diff --git a/src/pixelator/pna/resources/panels/proxiome-v1-FLAG-v1.0.csv b/src/pixelator/pna/resources/panels/proxiome-v1-FLAG-v1.0.csv new file mode 100644 index 000000000..a637e9549 --- /dev/null +++ b/src/pixelator/pna/resources/panels/proxiome-v1-FLAG-v1.0.csv @@ -0,0 +1,10 @@ +# --- +# name: proxiome-v1-FLAG-v1.0 +# product: proxiome-v1-FLAG-v1 +# description: >- +# Panel for the FLAG marker +# version: 1.0.1 +# panel_type: addon +# --- +marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2 +FLAG,,,,,CTTAACATCT,CTTAACATCT diff --git a/src/pixelator/pna/resources/panels/proxiome-v1-FMC63-v1.0.csv b/src/pixelator/pna/resources/panels/proxiome-v1-FMC63-v1.0.csv new file mode 100644 index 000000000..4bb165e12 --- /dev/null +++ b/src/pixelator/pna/resources/panels/proxiome-v1-FMC63-v1.0.csv @@ -0,0 +1,10 @@ +# --- +# name: proxiome-v1-FMC63-v1.0 +# product: proxiome-v1-FMC63-v1 +# description: >- +# Panel for the FMC63 marker +# version: 1.0.1 +# panel_type: addon +# --- +marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2 +FMC63,,,,,CGATTGGCAC,CGATTGGCAC diff --git a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-155-v1.0.csv b/src/pixelator/pna/resources/panels/proxiome-v1-immuno-155-v1.0.csv index 3a128bfcb..e2aee96bc 100644 --- a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-155-v1.0.csv +++ b/src/pixelator/pna/resources/panels/proxiome-v1-immuno-155-v1.0.csv @@ -4,6 +4,7 @@ # description: >- # Panel for the Proxiome Immuno Kit with 155 markers + 3 control markers # version: 1.0.2 +# panel_type: base # --- marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2 HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG diff --git a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-155-v1.1.csv b/src/pixelator/pna/resources/panels/proxiome-v1-immuno-155-v1.1.csv index 551d64f6f..a9e8ff049 100644 --- a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-155-v1.1.csv +++ b/src/pixelator/pna/resources/panels/proxiome-v1-immuno-155-v1.1.csv @@ -4,6 +4,7 @@ # description: >- # Panel for the Proxiome Immuno Kit with 155 markers + 3 control markers # version: 1.1.1 +# panel_type: base # --- marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2 HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG diff --git a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FLAG-v1.0.csv b/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FLAG-v1.0.csv deleted file mode 100644 index 8ffa09a3e..000000000 --- a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FLAG-v1.0.csv +++ /dev/null @@ -1,168 +0,0 @@ -# --- -# name: proxiome-v1-immuno-156-FLAG-v1.0 -# product: proxiome-v1-immuno-156-FLAG-v1 -# description: >- -# Panel for the with the 155 markers + 3 control markers -# of the Proximome Immuno 155 panel, plus the FLAG marker -# version: 1.0.2 -# --- -marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2 -HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG -B2M,,Beta-2-microglobulin,,P61769,CCAGGTTCCG,CCAGGTTCCG -CD11b,,Integrin α-M (ITGAM),ITGAM;Mac-1 α,P11215,CAGCTATGGT,CAGCTATGGT -CD11c,,Integrin α-X,Integrin αX,P20702,ATATGACGGT,ATATGACGGT -CD18,,Integrin beta 2,Integrin β2,P05107,GGGTAGGCTG,GGGTAGGCTG -CD82,,CD82 antigen,Tetraspanin-27,P27701,CCCGTCATGA,CCCGTCATGA -CD8,,T cell surface glycoprotein CD8 a/b chains,,P01732;P10966,CGGTGGATCA,CGGTGGATCA -TCRab,,T cell receptor alpha chain constant/beta constant 1,,P01848;P01850,CTGGTAGCAA,CTGGTAGCAA -HLA-DR,,"HLA class II histocompatibility antigen, DR",,P01903;P01911,TGTTGTCGAA,TGTTGTCGAA -CD45,,"Receptor-type tyrosine-protein phosphatase C. All 6 isoforms (ABC, AB, BC, B and O)",PTPRC,P08575,TGGAGGCTCT,TGGAGGCTCT -CD14,,Monocyte differentiation antigen CD14,,P08571,TGGCTATGTA,TGGCTATGTA -CD16,,Low-affinity immunoglobulin gamma Fc region receptor / III-A and -B,FcγRIII,P08637;O75015,ATAGGTTAGG,ATAGGTTAGG -CD19,,B-lymphocyte antigen CD19,,P15391,ACGGAATATT,ACGGAATATT -mIgG1,yes,,,,ATGCTAGTCG,ATGCTAGTCG -CD45RB,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, BC, and B)",,P08575,GAAGCAGTAT,GAAGCAGTAT -CD44,,CD44 antigen,,P16070,GTGAGTCAAT,GTGAGTCAAT -CD52,,CAMPATH-1 antigen,CAMPATH-1,P31358,CTTTAGCAGG,CTTTAGCAGG -CD59,,CD59 glycoprotein,Protectin;MAC-IP,P13987,GGTGTATGAG,GGTGTATGAG -CD45RA,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, and A)",,P08575,GGATTCGTGG,GGATTCGTGG -CD36,,Platelet glycoprotein 4,FAT;SCARB3,P16671,TACCCTGCGA,TACCCTGCGA -CD2,,T cell surface antigen CD2,,P06729,TGCCGATGCC,TGCCGATGCC -CD29,,Integrin beta-1,Integrin β1,P05556,TCCAGTGTCT,TCCAGTGTCT -CD5,,T cell surface glycoprotein CD5,,P06127,CACCCATCAA,CACCCATCAA -CD162,,P-selectin glycoprotein ligand 1,SELPLG;PSGL-1,Q14242,CTTCGTGGAC,CTTCGTGGAC -CD27,,CD27 antigen,,P26842,GGTTTGCAAA,GGTTTGCAAA -CR1,,Complement receptor type 1,CD35,P17927,CGCCACCTTT,CGCCACCTTT -CD26,,Dipeptidyl peptidase 4,DPP4,P27487,GATTCGCTGT,GATTCGCTGT -CD49d,,Integrin α-4,Integrin α4,P13612,AACTTAGGTT,AACTTAGGTT -CD37,,Leukocyte antigen CD37,Tetraspanin-26,P11049,AGAAGAAGAG,AGAAGAAGAG -CD41,,Integrin α-IIb,Integrin αIIb,P08514,TAAGGCATAA,TAAGGCATAA -CD20,,B-lymphocyte antigen CD20,,P11836,GCCACACCCA,GCCACACCCA -CD64,,High affinity immunoglobulin gamma Fc receptor I,FcγRI,P12314,CTTGTATATC,CTTGTATATC -CD22,,B-cell receptor CD22,,P20273,TGACCCGTTC,TGACCCGTTC -PD-L1,,Programmed cell death 1 ligand 1 (PDL1),CD274,Q9NZQ7,GCTTGAGATT,GCTTGAGATT -Siglec-7,,Sialic acid-binding Ig-like lectin 7 (SIGLEC-7),CD328,Q9Y286,TATATGCTGA,TATATGCTGA -CD25,,Interleukin-2 receptor subunit alpha,IL-2Rα,P01589,AGAGACGAAT,AGAGACGAAT -PD-1,,Programmed cell death protein 1 (PD-1),CD279,Q15116,TACAGAGCCC,TACAGAGCCC -NKp46,,Natural cytotoxicity triggering receptor 1 (NKp46),CD335,O76036,ATTACCCGCG,ATTACCCGCG -mIgG2a,yes,,,,ATTTCCACTA,ATTTCCACTA -mIgG2b,yes,,,,CTAAATGGCT,CTAAATGGCT -CTLA-4,,Cytotoxic T-lymphocyte protein 4,CD152,P16410,TTTCTGCATT,TTTCTGCATT -CD86,,T-lymphocyte activation antigen CD86,B7-2,P42081,ACCATCACTT,ACCATCACTT -CD13,,Aminopeptidase N,Aminopeptidase N,P15144,GCATGGGTAG,GCATGGGTAG -ADAM10,,Disintegrin and metalloproteinase domain-containing protein 10,CD156c,O14672,ATAAGTTCCA,ATAAGTTCCA -KIR2DL1,,Killer cell immunoglobulin-like receptor 2DL1,CD158a,P43626,TGTTACGGTC,TGTTACGGTC -KIR2DL2/DL3,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158b,P43627,ACTGCATTGA,ACTGCATTGA -NKG2A,,NKG2-A/NKG2-B type II integral membrane protein,CD159a,P26715,CGTACACGGT,CGTACACGGT -NKG2C,,NKG2-C type II integral membrane protein,CD159c,P26717,CAACAGTCGA,CAACAGTCGA -CD163,,Scavenger receptor cysteine-rich type 1 protein M130,,Q86VB7,GACCGTGATT,GACCGTGATT -CD169,,Sialoadhesin,Siglec-1,Q9BZZ2,TAATCGCGGG,TAATCGCGGG -CD1a,,T cell surface glycoprotein CD1a,,P06126,CGACTAATCA,CGACTAATCA -CD1c,,T cell surface glycoprotein CD1c,,P29017,GTGCACTGTC,GTGCACTGTC -CD206,,Macrophage mannose receptor 1,Mannose receptor,P22897,TGCCTAATAG,TGCCTAATAG -DNAM-1,,CD226 antigen,CD226,Q15762,CGGTCATTAA,CGGTCATTAA -PD-L2,,Programmed cell death 1 ligand 2 (PDL2),CD273,Q9BQ51,ATCGCGAAGC,ATCGCGAAGC -CD28,,T cell-specific surface glycoprotein CD28,,P10747,CATAACAATC,CATAACAATC -SLAMF6,,SLAM family member 6,CD352;NTB-A,Q96DU3,TCGGAGACAC,TCGGAGACAC -CD45RO,,"Receptor-type tyrosine-protein phosphatase C. Isoform O",,P08575,TTGATGACTC,TTGATGACTC -CD49e,,Integrin α-5,Integrin α5,P08648,TCTTTAGAAG,TCTTTAGAAG -CD56,,Neural cell adhesion molecule 1,NCAM,P13591,GTGCGTAAGC,GTGCGTAAGC -CD79a,,B-cell antigen receptor complex-associated protein alpha chain,MB-1,P11912,TCTCTCTGTT,TCTCTCTGTT -CD80,,T-lymphocyte activation antigen CD80,B7-1,P33681,AAGACGCGGA,AAGACGCGGA -CD81,,CD81 antigen,Tetraspanin-28,P60033,TGGGTTATGT,TGGGTTATGT -LILRB1,,Leukocyte immunoglobulin-like receptor subfamily B member 1,CD85j;ILT-2,Q8NHL6,CCTAAGTCTA,CCTAAGTCTA -CD93,,Complement component C1q receptor,,Q9NPY3,GCAGCGAACA,GCAGCGAACA -IgD,,Immunoglobulin delta heavy chain,,P0DOX3,AGATGAGGCA,AGATGAGGCA -IgE,,Immunoglobulin epsilon heavy chain,,P0DOX4,CGACGGTAAG,CGACGGTAAG -IgM,,Immunoglobulin mu heavy chain,,P0DOX6,GTGGATCCAA,GTGGATCCAA -KLRG1,,Killer cell lectin-like receptor subfamily G member 1,,Q96E93,TATACAGACA,TATACAGACA -NKp80,,Killer cell lectin-like receptor subfamily F member 1,KLRF1,Q9NZS2,CCATCGGATC,CCATCGGATC -TCRgd,,T cell receptor gamma constant 1 /delta constant,,P0CF51;B7Z8K6,CTTATGACCA,CTTATGACCA -CD10,,Neprilysin,Neprilysin,P08473,CGCAGGTAGC,CGCAGGTAGC -CD103,,Integrin alpha-E,Integrin αE,P38570,CCTATGCGAA,CCTATGCGAA -CCR9,,C-C chemokine receptor type 9,CD199,P51686,ACTCTTTCTG,ACTCTTTCTG -CD1b,,T cell surface glycoprotein CD1b,,P29016,GACACCACCG,GACACCACCG -CD21,,Complement receptor type 2,CR2,P20023,GTGGCGTTAA,GTGGCGTTAA -TALLA,,Tetraspanin-7,CD231;Tetraspanin-7,P41732,CACGATACTT,CACGATACTT -CD277,,Butyrophilin subfamily 3 member A1,BTN3,O00481,GAGTGATACG,GAGTGATACG -LAIR1,,Leukocyte-associated immunoglobulin-like receptor 1,CD305,Q6GTX8,GCAATGTGTA,GCAATGTGTA -CD371,,C-type lectin domain family 12 member A,CLEC12A,Q5QGZ9,AAGGTCCCAT,AAGGTCCCAT -CD89,,Immunoglobulin alpha Fc receptor,FcαRI;FCAR,P24071,GTATCATAAG,GTATCATAAG -CD90,,Thy-1 membrane glycoprotein,Thy-1,P04216,TAGCCGATTA,TAGCCGATTA -CD70,,CD70 antigen,CD27L,P32970,CTCAGCATGC,CTCAGCATGC -GPR56,,Adhesion G-protein coupled receptor G1,TM7XN1,Q9Y653,GCGTCTCTCT,GCGTCTCTCT -HLA-DQ,,"HLA class II histocompatibility antigen, DQ",,P01906;P05538;P01920;P01909,ATACTTGAGC,ATACTTGAGC -TCRVd2,,T cell receptor delta variable 2,,,CCGACCATTC,CCGACCATTC -HLA-DR-DP-DQ,,HLA class II histocompatibility antigen,,P01903;P20036;P01909,AACAGAGGAA,AACAGAGGAA -Siglec-9,,Sialic acid-binding Ig-like lectin 9,,Q9Y336,TTAACAAGCA,TTAACAAGCA -TCRVa7.2,,T cell receptor alpha variable 7,,A0A075B6U4,TCCCAGGTCC,TCCCAGGTCC -Fas,,Tumor necrosis factor receptor superfamily member 6,CD95,P25445,TACTGTTGGG,TACTGTTGGG -TCRVg9,,T cell receptor gamma variable 9,,,TCGTTTGTCA,TCGTTTGTCA -CD127,,Interleukin-7 receptor subunit alpha,IL-7Rα,P16871,TGTTAGAGGA,TGTTAGAGGA -CD141,,Thrombomodulin,TM,P07204,AATTGTTCGT,AATTGTTCGT -CD31,,Platelet endothelial cell adhesion molecule,PECAM-1,P16284,GGCAAAGAGC,GGCAAAGAGC -CD6,,T cell differentiation antigen CD6,,P30203,CTAAGATCTC,CTAAGATCTC -CD57,,Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1,,Q9P2W7,ACGACGGGAC,ACGACGGGAC -CD73,,5’-nucleotidase,NT5E,P21589,ACCAAGGACG,ACCAAGGACG -TIM-3,,Hepatitis A virus cellular receptor 2,CD366;HAVCR2,Q8TDQ0,CGCCAAGTGG,CGCCAAGTGG -GITR,,Tumor necrosis factor receptor superfamily member 18,CD357,Q9Y5U5,TGAGTCACTC,TGAGTCACTC -CCR3,,C-C chemokine receptor type 3,CD193,P51677,CCGTGACCCA,CCGTGACCCA -SLAMF7,,SLAM family member 7,CD319;CRACC,Q9NQ25,AGGCGGAAAT,AGGCGGAAAT -TIGIT,,T cell immunoreceptor with Ig and ITIM domains,,Q495A1,ACTGAGTCGC,ACTGAGTCGC -OX40,,Tumor necrosis factor receptor superfamily member 4,CD134,P43489,CCACTTCCGT,CCACTTCCGT -ICAM-2,,Intercellular adhesion molecule 2,CD102,P13598,TATCTGGGAT,TATCTGGGAT -CD123,,Interleukin-3 receptor subunit alpha,IL-3Rα,P26951,TGACTGCTAC,TGACTGCTAC -CD150,,Signaling lymphocytic activation molecule,SLAMF1,Q13291,TCGAATGGAT,TCGAATGGAT -CD40L,,CD40 ligand,CD154,P29965,CTAGATTTGC,CTAGATTTGC -KIR,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158,Q8N743,TCCTCTCCTG,TCCTCTCCTG -CD161,,Killer cell lectin-like receptor subfamily B member 1,KLRB1,Q12918,ACTGAACTAC,ACTGAACTAC -CD180,,CD180 antigen,RP105,Q99467,TGAGCTCCAA,TGAGCTCCAA -CCR1,,C-C chemokine receptor type 1,CD191,P32246,CCGGTGGTTC,CCGGTGGTTC -CCR2,,C-C chemokine receptor type 2,CD192,P41597,GGTTCTCCAC,GGTTCTCCAC -CD1d,,Antigen-presenting glycoprotein CD1d,,P15813,CAACGTCCCA,CAACGTCCCA -CD200,,OX-2 membrane glycoprotein,,P41217,CGCACGGGTT,CGCACGGGTT -Ly9,,T-lymphocyte surface antigen Ly-9,CD229;SLAMF3,Q9HBG7,TCGACGAGTG,TCGACGAGTG -CD24,,Signal transducer CD24,HSA,P25063,TCTTGTTCCC,TCTTGTTCCC -2B4,,Natural killer cell receptor 2B4,CD244;SLAMF4,Q9BZW8,TCTCAATCAA,TCTCAATCAA -BAFF-R,,Tumor necrosis factor receptor superfamily member 13C (BAFFR),CD268,Q96RJ3,ACGTAACCGC,ACGTAACCGC -ICOS,,Inducible T cell co-stimulator,CD278,Q9Y6W8,TTTCGGACAG,TTTCGGACAG -CD32,,Low-affinity immunoglobulin gamma Fc region receptor II-b,FcγRII,P31994,GATTTCCAGC,GATTTCCAGC -CD33,,Myeloid cell surface antigen CD33,Siglec-3,P20138,GCGATATAGT,GCGATATAGT -NKp30,,Natural cytotoxicity triggering receptor 3 (NKp30),CD337,O14931,CTTATCTCTT,CTTATCTCTT -CD38,,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,,P28907,TCCGATCTGG,TCCGATCTGG -CD39,,Ectonucleoside triphosphate diphosphohydrolase 1,ENTPD1,P49961,TCAGCGCCTT,TCAGCGCCTT -CD40,,Tumor necrosis factor receptor superfamily member 5,,P25942,TCTGGCGTGG,TCTGGCGTGG -CD48,,CD48 antigen,SLAMF2;BLAST-1,P09326,AGTACGAAGA,AGTACGAAGA -ICAM-3,,Intercellular adhesion molecule 3,CD50,P32942,CTCCGCGTTG,CTCCGCGTTG -CD55,,Complement decay-accelerating factor (DAF),DAF,P08174,TTAGCTAAAC,TTAGCTAAAC -CD58,,Lymphocyte function-associated antigen 3 (LFA3),LFA-3,P19256,ATGTTATGTG,ATGTTATGTG -CD62P,,P-selectin,P-selectin,P16109,ACTTAGCGCT,ACTTAGCGCT -CD69,,Early activation antigen CD69,,Q07108,GAAGGGTCTC,GAAGGGTCTC -CD72,,B-cell differentiation antigen CD72,Lyb-2,P21854,GCGGTGACTT,GCGGTGACTT -CD84,,SLAM family member 5,SLAMF5,Q9UIB8,GCCATTGGAA,GCCATTGGAA -CD9,,CD9 antigen,Tetraspanin-29,P21926,GTCTGGTCAT,GTCTGGTCAT -CD94,,Natural killer cells antigen CD94,KLRD1,Q13241,CTACAACCTT,CTACAACCTT -TCRVb5,,T cell receptor beta variable 5,,,GGCCTCAAGT,GGCCTCAAGT -CD3e,,T cell surface glycoprotein CD3 epsilon chain,,P07766,TGTAGAATTC,TGTAGAATTC -CD4,,T cell surface glycoprotein CD4,,P01730,GACAACTTCT,GACAACTTCT -CD11a,,Integrin α-L (LFA-1 α),ITGAL;LFA-1 α,P20701,ACACACTTGA,ACACACTTGA -CD43,,Leukosialin,Leukosialin,P16150,GAGATTACTA,GAGATTACTA -CD7,,T cell antigen CD7,,P09564,CTGGGTCCGT,CTGGGTCCGT -CD53,,Leukocyte surface antigen CD53,Tetraspanin-25,P19397,CAACCCGCTT,CAACCCGCTT -CD302,,C-type lectin domain family 13 member A,CLEC13A,Q8IX05,TAGACATTGG,TAGACATTGG -VISTA,,V-type immunoglobulin domain-containing suppressor of T cell activation,VSIR,Q9H7M9,AATGTTAACG,AATGTTAACG -BCMA,,Tumor necrosis factor receptor superfamily member 17,CD269,Q02223,CTGGACTATG,CTGGACTATG -CD138,,Syndecan-1,Syndecan-1,P18827,CTGGGCTTAC,CTGGGCTTAC -4-1BB,,Tumor necrosis factor receptor superfamily member 9,CD137,Q07011,CCAGCTAGAA,CCAGCTAGAA -CD66b,,Cell adhesion molecule CEACAM8,CEACAM8,P31997,CTAGGCAGTT,CTAGGCAGTT -CX3CR1,,CX3C chemokine receptor 1,Fractalkine receptor,P49238,TACTCCCGCC,TACTCCCGCC -EpCAM,,Epithelial cell adhesion molecule,CD326,P16422,CGTTCTTACA,CGTTCTTACA -DC-SIGN,,CD209 antigen,CD209,Q9NNX6,TGGACGTGAA,TGGACGTGAA -CD34,,Hematopoietic progenitor cell antigen CD34,,P28906,CCGTCTAGCC,CCGTCTAGCC -Dectin-1,,C-type lectin domain family 7 member A,CD369;CLEC7A,Q9BXN2,CTGCCAAGAC,CTGCCAAGAC -ICAM-1,,Intercellular adhesion molecule 1,CD54,P05362,AGCAGCTGAT,AGCAGCTGAT -CD71,,Transferrin receptor protein 1,Transferrin receptor,P02786,TCAGGACAGA,TCAGGACAGA -CD47,,Leukocyte surface antigen CD47,Integrin associated protein,Q08722,AGCTACTATT,AGCTACTATT -c-Kit,,Mast/Stem cell growth factor receptor Kit,CD117,P10721,GCTATAATTG,GCTATAATTG -NKG2D,,NKG2-D type II integral membrane protein,CD314;KG2DN,P26718,TGGCGCACAC,TGGCGCACAC -FLAG,,,,,CTTAACATCT,CTTAACATCT diff --git a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FLAG-v1.1.csv b/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FLAG-v1.1.csv deleted file mode 100644 index d78526409..000000000 --- a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FLAG-v1.1.csv +++ /dev/null @@ -1,168 +0,0 @@ -# --- -# name: proxiome-v1-immuno-156-FLAG-v1.1 -# product: proxiome-v1-immuno-156-FLAG-v1 -# description: >- -# Panel for the with the 155 markers + 3 control markers -# of the Proximome Immuno 155 panel, plus the FLAG marker -# version: 1.1.1 -# --- -marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2 -HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG -B2M,,Beta-2-microglobulin,,P61769,CCAGGTTCCG,CCAGGTTCCG -CD11b,,Integrin α-M (ITGAM),ITGAM;Mac-1 α,P11215,CAGCTATGGT,CAGCTATGGT -CD11c,,Integrin α-X,Integrin αX,P20702,ATATGACGGT,ATATGACGGT -CD18,,Integrin beta 2,Integrin β2,P05107,GGGTAGGCTG,GGGTAGGCTG -CD82,,CD82 antigen,Tetraspanin-27,P27701,CCCGTCATGA,CCCGTCATGA -CD8,,T cell surface glycoprotein CD8 a/b chains,,P01732;P10966,CGGTGGATCA,CGGTGGATCA -TCRab,,T cell receptor alpha chain constant/beta constant 1,,P01848;P01850,CTGGTAGCAA,CTGGTAGCAA -HLA-DR,,"HLA class II histocompatibility antigen, DR",,P01903;P01911,TGTTGTCGAA,TGTTGTCGAA -CD45,,"Receptor-type tyrosine-protein phosphatase C. All 6 isoforms (ABC, AB, BC, B and O)",PTPRC,P08575,TGGAGGCTCT,TGGAGGCTCT -CD14,,Monocyte differentiation antigen CD14,,P08571,TGGCTATGTA,TGGCTATGTA -CD16,,Low-affinity immunoglobulin gamma Fc region receptor / III-A and -B,FcγRIII,P08637;O75015,ATAGGTTAGG,ATAGGTTAGG -CD19,,B-lymphocyte antigen CD19,,P15391,ACGGAATATT,ACGGAATATT -mIgG1,yes,,,,ATGCTAGTCG,ATGCTAGTCG -CD45RB,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, BC, and B)",,P08575,GAAGCAGTAT,GAAGCAGTAT -CD44,,CD44 antigen,,P16070,GTGAGTCAAT,GTGAGTCAAT -CD52,,CAMPATH-1 antigen,CAMPATH-1,P31358,CTTTAGCAGG,CTTTAGCAGG -CD59,,CD59 glycoprotein,Protectin;MAC-IP,P13987,GGTGTATGAG,GGTGTATGAG -CD45RA,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, and A)",,P08575,GGATTCGTGG,GGATTCGTGG -CD36,,Platelet glycoprotein 4,FAT;SCARB3,P16671,TACCCTGCGA,TACCCTGCGA -CD2,,T cell surface antigen CD2,,P06729,TGCCGATGCC,TGCCGATGCC -CD29,,Integrin beta-1,Integrin β1,P05556,TCCAGTGTCT,TCCAGTGTCT -CD5,,T cell surface glycoprotein CD5,,P06127,CACCCATCAA,CACCCATCAA -CD162,,P-selectin glycoprotein ligand 1,SELPLG;PSGL-1,Q14242,CTTCGTGGAC,CTTCGTGGAC -CD27,,CD27 antigen,,P26842,GGTTTGCAAA,GGTTTGCAAA -CR1,,Complement receptor type 1,CD35,P17927,CGCCACCTTT,CGCCACCTTT -CD26,,Dipeptidyl peptidase 4,DPP4,P27487,GATTCGCTGT,GATTCGCTGT -CD49d,,Integrin α-4,Integrin α4,P13612,AACTTAGGTT,AACTTAGGTT -CD37,,Leukocyte antigen CD37,Tetraspanin-26,P11049,AGAAGAAGAG,AGAAGAAGAG -CD41,,Integrin α-IIb,Integrin αIIb,P08514,TAAGGCATAA,TAAGGCATAA -CD20,,B-lymphocyte antigen CD20,,P11836,GCCACACCCA,GCCACACCCA -CD64,,High affinity immunoglobulin gamma Fc receptor I,FcγRI,P12314,CTTGTATATC,CTTGTATATC -CD22,,B-cell receptor CD22,,P20273,TGACCCGTTC,TGACCCGTTC -PD-L1,,Programmed cell death 1 ligand 1 (PDL1),CD274,Q9NZQ7,GCTTGAGATT,GCTTGAGATT -Siglec-7,,Sialic acid-binding Ig-like lectin 7 (SIGLEC-7),CD328,Q9Y286,TATATGCTGA,TATATGCTGA -CD25,,Interleukin-2 receptor subunit alpha,IL-2Rα,P01589,AGAGACGAAT,AGAGACGAAT -PD-1,,Programmed cell death protein 1 (PD-1),CD279,Q15116,TACAGAGCCC,TACAGAGCCC -NKp46,,Natural cytotoxicity triggering receptor 1 (NKp46),CD335,O76036,ATTACCCGCG,ATTACCCGCG -mIgG2a,yes,,,,ATTTCCACTA,ATTTCCACTA -mIgG2b,yes,,,,CTAAATGGCT,CTAAATGGCT -CTLA-4,,Cytotoxic T-lymphocyte protein 4,CD152,P16410,TTTCTGCATT,TTTCTGCATT -CD86,,T-lymphocyte activation antigen CD86,B7-2,P42081,ACCATCACTT,ACCATCACTT -CD13,,Aminopeptidase N,Aminopeptidase N,P15144,GCATGGGTAG,GCATGGGTAG -ADAM10,,Disintegrin and metalloproteinase domain-containing protein 10,CD156c,O14672,ATAAGTTCCA,ATAAGTTCCA -KIR2DL1,,Killer cell immunoglobulin-like receptor 2DL1,CD158a,P43626,TGTTACGGTC,TGTTACGGTC -KIR2DL2/DL3,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158b,P43627,ACTGCATTGA,ACTGCATTGA -NKG2A,,NKG2-A/NKG2-B type II integral membrane protein,CD159a,P26715,CGTACACGGT,CGTACACGGT -NKG2C,,NKG2-C type II integral membrane protein,CD159c,P26717,CAACAGTCGA,CAACAGTCGA -CD163,,Scavenger receptor cysteine-rich type 1 protein M130,,Q86VB7,GACCGTGATT,GACCGTGATT -CD169,,Sialoadhesin,Siglec-1,Q9BZZ2,TAATCGCGGG,TAATCGCGGG -CD1a,,T cell surface glycoprotein CD1a,,P06126,CGACTAATCA,CGACTAATCA -CD1c,,T cell surface glycoprotein CD1c,,P29017,GTGCACTGTC,GTGCACTGTC -CD206,,Macrophage mannose receptor 1,Mannose receptor,P22897,TGCCTAATAG,TGCCTAATAG -DNAM-1,,CD226 antigen,CD226,Q15762,CGGTCATTAA,CGGTCATTAA -PD-L2,,Programmed cell death 1 ligand 2 (PDL2),CD273,Q9BQ51,ATCGCGAAGC,ATCGCGAAGC -CD28,,T cell-specific surface glycoprotein CD28,,P10747,CATAACAATC,CATAACAATC -SLAMF6,,SLAM family member 6,CD352;NTB-A,Q96DU3,TCGGAGACAC,TCGGAGACAC -CD45RO,,"Receptor-type tyrosine-protein phosphatase C. Isoform O",,P08575,TTGATGACTC,TTGATGACTC -CD49e,,Integrin α-5,Integrin α5,P08648,AACTCCTGAA,AACTCCTGAA -CD56,,Neural cell adhesion molecule 1,NCAM,P13591,GTGCGTAAGC,GTGCGTAAGC -CD79a,,B-cell antigen receptor complex-associated protein alpha chain,MB-1,P11912,AGATCGACAG,AGATCGACAG -CD80,,T-lymphocyte activation antigen CD80,B7-1,P33681,AAGACGCGGA,AAGACGCGGA -CD81,,CD81 antigen,Tetraspanin-28,P60033,TGGGTTATGT,TGGGTTATGT -LILRB1,,Leukocyte immunoglobulin-like receptor subfamily B member 1,CD85j;ILT-2,Q8NHL6,CCTAAGTCTA,CCTAAGTCTA -CD93,,Complement component C1q receptor,,Q9NPY3,GCAGCGAACA,GCAGCGAACA -IgD,,Immunoglobulin delta heavy chain,,P0DOX3,AGATGAGGCA,AGATGAGGCA -IgE,,Immunoglobulin epsilon heavy chain,,P0DOX4,CGACGGTAAG,CGACGGTAAG -IgM,,Immunoglobulin mu heavy chain,,P0DOX6,GTGGATCCAA,GTGGATCCAA -KLRG1,,Killer cell lectin-like receptor subfamily G member 1,,Q96E93,TATACAGACA,TATACAGACA -NKp80,,Killer cell lectin-like receptor subfamily F member 1,KLRF1,Q9NZS2,CCATCGGATC,CCATCGGATC -TCRgd,,T cell receptor gamma constant 1 /delta constant,,P0CF51;B7Z8K6,CTTATGACCA,CTTATGACCA -CD10,,Neprilysin,Neprilysin,P08473,CGCAGGTAGC,CGCAGGTAGC -CD103,,Integrin alpha-E,Integrin αE,P38570,CCTATGCGAA,CCTATGCGAA -CCR9,,C-C chemokine receptor type 9,CD199,P51686,ACTCTTTCTG,ACTCTTTCTG -CD1b,,T cell surface glycoprotein CD1b,,P29016,GACACCACCG,GACACCACCG -CD21,,Complement receptor type 2,CR2,P20023,GTGGCGTTAA,GTGGCGTTAA -TALLA,,Tetraspanin-7,CD231;Tetraspanin-7,P41732,CACGATACTT,CACGATACTT -CD277,,Butyrophilin subfamily 3 member A1,BTN3,O00481,GAGTGATACG,GAGTGATACG -LAIR1,,Leukocyte-associated immunoglobulin-like receptor 1,CD305,Q6GTX8,GCAATGTGTA,GCAATGTGTA -CD371,,C-type lectin domain family 12 member A,CLEC12A,Q5QGZ9,AAGGTCCCAT,AAGGTCCCAT -CD89,,Immunoglobulin alpha Fc receptor,FcαRI;FCAR,P24071,GTATCATAAG,GTATCATAAG -CD90,,Thy-1 membrane glycoprotein,Thy-1,P04216,TAGCCGATTA,TAGCCGATTA -CD70,,CD70 antigen,CD27L,P32970,CTCAGCATGC,CTCAGCATGC -GPR56,,Adhesion G-protein coupled receptor G1,TM7XN1,Q9Y653,GCGTCTCTCT,GCGTCTCTCT -HLA-DQ,,"HLA class II histocompatibility antigen, DQ",,P01906;P05538;P01920;P01909,ATACTTGAGC,ATACTTGAGC -TCRVd2,,T cell receptor delta variable 2,,,CCGACCATTC,CCGACCATTC -HLA-DR-DP-DQ,,HLA class II histocompatibility antigen,,P01903;P20036;P01909,AACAGAGGAA,AACAGAGGAA -Siglec-9,,Sialic acid-binding Ig-like lectin 9,,Q9Y336,TTAACAAGCA,TTAACAAGCA -TCRVa7.2,,T cell receptor alpha variable 7,,A0A075B6U4,TCCCAGGTCC,TCCCAGGTCC -Fas,,Tumor necrosis factor receptor superfamily member 6,CD95,P25445,TACTGTTGGG,TACTGTTGGG -TCRVg9,,T cell receptor gamma variable 9,,,TCGTTTGTCA,TCGTTTGTCA -CD127,,Interleukin-7 receptor subunit alpha,IL-7Rα,P16871,TGTTAGAGGA,TGTTAGAGGA -CD141,,Thrombomodulin,TM,P07204,AATTGTTCGT,AATTGTTCGT -CD31,,Platelet endothelial cell adhesion molecule,PECAM-1,P16284,GGCAAAGAGC,GGCAAAGAGC -CD6,,T cell differentiation antigen CD6,,P30203,CTAAGATCTC,CTAAGATCTC -CD57,,Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1,,Q9P2W7,ACGACGGGAC,ACGACGGGAC -CD73,,5’-nucleotidase,NT5E,P21589,ACCAAGGACG,ACCAAGGACG -TIM-3,,Hepatitis A virus cellular receptor 2,CD366;HAVCR2,Q8TDQ0,CGCCAAGTGG,CGCCAAGTGG -GITR,,Tumor necrosis factor receptor superfamily member 18,CD357,Q9Y5U5,TGAGTCACTC,TGAGTCACTC -CCR3,,C-C chemokine receptor type 3,CD193,P51677,CCGTGACCCA,CCGTGACCCA -SLAMF7,,SLAM family member 7,CD319;CRACC,Q9NQ25,AGGCGGAAAT,AGGCGGAAAT -TIGIT,,T cell immunoreceptor with Ig and ITIM domains,,Q495A1,ACTGAGTCGC,ACTGAGTCGC -OX40,,Tumor necrosis factor receptor superfamily member 4,CD134,P43489,CCACTTCCGT,CCACTTCCGT -ICAM-2,,Intercellular adhesion molecule 2,CD102,P13598,TATCTGGGAT,TATCTGGGAT -CD123,,Interleukin-3 receptor subunit alpha,IL-3Rα,P26951,TGACTGCTAC,TGACTGCTAC -CD150,,Signaling lymphocytic activation molecule,SLAMF1,Q13291,TCGAATGGAT,TCGAATGGAT -CD40L,,CD40 ligand,CD154,P29965,CTAGATTTGC,CTAGATTTGC -KIR,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158,Q8N743,TCCTCTCCTG,TCCTCTCCTG -CD161,,Killer cell lectin-like receptor subfamily B member 1,KLRB1,Q12918,ACTGAACTAC,ACTGAACTAC -CD180,,CD180 antigen,RP105,Q99467,TGAGCTCCAA,TGAGCTCCAA -CCR1,,C-C chemokine receptor type 1,CD191,P32246,CCGGTGGTTC,CCGGTGGTTC -CCR2,,C-C chemokine receptor type 2,CD192,P41597,GGTTCTCCAC,GGTTCTCCAC -CD1d,,Antigen-presenting glycoprotein CD1d,,P15813,CAACGTCCCA,CAACGTCCCA -CD200,,OX-2 membrane glycoprotein,,P41217,CGCACGGGTT,CGCACGGGTT -Ly9,,T-lymphocyte surface antigen Ly-9,CD229;SLAMF3,Q9HBG7,TCGACGAGTG,TCGACGAGTG -CD24,,Signal transducer CD24,HSA,P25063,TCTTGTTCCC,TCTTGTTCCC -2B4,,Natural killer cell receptor 2B4,CD244;SLAMF4,Q9BZW8,TCTCAATCAA,TCTCAATCAA -BAFF-R,,Tumor necrosis factor receptor superfamily member 13C (BAFFR),CD268,Q96RJ3,ACGTAACCGC,ACGTAACCGC -ICOS,,Inducible T cell co-stimulator,CD278,Q9Y6W8,CAGGCACCTG,CAGGCACCTG -CD32,,Low-affinity immunoglobulin gamma Fc region receptor II-b,FcγRII,P31994,GATTTCCAGC,GATTTCCAGC -CD33,,Myeloid cell surface antigen CD33,Siglec-3,P20138,GCGATATAGT,GCGATATAGT -NKp30,,Natural cytotoxicity triggering receptor 3 (NKp30),CD337,O14931,CTTATCTCTT,CTTATCTCTT -CD38,,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,,P28907,TCCGATCTGG,TCCGATCTGG -CD39,,Ectonucleoside triphosphate diphosphohydrolase 1,ENTPD1,P49961,TCAGCGCCTT,TCAGCGCCTT -CD40,,Tumor necrosis factor receptor superfamily member 5,,P25942,TCTGGCGTGG,TCTGGCGTGG -CD48,,CD48 antigen,SLAMF2;BLAST-1,P09326,AGTACGAAGA,AGTACGAAGA -ICAM-3,,Intercellular adhesion molecule 3,CD50,P32942,CTCCGCGTTG,CTCCGCGTTG -CD55,,Complement decay-accelerating factor (DAF),DAF,P08174,TTAGCTAAAC,TTAGCTAAAC -CD58,,Lymphocyte function-associated antigen 3 (LFA3),LFA-3,P19256,ATGTTATGTG,ATGTTATGTG -CD62P,,P-selectin,P-selectin,P16109,ACTTAGCGCT,ACTTAGCGCT -CD69,,Early activation antigen CD69,,Q07108,GAAGGGTCTC,GAAGGGTCTC -CD72,,B-cell differentiation antigen CD72,Lyb-2,P21854,GCGGTGACTT,GCGGTGACTT -CD84,,SLAM family member 5,SLAMF5,Q9UIB8,GCCATTGGAA,GCCATTGGAA -CD9,,CD9 antigen,Tetraspanin-29,P21926,GTCTGGTCAT,GTCTGGTCAT -CD94,,Natural killer cells antigen CD94,KLRD1,Q13241,CTACAACCTT,CTACAACCTT -TCRVb5,,T cell receptor beta variable 5,,,GGCCTCAAGT,GGCCTCAAGT -CD3e,,T cell surface glycoprotein CD3 epsilon chain,,P07766,TGTAGAATTC,TGTAGAATTC -CD4,,T cell surface glycoprotein CD4,,P01730,GACAACTTCT,GACAACTTCT -CD11a,,Integrin α-L (LFA-1 α),ITGAL;LFA-1 α,P20701,ACACACTTGA,ACACACTTGA -CD43,,Leukosialin,Leukosialin,P16150,GAGATTACTA,GAGATTACTA -CD7,,T cell antigen CD7,,P09564,CTGGGTCCGT,CTGGGTCCGT -CD53,,Leukocyte surface antigen CD53,Tetraspanin-25,P19397,CAACCCGCTT,CAACCCGCTT -CD302,,C-type lectin domain family 13 member A,CLEC13A,Q8IX05,TAGACATTGG,TAGACATTGG -VISTA,,V-type immunoglobulin domain-containing suppressor of T cell activation,VSIR,Q9H7M9,AATGTTAACG,AATGTTAACG -BCMA,,Tumor necrosis factor receptor superfamily member 17,CD269,Q02223,CTGGACTATG,CTGGACTATG -CD138,,Syndecan-1,Syndecan-1,P18827,CTGGGCTTAC,CTGGGCTTAC -4-1BB,,Tumor necrosis factor receptor superfamily member 9,CD137,Q07011,CCAGCTAGAA,CCAGCTAGAA -CD66b,,Cell adhesion molecule CEACAM8,CEACAM8,P31997,CTAGGCAGTT,CTAGGCAGTT -CX3CR1,,CX3C chemokine receptor 1,Fractalkine receptor,P49238,TACTCCCGCC,TACTCCCGCC -EpCAM,,Epithelial cell adhesion molecule,CD326,P16422,CGTTCTTACA,CGTTCTTACA -DC-SIGN,,CD209 antigen,CD209,Q9NNX6,TGGACGTGAA,TGGACGTGAA -CD34,,Hematopoietic progenitor cell antigen CD34,,P28906,CCGTCTAGCC,CCGTCTAGCC -Dectin-1,,C-type lectin domain family 7 member A,CD369;CLEC7A,Q9BXN2,CTGCCAAGAC,CTGCCAAGAC -ICAM-1,,Intercellular adhesion molecule 1,CD54,P05362,AGCAGCTGAT,AGCAGCTGAT -CD71,,Transferrin receptor protein 1,Transferrin receptor,P02786,TCAGGACAGA,TCAGGACAGA -CD47,,Leukocyte surface antigen CD47,Integrin associated protein,Q08722,AGCTACTATT,AGCTACTATT -c-Kit,,Mast/Stem cell growth factor receptor Kit,CD117,P10721,GCTATAATTG,GCTATAATTG -NKG2D,,NKG2-D type II integral membrane protein,CD314;KG2DN,P26718,TGGCGCACAC,TGGCGCACAC -FLAG,,,,,CTTAACATCT,CTTAACATCT diff --git a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FMC63-v1.0.csv b/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FMC63-v1.0.csv deleted file mode 100644 index d9155469e..000000000 --- a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FMC63-v1.0.csv +++ /dev/null @@ -1,168 +0,0 @@ -# --- -# name: proxiome-v1-immuno-156-FMC63-v1.0 -# product: proxiome-v1-immuno-156-FMC63-v1 -# description: >- -# Panel for the with the 155 markers + 3 control markers -# of the Proximome Immuno 155 panel, plus the FMC63 marker -# version: 1.0.2 -# --- -marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2 -HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG -B2M,,Beta-2-microglobulin,,P61769,CCAGGTTCCG,CCAGGTTCCG -CD11b,,Integrin α-M (ITGAM),ITGAM;Mac-1 α,P11215,CAGCTATGGT,CAGCTATGGT -CD11c,,Integrin α-X,Integrin αX,P20702,ATATGACGGT,ATATGACGGT -CD18,,Integrin beta 2,Integrin β2,P05107,GGGTAGGCTG,GGGTAGGCTG -CD82,,CD82 antigen,Tetraspanin-27,P27701,CCCGTCATGA,CCCGTCATGA -CD8,,T cell surface glycoprotein CD8 a/b chains,,P01732;P10966,CGGTGGATCA,CGGTGGATCA -TCRab,,T cell receptor alpha chain constant/beta constant 1,,P01848;P01850,CTGGTAGCAA,CTGGTAGCAA -HLA-DR,,"HLA class II histocompatibility antigen, DR",,P01903;P01911,TGTTGTCGAA,TGTTGTCGAA -CD45,,"Receptor-type tyrosine-protein phosphatase C. All 6 isoforms (ABC, AB, BC, B and O)",PTPRC,P08575,TGGAGGCTCT,TGGAGGCTCT -CD14,,Monocyte differentiation antigen CD14,,P08571,TGGCTATGTA,TGGCTATGTA -CD16,,Low-affinity immunoglobulin gamma Fc region receptor / III-A and -B,FcγRIII,P08637;O75015,ATAGGTTAGG,ATAGGTTAGG -CD19,,B-lymphocyte antigen CD19,,P15391,ACGGAATATT,ACGGAATATT -mIgG1,yes,,,,ATGCTAGTCG,ATGCTAGTCG -CD45RB,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, BC, and B)",,P08575,GAAGCAGTAT,GAAGCAGTAT -CD44,,CD44 antigen,,P16070,GTGAGTCAAT,GTGAGTCAAT -CD52,,CAMPATH-1 antigen,CAMPATH-1,P31358,CTTTAGCAGG,CTTTAGCAGG -CD59,,CD59 glycoprotein,Protectin;MAC-IP,P13987,GGTGTATGAG,GGTGTATGAG -CD45RA,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, and A)",,P08575,GGATTCGTGG,GGATTCGTGG -CD36,,Platelet glycoprotein 4,FAT;SCARB3,P16671,TACCCTGCGA,TACCCTGCGA -CD2,,T cell surface antigen CD2,,P06729,TGCCGATGCC,TGCCGATGCC -CD29,,Integrin beta-1,Integrin β1,P05556,TCCAGTGTCT,TCCAGTGTCT -CD5,,T cell surface glycoprotein CD5,,P06127,CACCCATCAA,CACCCATCAA -CD162,,P-selectin glycoprotein ligand 1,SELPLG;PSGL-1,Q14242,CTTCGTGGAC,CTTCGTGGAC -CD27,,CD27 antigen,,P26842,GGTTTGCAAA,GGTTTGCAAA -CR1,,Complement receptor type 1,CD35,P17927,CGCCACCTTT,CGCCACCTTT -CD26,,Dipeptidyl peptidase 4,DPP4,P27487,GATTCGCTGT,GATTCGCTGT -CD49d,,Integrin α-4,Integrin α4,P13612,AACTTAGGTT,AACTTAGGTT -CD37,,Leukocyte antigen CD37,Tetraspanin-26,P11049,AGAAGAAGAG,AGAAGAAGAG -CD41,,Integrin α-IIb,Integrin αIIb,P08514,TAAGGCATAA,TAAGGCATAA -CD20,,B-lymphocyte antigen CD20,,P11836,GCCACACCCA,GCCACACCCA -CD64,,High affinity immunoglobulin gamma Fc receptor I,FcγRI,P12314,CTTGTATATC,CTTGTATATC -CD22,,B-cell receptor CD22,,P20273,TGACCCGTTC,TGACCCGTTC -PD-L1,,Programmed cell death 1 ligand 1 (PDL1),CD274,Q9NZQ7,GCTTGAGATT,GCTTGAGATT -Siglec-7,,Sialic acid-binding Ig-like lectin 7 (SIGLEC-7),CD328,Q9Y286,TATATGCTGA,TATATGCTGA -CD25,,Interleukin-2 receptor subunit alpha,IL-2Rα,P01589,AGAGACGAAT,AGAGACGAAT -PD-1,,Programmed cell death protein 1 (PD-1),CD279,Q15116,TACAGAGCCC,TACAGAGCCC -NKp46,,Natural cytotoxicity triggering receptor 1 (NKp46),CD335,O76036,ATTACCCGCG,ATTACCCGCG -mIgG2a,yes,,,,ATTTCCACTA,ATTTCCACTA -mIgG2b,yes,,,,CTAAATGGCT,CTAAATGGCT -CTLA-4,,Cytotoxic T-lymphocyte protein 4,CD152,P16410,TTTCTGCATT,TTTCTGCATT -CD86,,T-lymphocyte activation antigen CD86,B7-2,P42081,ACCATCACTT,ACCATCACTT -CD13,,Aminopeptidase N,Aminopeptidase N,P15144,GCATGGGTAG,GCATGGGTAG -ADAM10,,Disintegrin and metalloproteinase domain-containing protein 10,CD156c,O14672,ATAAGTTCCA,ATAAGTTCCA -KIR2DL1,,Killer cell immunoglobulin-like receptor 2DL1,CD158a,P43626,TGTTACGGTC,TGTTACGGTC -KIR2DL2/DL3,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158b,P43627,ACTGCATTGA,ACTGCATTGA -NKG2A,,NKG2-A/NKG2-B type II integral membrane protein,CD159a,P26715,CGTACACGGT,CGTACACGGT -NKG2C,,NKG2-C type II integral membrane protein,CD159c,P26717,CAACAGTCGA,CAACAGTCGA -CD163,,Scavenger receptor cysteine-rich type 1 protein M130,,Q86VB7,GACCGTGATT,GACCGTGATT -CD169,,Sialoadhesin,Siglec-1,Q9BZZ2,TAATCGCGGG,TAATCGCGGG -CD1a,,T cell surface glycoprotein CD1a,,P06126,CGACTAATCA,CGACTAATCA -CD1c,,T cell surface glycoprotein CD1c,,P29017,GTGCACTGTC,GTGCACTGTC -CD206,,Macrophage mannose receptor 1,Mannose receptor,P22897,TGCCTAATAG,TGCCTAATAG -DNAM-1,,CD226 antigen,CD226,Q15762,CGGTCATTAA,CGGTCATTAA -PD-L2,,Programmed cell death 1 ligand 2 (PDL2),CD273,Q9BQ51,ATCGCGAAGC,ATCGCGAAGC -CD28,,T cell-specific surface glycoprotein CD28,,P10747,CATAACAATC,CATAACAATC -SLAMF6,,SLAM family member 6,CD352;NTB-A,Q96DU3,TCGGAGACAC,TCGGAGACAC -CD45RO,,"Receptor-type tyrosine-protein phosphatase C. Isoform O",,P08575,TTGATGACTC,TTGATGACTC -CD49e,,Integrin α-5,Integrin α5,P08648,TCTTTAGAAG,TCTTTAGAAG -CD56,,Neural cell adhesion molecule 1,NCAM,P13591,GTGCGTAAGC,GTGCGTAAGC -CD79a,,B-cell antigen receptor complex-associated protein alpha chain,MB-1,P11912,TCTCTCTGTT,TCTCTCTGTT -CD80,,T-lymphocyte activation antigen CD80,B7-1,P33681,AAGACGCGGA,AAGACGCGGA -CD81,,CD81 antigen,Tetraspanin-28,P60033,TGGGTTATGT,TGGGTTATGT -LILRB1,,Leukocyte immunoglobulin-like receptor subfamily B member 1,CD85j;ILT-2,Q8NHL6,CCTAAGTCTA,CCTAAGTCTA -CD93,,Complement component C1q receptor,,Q9NPY3,GCAGCGAACA,GCAGCGAACA -IgD,,Immunoglobulin delta heavy chain,,P0DOX3,AGATGAGGCA,AGATGAGGCA -IgE,,Immunoglobulin epsilon heavy chain,,P0DOX4,CGACGGTAAG,CGACGGTAAG -IgM,,Immunoglobulin mu heavy chain,,P0DOX6,GTGGATCCAA,GTGGATCCAA -KLRG1,,Killer cell lectin-like receptor subfamily G member 1,,Q96E93,TATACAGACA,TATACAGACA -NKp80,,Killer cell lectin-like receptor subfamily F member 1,KLRF1,Q9NZS2,CCATCGGATC,CCATCGGATC -TCRgd,,T cell receptor gamma constant 1 /delta constant,,P0CF51;B7Z8K6,CTTATGACCA,CTTATGACCA -CD10,,Neprilysin,Neprilysin,P08473,CGCAGGTAGC,CGCAGGTAGC -CD103,,Integrin alpha-E,Integrin αE,P38570,CCTATGCGAA,CCTATGCGAA -CCR9,,C-C chemokine receptor type 9,CD199,P51686,ACTCTTTCTG,ACTCTTTCTG -CD1b,,T cell surface glycoprotein CD1b,,P29016,GACACCACCG,GACACCACCG -CD21,,Complement receptor type 2,CR2,P20023,GTGGCGTTAA,GTGGCGTTAA -TALLA,,Tetraspanin-7,CD231;Tetraspanin-7,P41732,CACGATACTT,CACGATACTT -CD277,,Butyrophilin subfamily 3 member A1,BTN3,O00481,GAGTGATACG,GAGTGATACG -LAIR1,,Leukocyte-associated immunoglobulin-like receptor 1,CD305,Q6GTX8,GCAATGTGTA,GCAATGTGTA -CD371,,C-type lectin domain family 12 member A,CLEC12A,Q5QGZ9,AAGGTCCCAT,AAGGTCCCAT -CD89,,Immunoglobulin alpha Fc receptor,FcαRI;FCAR,P24071,GTATCATAAG,GTATCATAAG -CD90,,Thy-1 membrane glycoprotein,Thy-1,P04216,TAGCCGATTA,TAGCCGATTA -CD70,,CD70 antigen,CD27L,P32970,CTCAGCATGC,CTCAGCATGC -GPR56,,Adhesion G-protein coupled receptor G1,TM7XN1,Q9Y653,GCGTCTCTCT,GCGTCTCTCT -HLA-DQ,,"HLA class II histocompatibility antigen, DQ",,P01906;P05538;P01920;P01909,ATACTTGAGC,ATACTTGAGC -TCRVd2,,T cell receptor delta variable 2,,,CCGACCATTC,CCGACCATTC -HLA-DR-DP-DQ,,HLA class II histocompatibility antigen,,P01903;P20036;P01909,AACAGAGGAA,AACAGAGGAA -Siglec-9,,Sialic acid-binding Ig-like lectin 9,,Q9Y336,TTAACAAGCA,TTAACAAGCA -TCRVa7.2,,T cell receptor alpha variable 7,,A0A075B6U4,TCCCAGGTCC,TCCCAGGTCC -Fas,,Tumor necrosis factor receptor superfamily member 6,CD95,P25445,TACTGTTGGG,TACTGTTGGG -TCRVg9,,T cell receptor gamma variable 9,,,TCGTTTGTCA,TCGTTTGTCA -CD127,,Interleukin-7 receptor subunit alpha,IL-7Rα,P16871,TGTTAGAGGA,TGTTAGAGGA -CD141,,Thrombomodulin,TM,P07204,AATTGTTCGT,AATTGTTCGT -CD31,,Platelet endothelial cell adhesion molecule,PECAM-1,P16284,GGCAAAGAGC,GGCAAAGAGC -CD6,,T cell differentiation antigen CD6,,P30203,CTAAGATCTC,CTAAGATCTC -CD57,,Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1,,Q9P2W7,ACGACGGGAC,ACGACGGGAC -CD73,,5’-nucleotidase,NT5E,P21589,ACCAAGGACG,ACCAAGGACG -TIM-3,,Hepatitis A virus cellular receptor 2,CD366;HAVCR2,Q8TDQ0,CGCCAAGTGG,CGCCAAGTGG -GITR,,Tumor necrosis factor receptor superfamily member 18,CD357,Q9Y5U5,TGAGTCACTC,TGAGTCACTC -CCR3,,C-C chemokine receptor type 3,CD193,P51677,CCGTGACCCA,CCGTGACCCA -SLAMF7,,SLAM family member 7,CD319;CRACC,Q9NQ25,AGGCGGAAAT,AGGCGGAAAT -TIGIT,,T cell immunoreceptor with Ig and ITIM domains,,Q495A1,ACTGAGTCGC,ACTGAGTCGC -OX40,,Tumor necrosis factor receptor superfamily member 4,CD134,P43489,CCACTTCCGT,CCACTTCCGT -ICAM-2,,Intercellular adhesion molecule 2,CD102,P13598,TATCTGGGAT,TATCTGGGAT -CD123,,Interleukin-3 receptor subunit alpha,IL-3Rα,P26951,TGACTGCTAC,TGACTGCTAC -CD150,,Signaling lymphocytic activation molecule,SLAMF1,Q13291,TCGAATGGAT,TCGAATGGAT -CD40L,,CD40 ligand,CD154,P29965,CTAGATTTGC,CTAGATTTGC -KIR,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158,Q8N743,TCCTCTCCTG,TCCTCTCCTG -CD161,,Killer cell lectin-like receptor subfamily B member 1,KLRB1,Q12918,ACTGAACTAC,ACTGAACTAC -CD180,,CD180 antigen,RP105,Q99467,TGAGCTCCAA,TGAGCTCCAA -CCR1,,C-C chemokine receptor type 1,CD191,P32246,CCGGTGGTTC,CCGGTGGTTC -CCR2,,C-C chemokine receptor type 2,CD192,P41597,GGTTCTCCAC,GGTTCTCCAC -CD1d,,Antigen-presenting glycoprotein CD1d,,P15813,CAACGTCCCA,CAACGTCCCA -CD200,,OX-2 membrane glycoprotein,,P41217,CGCACGGGTT,CGCACGGGTT -Ly9,,T-lymphocyte surface antigen Ly-9,CD229;SLAMF3,Q9HBG7,TCGACGAGTG,TCGACGAGTG -CD24,,Signal transducer CD24,HSA,P25063,TCTTGTTCCC,TCTTGTTCCC -2B4,,Natural killer cell receptor 2B4,CD244;SLAMF4,Q9BZW8,TCTCAATCAA,TCTCAATCAA -BAFF-R,,Tumor necrosis factor receptor superfamily member 13C (BAFFR),CD268,Q96RJ3,ACGTAACCGC,ACGTAACCGC -ICOS,,Inducible T cell co-stimulator,CD278,Q9Y6W8,TTTCGGACAG,TTTCGGACAG -CD32,,Low-affinity immunoglobulin gamma Fc region receptor II-b,FcγRII,P31994,GATTTCCAGC,GATTTCCAGC -CD33,,Myeloid cell surface antigen CD33,Siglec-3,P20138,GCGATATAGT,GCGATATAGT -NKp30,,Natural cytotoxicity triggering receptor 3 (NKp30),CD337,O14931,CTTATCTCTT,CTTATCTCTT -CD38,,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,,P28907,TCCGATCTGG,TCCGATCTGG -CD39,,Ectonucleoside triphosphate diphosphohydrolase 1,ENTPD1,P49961,TCAGCGCCTT,TCAGCGCCTT -CD40,,Tumor necrosis factor receptor superfamily member 5,,P25942,TCTGGCGTGG,TCTGGCGTGG -CD48,,CD48 antigen,SLAMF2;BLAST-1,P09326,AGTACGAAGA,AGTACGAAGA -ICAM-3,,Intercellular adhesion molecule 3,CD50,P32942,CTCCGCGTTG,CTCCGCGTTG -CD55,,Complement decay-accelerating factor (DAF),DAF,P08174,TTAGCTAAAC,TTAGCTAAAC -CD58,,Lymphocyte function-associated antigen 3 (LFA3),LFA-3,P19256,ATGTTATGTG,ATGTTATGTG -CD62P,,P-selectin,P-selectin,P16109,ACTTAGCGCT,ACTTAGCGCT -CD69,,Early activation antigen CD69,,Q07108,GAAGGGTCTC,GAAGGGTCTC -CD72,,B-cell differentiation antigen CD72,Lyb-2,P21854,GCGGTGACTT,GCGGTGACTT -CD84,,SLAM family member 5,SLAMF5,Q9UIB8,GCCATTGGAA,GCCATTGGAA -CD9,,CD9 antigen,Tetraspanin-29,P21926,GTCTGGTCAT,GTCTGGTCAT -CD94,,Natural killer cells antigen CD94,KLRD1,Q13241,CTACAACCTT,CTACAACCTT -TCRVb5,,T cell receptor beta variable 5,,,GGCCTCAAGT,GGCCTCAAGT -CD3e,,T cell surface glycoprotein CD3 epsilon chain,,P07766,TGTAGAATTC,TGTAGAATTC -CD4,,T cell surface glycoprotein CD4,,P01730,GACAACTTCT,GACAACTTCT -CD11a,,Integrin α-L (LFA-1 α),ITGAL;LFA-1 α,P20701,ACACACTTGA,ACACACTTGA -CD43,,Leukosialin,Leukosialin,P16150,GAGATTACTA,GAGATTACTA -CD7,,T cell antigen CD7,,P09564,CTGGGTCCGT,CTGGGTCCGT -CD53,,Leukocyte surface antigen CD53,Tetraspanin-25,P19397,CAACCCGCTT,CAACCCGCTT -CD302,,C-type lectin domain family 13 member A,CLEC13A,Q8IX05,TAGACATTGG,TAGACATTGG -VISTA,,V-type immunoglobulin domain-containing suppressor of T cell activation,VSIR,Q9H7M9,AATGTTAACG,AATGTTAACG -BCMA,,Tumor necrosis factor receptor superfamily member 17,CD269,Q02223,CTGGACTATG,CTGGACTATG -CD138,,Syndecan-1,Syndecan-1,P18827,CTGGGCTTAC,CTGGGCTTAC -4-1BB,,Tumor necrosis factor receptor superfamily member 9,CD137,Q07011,CCAGCTAGAA,CCAGCTAGAA -CD66b,,Cell adhesion molecule CEACAM8,CEACAM8,P31997,CTAGGCAGTT,CTAGGCAGTT -CX3CR1,,CX3C chemokine receptor 1,Fractalkine receptor,P49238,TACTCCCGCC,TACTCCCGCC -EpCAM,,Epithelial cell adhesion molecule,CD326,P16422,CGTTCTTACA,CGTTCTTACA -DC-SIGN,,CD209 antigen,CD209,Q9NNX6,TGGACGTGAA,TGGACGTGAA -CD34,,Hematopoietic progenitor cell antigen CD34,,P28906,CCGTCTAGCC,CCGTCTAGCC -Dectin-1,,C-type lectin domain family 7 member A,CD369;CLEC7A,Q9BXN2,CTGCCAAGAC,CTGCCAAGAC -ICAM-1,,Intercellular adhesion molecule 1,CD54,P05362,AGCAGCTGAT,AGCAGCTGAT -CD71,,Transferrin receptor protein 1,Transferrin receptor,P02786,TCAGGACAGA,TCAGGACAGA -CD47,,Leukocyte surface antigen CD47,Integrin associated protein,Q08722,AGCTACTATT,AGCTACTATT -c-Kit,,Mast/Stem cell growth factor receptor Kit,CD117,P10721,GCTATAATTG,GCTATAATTG -NKG2D,,NKG2-D type II integral membrane protein,CD314;KG2DN,P26718,TGGCGCACAC,TGGCGCACAC -FMC63,,,,,CGATTGGCAC,CGATTGGCAC diff --git a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FMC63-v1.1.csv b/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FMC63-v1.1.csv deleted file mode 100644 index 9de13bf6c..000000000 --- a/src/pixelator/pna/resources/panels/proxiome-v1-immuno-156-FMC63-v1.1.csv +++ /dev/null @@ -1,168 +0,0 @@ -# --- -# name: proxiome-v1-immuno-156-FMC63-v1.1 -# product: proxiome-v1-immuno-156-FMC63-v1 -# description: >- -# Panel for the with the 155 markers + 3 control markers -# of the Proximome Immuno 155 panel, plus the FMC63 marker -# version: 1.1.1 -# --- -marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2 -HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG -B2M,,Beta-2-microglobulin,,P61769,CCAGGTTCCG,CCAGGTTCCG -CD11b,,Integrin α-M (ITGAM),ITGAM;Mac-1 α,P11215,CAGCTATGGT,CAGCTATGGT -CD11c,,Integrin α-X,Integrin αX,P20702,ATATGACGGT,ATATGACGGT -CD18,,Integrin beta 2,Integrin β2,P05107,GGGTAGGCTG,GGGTAGGCTG -CD82,,CD82 antigen,Tetraspanin-27,P27701,CCCGTCATGA,CCCGTCATGA -CD8,,T cell surface glycoprotein CD8 a/b chains,,P01732;P10966,CGGTGGATCA,CGGTGGATCA -TCRab,,T cell receptor alpha chain constant/beta constant 1,,P01848;P01850,CTGGTAGCAA,CTGGTAGCAA -HLA-DR,,"HLA class II histocompatibility antigen, DR",,P01903;P01911,TGTTGTCGAA,TGTTGTCGAA -CD45,,"Receptor-type tyrosine-protein phosphatase C. All 6 isoforms (ABC, AB, BC, B and O)",PTPRC,P08575,TGGAGGCTCT,TGGAGGCTCT -CD14,,Monocyte differentiation antigen CD14,,P08571,TGGCTATGTA,TGGCTATGTA -CD16,,Low-affinity immunoglobulin gamma Fc region receptor / III-A and -B,FcγRIII,P08637;O75015,ATAGGTTAGG,ATAGGTTAGG -CD19,,B-lymphocyte antigen CD19,,P15391,ACGGAATATT,ACGGAATATT -mIgG1,yes,,,,ATGCTAGTCG,ATGCTAGTCG -CD45RB,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, BC, and B)",,P08575,GAAGCAGTAT,GAAGCAGTAT -CD44,,CD44 antigen,,P16070,GTGAGTCAAT,GTGAGTCAAT -CD52,,CAMPATH-1 antigen,CAMPATH-1,P31358,CTTTAGCAGG,CTTTAGCAGG -CD59,,CD59 glycoprotein,Protectin;MAC-IP,P13987,GGTGTATGAG,GGTGTATGAG -CD45RA,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, and A)",,P08575,GGATTCGTGG,GGATTCGTGG -CD36,,Platelet glycoprotein 4,FAT;SCARB3,P16671,TACCCTGCGA,TACCCTGCGA -CD2,,T cell surface antigen CD2,,P06729,TGCCGATGCC,TGCCGATGCC -CD29,,Integrin beta-1,Integrin β1,P05556,TCCAGTGTCT,TCCAGTGTCT -CD5,,T cell surface glycoprotein CD5,,P06127,CACCCATCAA,CACCCATCAA -CD162,,P-selectin glycoprotein ligand 1,SELPLG;PSGL-1,Q14242,CTTCGTGGAC,CTTCGTGGAC -CD27,,CD27 antigen,,P26842,GGTTTGCAAA,GGTTTGCAAA -CR1,,Complement receptor type 1,CD35,P17927,CGCCACCTTT,CGCCACCTTT -CD26,,Dipeptidyl peptidase 4,DPP4,P27487,GATTCGCTGT,GATTCGCTGT -CD49d,,Integrin α-4,Integrin α4,P13612,AACTTAGGTT,AACTTAGGTT -CD37,,Leukocyte antigen CD37,Tetraspanin-26,P11049,AGAAGAAGAG,AGAAGAAGAG -CD41,,Integrin α-IIb,Integrin αIIb,P08514,TAAGGCATAA,TAAGGCATAA -CD20,,B-lymphocyte antigen CD20,,P11836,GCCACACCCA,GCCACACCCA -CD64,,High affinity immunoglobulin gamma Fc receptor I,FcγRI,P12314,CTTGTATATC,CTTGTATATC -CD22,,B-cell receptor CD22,,P20273,TGACCCGTTC,TGACCCGTTC -PD-L1,,Programmed cell death 1 ligand 1 (PDL1),CD274,Q9NZQ7,GCTTGAGATT,GCTTGAGATT -Siglec-7,,Sialic acid-binding Ig-like lectin 7 (SIGLEC-7),CD328,Q9Y286,TATATGCTGA,TATATGCTGA -CD25,,Interleukin-2 receptor subunit alpha,IL-2Rα,P01589,AGAGACGAAT,AGAGACGAAT -PD-1,,Programmed cell death protein 1 (PD-1),CD279,Q15116,TACAGAGCCC,TACAGAGCCC -NKp46,,Natural cytotoxicity triggering receptor 1 (NKp46),CD335,O76036,ATTACCCGCG,ATTACCCGCG -mIgG2a,yes,,,,ATTTCCACTA,ATTTCCACTA -mIgG2b,yes,,,,CTAAATGGCT,CTAAATGGCT -CTLA-4,,Cytotoxic T-lymphocyte protein 4,CD152,P16410,TTTCTGCATT,TTTCTGCATT -CD86,,T-lymphocyte activation antigen CD86,B7-2,P42081,ACCATCACTT,ACCATCACTT -CD13,,Aminopeptidase N,Aminopeptidase N,P15144,GCATGGGTAG,GCATGGGTAG -ADAM10,,Disintegrin and metalloproteinase domain-containing protein 10,CD156c,O14672,ATAAGTTCCA,ATAAGTTCCA -KIR2DL1,,Killer cell immunoglobulin-like receptor 2DL1,CD158a,P43626,TGTTACGGTC,TGTTACGGTC -KIR2DL2/DL3,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158b,P43627,ACTGCATTGA,ACTGCATTGA -NKG2A,,NKG2-A/NKG2-B type II integral membrane protein,CD159a,P26715,CGTACACGGT,CGTACACGGT -NKG2C,,NKG2-C type II integral membrane protein,CD159c,P26717,CAACAGTCGA,CAACAGTCGA -CD163,,Scavenger receptor cysteine-rich type 1 protein M130,,Q86VB7,GACCGTGATT,GACCGTGATT -CD169,,Sialoadhesin,Siglec-1,Q9BZZ2,TAATCGCGGG,TAATCGCGGG -CD1a,,T cell surface glycoprotein CD1a,,P06126,CGACTAATCA,CGACTAATCA -CD1c,,T cell surface glycoprotein CD1c,,P29017,GTGCACTGTC,GTGCACTGTC -CD206,,Macrophage mannose receptor 1,Mannose receptor,P22897,TGCCTAATAG,TGCCTAATAG -DNAM-1,,CD226 antigen,CD226,Q15762,CGGTCATTAA,CGGTCATTAA -PD-L2,,Programmed cell death 1 ligand 2 (PDL2),CD273,Q9BQ51,ATCGCGAAGC,ATCGCGAAGC -CD28,,T cell-specific surface glycoprotein CD28,,P10747,CATAACAATC,CATAACAATC -SLAMF6,,SLAM family member 6,CD352;NTB-A,Q96DU3,TCGGAGACAC,TCGGAGACAC -CD45RO,,"Receptor-type tyrosine-protein phosphatase C. Isoform O",,P08575,TTGATGACTC,TTGATGACTC -CD49e,,Integrin α-5,Integrin α5,P08648,AACTCCTGAA,AACTCCTGAA -CD56,,Neural cell adhesion molecule 1,NCAM,P13591,GTGCGTAAGC,GTGCGTAAGC -CD79a,,B-cell antigen receptor complex-associated protein alpha chain,MB-1,P11912,AGATCGACAG,AGATCGACAG -CD80,,T-lymphocyte activation antigen CD80,B7-1,P33681,AAGACGCGGA,AAGACGCGGA -CD81,,CD81 antigen,Tetraspanin-28,P60033,TGGGTTATGT,TGGGTTATGT -LILRB1,,Leukocyte immunoglobulin-like receptor subfamily B member 1,CD85j;ILT-2,Q8NHL6,CCTAAGTCTA,CCTAAGTCTA -CD93,,Complement component C1q receptor,,Q9NPY3,GCAGCGAACA,GCAGCGAACA -IgD,,Immunoglobulin delta heavy chain,,P0DOX3,AGATGAGGCA,AGATGAGGCA -IgE,,Immunoglobulin epsilon heavy chain,,P0DOX4,CGACGGTAAG,CGACGGTAAG -IgM,,Immunoglobulin mu heavy chain,,P0DOX6,GTGGATCCAA,GTGGATCCAA -KLRG1,,Killer cell lectin-like receptor subfamily G member 1,,Q96E93,TATACAGACA,TATACAGACA -NKp80,,Killer cell lectin-like receptor subfamily F member 1,KLRF1,Q9NZS2,CCATCGGATC,CCATCGGATC -TCRgd,,T cell receptor gamma constant 1 /delta constant,,P0CF51;B7Z8K6,CTTATGACCA,CTTATGACCA -CD10,,Neprilysin,Neprilysin,P08473,CGCAGGTAGC,CGCAGGTAGC -CD103,,Integrin alpha-E,Integrin αE,P38570,CCTATGCGAA,CCTATGCGAA -CCR9,,C-C chemokine receptor type 9,CD199,P51686,ACTCTTTCTG,ACTCTTTCTG -CD1b,,T cell surface glycoprotein CD1b,,P29016,GACACCACCG,GACACCACCG -CD21,,Complement receptor type 2,CR2,P20023,GTGGCGTTAA,GTGGCGTTAA -TALLA,,Tetraspanin-7,CD231;Tetraspanin-7,P41732,CACGATACTT,CACGATACTT -CD277,,Butyrophilin subfamily 3 member A1,BTN3,O00481,GAGTGATACG,GAGTGATACG -LAIR1,,Leukocyte-associated immunoglobulin-like receptor 1,CD305,Q6GTX8,GCAATGTGTA,GCAATGTGTA -CD371,,C-type lectin domain family 12 member A,CLEC12A,Q5QGZ9,AAGGTCCCAT,AAGGTCCCAT -CD89,,Immunoglobulin alpha Fc receptor,FcαRI;FCAR,P24071,GTATCATAAG,GTATCATAAG -CD90,,Thy-1 membrane glycoprotein,Thy-1,P04216,TAGCCGATTA,TAGCCGATTA -CD70,,CD70 antigen,CD27L,P32970,CTCAGCATGC,CTCAGCATGC -GPR56,,Adhesion G-protein coupled receptor G1,TM7XN1,Q9Y653,GCGTCTCTCT,GCGTCTCTCT -HLA-DQ,,"HLA class II histocompatibility antigen, DQ",,P01906;P05538;P01920;P01909,ATACTTGAGC,ATACTTGAGC -TCRVd2,,T cell receptor delta variable 2,,,CCGACCATTC,CCGACCATTC -HLA-DR-DP-DQ,,HLA class II histocompatibility antigen,,P01903;P20036;P01909,AACAGAGGAA,AACAGAGGAA -Siglec-9,,Sialic acid-binding Ig-like lectin 9,,Q9Y336,TTAACAAGCA,TTAACAAGCA -TCRVa7.2,,T cell receptor alpha variable 7,,A0A075B6U4,TCCCAGGTCC,TCCCAGGTCC -Fas,,Tumor necrosis factor receptor superfamily member 6,CD95,P25445,TACTGTTGGG,TACTGTTGGG -TCRVg9,,T cell receptor gamma variable 9,,,TCGTTTGTCA,TCGTTTGTCA -CD127,,Interleukin-7 receptor subunit alpha,IL-7Rα,P16871,TGTTAGAGGA,TGTTAGAGGA -CD141,,Thrombomodulin,TM,P07204,AATTGTTCGT,AATTGTTCGT -CD31,,Platelet endothelial cell adhesion molecule,PECAM-1,P16284,GGCAAAGAGC,GGCAAAGAGC -CD6,,T cell differentiation antigen CD6,,P30203,CTAAGATCTC,CTAAGATCTC -CD57,,Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1,,Q9P2W7,ACGACGGGAC,ACGACGGGAC -CD73,,5’-nucleotidase,NT5E,P21589,ACCAAGGACG,ACCAAGGACG -TIM-3,,Hepatitis A virus cellular receptor 2,CD366;HAVCR2,Q8TDQ0,CGCCAAGTGG,CGCCAAGTGG -GITR,,Tumor necrosis factor receptor superfamily member 18,CD357,Q9Y5U5,TGAGTCACTC,TGAGTCACTC -CCR3,,C-C chemokine receptor type 3,CD193,P51677,CCGTGACCCA,CCGTGACCCA -SLAMF7,,SLAM family member 7,CD319;CRACC,Q9NQ25,AGGCGGAAAT,AGGCGGAAAT -TIGIT,,T cell immunoreceptor with Ig and ITIM domains,,Q495A1,ACTGAGTCGC,ACTGAGTCGC -OX40,,Tumor necrosis factor receptor superfamily member 4,CD134,P43489,CCACTTCCGT,CCACTTCCGT -ICAM-2,,Intercellular adhesion molecule 2,CD102,P13598,TATCTGGGAT,TATCTGGGAT -CD123,,Interleukin-3 receptor subunit alpha,IL-3Rα,P26951,TGACTGCTAC,TGACTGCTAC -CD150,,Signaling lymphocytic activation molecule,SLAMF1,Q13291,TCGAATGGAT,TCGAATGGAT -CD40L,,CD40 ligand,CD154,P29965,CTAGATTTGC,CTAGATTTGC -KIR,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158,Q8N743,TCCTCTCCTG,TCCTCTCCTG -CD161,,Killer cell lectin-like receptor subfamily B member 1,KLRB1,Q12918,ACTGAACTAC,ACTGAACTAC -CD180,,CD180 antigen,RP105,Q99467,TGAGCTCCAA,TGAGCTCCAA -CCR1,,C-C chemokine receptor type 1,CD191,P32246,CCGGTGGTTC,CCGGTGGTTC -CCR2,,C-C chemokine receptor type 2,CD192,P41597,GGTTCTCCAC,GGTTCTCCAC -CD1d,,Antigen-presenting glycoprotein CD1d,,P15813,CAACGTCCCA,CAACGTCCCA -CD200,,OX-2 membrane glycoprotein,,P41217,CGCACGGGTT,CGCACGGGTT -Ly9,,T-lymphocyte surface antigen Ly-9,CD229;SLAMF3,Q9HBG7,TCGACGAGTG,TCGACGAGTG -CD24,,Signal transducer CD24,HSA,P25063,TCTTGTTCCC,TCTTGTTCCC -2B4,,Natural killer cell receptor 2B4,CD244;SLAMF4,Q9BZW8,TCTCAATCAA,TCTCAATCAA -BAFF-R,,Tumor necrosis factor receptor superfamily member 13C (BAFFR),CD268,Q96RJ3,ACGTAACCGC,ACGTAACCGC -ICOS,,Inducible T cell co-stimulator,CD278,Q9Y6W8,CAGGCACCTG,CAGGCACCTG -CD32,,Low-affinity immunoglobulin gamma Fc region receptor II-b,FcγRII,P31994,GATTTCCAGC,GATTTCCAGC -CD33,,Myeloid cell surface antigen CD33,Siglec-3,P20138,GCGATATAGT,GCGATATAGT -NKp30,,Natural cytotoxicity triggering receptor 3 (NKp30),CD337,O14931,CTTATCTCTT,CTTATCTCTT -CD38,,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,,P28907,TCCGATCTGG,TCCGATCTGG -CD39,,Ectonucleoside triphosphate diphosphohydrolase 1,ENTPD1,P49961,TCAGCGCCTT,TCAGCGCCTT -CD40,,Tumor necrosis factor receptor superfamily member 5,,P25942,TCTGGCGTGG,TCTGGCGTGG -CD48,,CD48 antigen,SLAMF2;BLAST-1,P09326,AGTACGAAGA,AGTACGAAGA -ICAM-3,,Intercellular adhesion molecule 3,CD50,P32942,CTCCGCGTTG,CTCCGCGTTG -CD55,,Complement decay-accelerating factor (DAF),DAF,P08174,TTAGCTAAAC,TTAGCTAAAC -CD58,,Lymphocyte function-associated antigen 3 (LFA3),LFA-3,P19256,ATGTTATGTG,ATGTTATGTG -CD62P,,P-selectin,P-selectin,P16109,ACTTAGCGCT,ACTTAGCGCT -CD69,,Early activation antigen CD69,,Q07108,GAAGGGTCTC,GAAGGGTCTC -CD72,,B-cell differentiation antigen CD72,Lyb-2,P21854,GCGGTGACTT,GCGGTGACTT -CD84,,SLAM family member 5,SLAMF5,Q9UIB8,GCCATTGGAA,GCCATTGGAA -CD9,,CD9 antigen,Tetraspanin-29,P21926,GTCTGGTCAT,GTCTGGTCAT -CD94,,Natural killer cells antigen CD94,KLRD1,Q13241,CTACAACCTT,CTACAACCTT -TCRVb5,,T cell receptor beta variable 5,,,GGCCTCAAGT,GGCCTCAAGT -CD3e,,T cell surface glycoprotein CD3 epsilon chain,,P07766,TGTAGAATTC,TGTAGAATTC -CD4,,T cell surface glycoprotein CD4,,P01730,GACAACTTCT,GACAACTTCT -CD11a,,Integrin α-L (LFA-1 α),ITGAL;LFA-1 α,P20701,ACACACTTGA,ACACACTTGA -CD43,,Leukosialin,Leukosialin,P16150,GAGATTACTA,GAGATTACTA -CD7,,T cell antigen CD7,,P09564,CTGGGTCCGT,CTGGGTCCGT -CD53,,Leukocyte surface antigen CD53,Tetraspanin-25,P19397,CAACCCGCTT,CAACCCGCTT -CD302,,C-type lectin domain family 13 member A,CLEC13A,Q8IX05,TAGACATTGG,TAGACATTGG -VISTA,,V-type immunoglobulin domain-containing suppressor of T cell activation,VSIR,Q9H7M9,AATGTTAACG,AATGTTAACG -BCMA,,Tumor necrosis factor receptor superfamily member 17,CD269,Q02223,CTGGACTATG,CTGGACTATG -CD138,,Syndecan-1,Syndecan-1,P18827,CTGGGCTTAC,CTGGGCTTAC -4-1BB,,Tumor necrosis factor receptor superfamily member 9,CD137,Q07011,CCAGCTAGAA,CCAGCTAGAA -CD66b,,Cell adhesion molecule CEACAM8,CEACAM8,P31997,CTAGGCAGTT,CTAGGCAGTT -CX3CR1,,CX3C chemokine receptor 1,Fractalkine receptor,P49238,TACTCCCGCC,TACTCCCGCC -EpCAM,,Epithelial cell adhesion molecule,CD326,P16422,CGTTCTTACA,CGTTCTTACA -DC-SIGN,,CD209 antigen,CD209,Q9NNX6,TGGACGTGAA,TGGACGTGAA -CD34,,Hematopoietic progenitor cell antigen CD34,,P28906,CCGTCTAGCC,CCGTCTAGCC -Dectin-1,,C-type lectin domain family 7 member A,CD369;CLEC7A,Q9BXN2,CTGCCAAGAC,CTGCCAAGAC -ICAM-1,,Intercellular adhesion molecule 1,CD54,P05362,AGCAGCTGAT,AGCAGCTGAT -CD71,,Transferrin receptor protein 1,Transferrin receptor,P02786,TCAGGACAGA,TCAGGACAGA -CD47,,Leukocyte surface antigen CD47,Integrin associated protein,Q08722,AGCTACTATT,AGCTACTATT -c-Kit,,Mast/Stem cell growth factor receptor Kit,CD117,P10721,GCTATAATTG,GCTATAATTG -NKG2D,,NKG2-D type II integral membrane protein,CD314;KG2DN,P26718,TGGCGCACAC,TGGCGCACAC -FMC63,,,,,CGATTGGCAC,CGATTGGCAC diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-FLAG-v2.0.csv b/src/pixelator/pna/resources/panels/proxiome-v2-FLAG-v2.0.csv new file mode 100644 index 000000000..d07362db2 --- /dev/null +++ b/src/pixelator/pna/resources/panels/proxiome-v2-FLAG-v2.0.csv @@ -0,0 +1,10 @@ +# --- +# name: proxiome-v2-FLAG-v2.0 +# product: proxiome-v2-FLAG +# description: >- +# Panel for the FLAG marker +# version: 2.0.0 +# panel_type: addon +# --- +marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing +FLAG,,,,,CTTAACATCT,CTTAACATCT diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-FMC63-v2.0.csv b/src/pixelator/pna/resources/panels/proxiome-v2-FMC63-v2.0.csv new file mode 100644 index 000000000..1bf41be14 --- /dev/null +++ b/src/pixelator/pna/resources/panels/proxiome-v2-FMC63-v2.0.csv @@ -0,0 +1,10 @@ +# --- +# name: proxiome-v2-FMC63-v2.0 +# product: proxiome-v2-FMC63 +# description: >- +# Panel for the FMC63 marker +# version: 2.0.0 +# panel_type: addon +# --- +marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing +FMC63,,,,,CGATTGGCAC,CGATTGGCAC diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-G4S-v2.0.csv b/src/pixelator/pna/resources/panels/proxiome-v2-G4S-v2.0.csv new file mode 100644 index 000000000..21a4c198d --- /dev/null +++ b/src/pixelator/pna/resources/panels/proxiome-v2-G4S-v2.0.csv @@ -0,0 +1,10 @@ +# --- +# name: proxiome-v2-G4S-v2.0 +# product: proxiome-v2-G4S +# description: >- +# Panel for the G4S marker +# version: 2.0.0 +# panel_type: addon +# --- +marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing +G4S,,,,,TTCTTTGATG,TTCTTTGATG diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-hashing-prerelease.csv b/src/pixelator/pna/resources/panels/proxiome-v2-hashing-prerelease.csv new file mode 100644 index 000000000..38cf5cda7 --- /dev/null +++ b/src/pixelator/pna/resources/panels/proxiome-v2-hashing-prerelease.csv @@ -0,0 +1,33 @@ +# --- +# name: proxiome-v2-hashing-prerelease +# product: proxiome-v2-hashing +# description: >- +# 3*8 hashing antibodies +# version: 1.0.0 +# panel_type: sample_hashing +# --- +marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing +B2M-1,,,,,TGAGTGGTGA,TGAGTGGTGA,yes +B2M-2,,,,,TAGAGGAGGC,TAGAGGAGGC,yes +B2M-3,,,,,CCCACTAAGC,CCCACTAAGC,yes +B2M-4,,,,,TGGTTTACAA,TGGTTTACAA,yes +B2M-5,,,,,CTAACTACGG,CTAACTACGG,yes +B2M-6,,,,,TATTGAACCT,TATTGAACCT,yes +B2M-7,,,,,ATCAACCCTA,ATCAACCCTA,yes +B2M-8,,,,,GTATCCCTAC,GTATCCCTAC,yes +CD298-1,,,,,GCTAGCAACG,GCTAGCAACG,yes +CD298-2,,,,,AAATAGTACG,AAATAGTACG,yes +CD298-3,,,,,GACGGCTTAG,GACGGCTTAG,yes +CD298-4,,,,,GTCAAGGTAA,GTCAAGGTAA,yes +CD298-5,,,,,GGTAAGCCCT,GGTAAGCCCT,yes +CD298-6,,,,,GCCGCCTATG,GCCGCCTATG,yes +CD298-7,,,,,GCTCCGCAAC,GCTCCGCAAC,yes +CD298-8,,,,,AGCCTCAGCA,AGCCTCAGCA,yes +CD98-1,,,,,CACTTGGCCA,CACTTGGCCA,yes +CD98-2,,,,,ATTGTGTGGG,ATTGTGTGGG,yes +CD98-3,,,,,CATAGACCAT,CATAGACCAT,yes +CD98-4,,,,,ATGTTCCTCT,ATGTTCCTCT,yes +CD98-5,,,,,TTCGTAACTA,TTCGTAACTA,yes +CD98-6,,,,,CTGACCGCTA,CTGACCGCTA,yes +CD98-7,,,,,CCCTCGGTCT,CCCTCGGTCT,yes +CD98-8,,,,,ATCGCACGTA,ATCGCACGTA,yes diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-hashing-v2.0.csv b/src/pixelator/pna/resources/panels/proxiome-v2-hashing-v2.0.csv new file mode 100644 index 000000000..8afa544d4 --- /dev/null +++ b/src/pixelator/pna/resources/panels/proxiome-v2-hashing-v2.0.csv @@ -0,0 +1,33 @@ +# --- +# name: proxiome-v2-hashing-v2.0 +# product: proxiome-v2-hashing +# description: >- +# 3*8 hashing antibodies +# version: 2.0.0 +# panel_type: sample_hashing +# --- +marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing +B2M-1,,,,,GAGGGACGGT,GAGGGACGGT,yes +B2M-2,,,,,TAGAGGAGGC,TAGAGGAGGC,yes +B2M-3,,,,,CCCACTAAGC,CCCACTAAGC,yes +B2M-4,,,,,TGGTTTACAA,TGGTTTACAA,yes +B2M-5,,,,,CTAACTACGG,CTAACTACGG,yes +B2M-6,,,,,TATTGAACCT,TATTGAACCT,yes +B2M-7,,,,,ATCAACCCTA,ATCAACCCTA,yes +B2M-8,,,,,GTATCCCTAC,GTATCCCTAC,yes +CD298-1,,,,,AAAGTCTCTG,AAAGTCTCTG,yes +CD298-2,,,,,AAATAGTACG,AAATAGTACG,yes +CD298-3,,,,,GACGGCTTAG,GACGGCTTAG,yes +CD298-4,,,,,GTCAAGGTAA,GTCAAGGTAA,yes +CD298-5,,,,,GGTAAGCCCT,GGTAAGCCCT,yes +CD298-6,,,,,GCCGCCTATG,GCCGCCTATG,yes +CD298-7,,,,,GCTCCGCAAC,GCTCCGCAAC,yes +CD298-8,,,,,AGCCTCAGCA,AGCCTCAGCA,yes +CD98-1,,,,,TGGCTTAGCC,TGGCTTAGCC,yes +CD98-2,,,,,ATTGTGTGGG,ATTGTGTGGG,yes +CD98-3,,,,,CATAGACCAT,CATAGACCAT,yes +CD98-4,,,,,ATGTTCCTCT,ATGTTCCTCT,yes +CD98-5,,,,,TTCGTAACTA,TTCGTAACTA,yes +CD98-6,,,,,CTGACCGCTA,CTGACCGCTA,yes +CD98-7,,,,,CCCTCGGTCT,CCCTCGGTCT,yes +CD98-8,,,,,ATCGCACGTA,ATCGCACGTA,yes diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-155-prerelease.csv b/src/pixelator/pna/resources/panels/proxiome-v2-immuno-155-prerelease.csv deleted file mode 100644 index 785d88718..000000000 --- a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-155-prerelease.csv +++ /dev/null @@ -1,192 +0,0 @@ -# --- -# name: proxiome-v2-immuno-155-prerelease -# product: proxiome-v2-immuno-155 -# aliases: -# - proxiome-v2-immuno-155-v1.0 -# description: >- -# Panel for the Proxiome Immuno Kit with 155 markers + 3 control markers + 3*8 hashing antibodies -# version: 1.0.1 -# --- -marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing -HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG -B2M,,Beta-2-microglobulin,,P61769,CCAGGTTCCG,CCAGGTTCCG -CD11b,,Integrin α-M (ITGAM),ITGAM;Mac-1 α,P11215,CAGCTATGGT,CAGCTATGGT -CD11c,,Integrin α-X,Integrin αX,P20702,ATATGACGGT,ATATGACGGT -CD18,,Integrin beta 2,Integrin β2,P05107,GGGTAGGCTG,GGGTAGGCTG -CD82,,CD82 antigen,Tetraspanin-27,P27701,CCCGTCATGA,CCCGTCATGA -CD8,,T cell surface glycoprotein CD8 a/b chains,,P01732;P10966,CGGTGGATCA,CGGTGGATCA -TCRab,,T cell receptor alpha chain constant/beta constant 1,,P01848;P01850,CTGGTAGCAA,CTGGTAGCAA -HLA-DR,,"HLA class II histocompatibility antigen, DR",,P01903;P01911,TGTTGTCGAA,TGTTGTCGAA -CD45,,"Receptor-type tyrosine-protein phosphatase C. All 6 isoforms (ABC, AB, BC, B and O)",PTPRC,P08575,TGGAGGCTCT,TGGAGGCTCT -CD14,,Monocyte differentiation antigen CD14,,P08571,TGGCTATGTA,TGGCTATGTA -CD16,,Low-affinity immunoglobulin gamma Fc region receptor / III-A and -B,FcγRIII,P08637;O75015,ATAGGTTAGG,ATAGGTTAGG -CD19,,B-lymphocyte antigen CD19,,P15391,ACGGAATATT,ACGGAATATT -mIgG1,yes,,,,ATGCTAGTCG,ATGCTAGTCG -CD45RB,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, BC, and B)",,P08575,GAAGCAGTAT,GAAGCAGTAT -CD44,,CD44 antigen,,P16070,GTGAGTCAAT,GTGAGTCAAT -CD52,,CAMPATH-1 antigen,CAMPATH-1,P31358,CTTTAGCAGG,CTTTAGCAGG -CD59,,CD59 glycoprotein,Protectin;MAC-IP,P13987,GGTGTATGAG,GGTGTATGAG -CD45RA,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, and A)",,P08575,GGATTCGTGG,GGATTCGTGG -CD36,,Platelet glycoprotein 4,FAT;SCARB3,P16671,TACCCTGCGA,TACCCTGCGA -CD2,,T cell surface antigen CD2,,P06729,TGCCGATGCC,TGCCGATGCC -CD29,,Integrin beta-1,Integrin β1,P05556,TCCAGTGTCT,TCCAGTGTCT -CD5,,T cell surface glycoprotein CD5,,P06127,CACCCATCAA,CACCCATCAA -CD162,,P-selectin glycoprotein ligand 1,SELPLG;PSGL-1,Q14242,CTTCGTGGAC,CTTCGTGGAC -CD27,,CD27 antigen,,P26842,GGTTTGCAAA,GGTTTGCAAA -CR1,,Complement receptor type 1,CD35,P17927,CGCCACCTTT,CGCCACCTTT -CD26,,Dipeptidyl peptidase 4,DPP4,P27487,GATTCGCTGT,GATTCGCTGT -CD49d,,Integrin α-4,Integrin α4,P13612,AACTTAGGTT,AACTTAGGTT -CD37,,Leukocyte antigen CD37,Tetraspanin-26,P11049,AGAAGAAGAG,AGAAGAAGAG -CD41,,Integrin α-IIb,Integrin αIIb,P08514,TAAGGCATAA,TAAGGCATAA -CD20,,B-lymphocyte antigen CD20,,P11836,GCCACACCCA,GCCACACCCA -CD64,,High affinity immunoglobulin gamma Fc receptor I,FcγRI,P12314,CTTGTATATC,CTTGTATATC -CD22,,B-cell receptor CD22,,P20273,TGACCCGTTC,TGACCCGTTC -PD-L1,,Programmed cell death 1 ligand 1 (PDL1),CD274,Q9NZQ7,GCTTGAGATT,GCTTGAGATT -Siglec-7,,Sialic acid-binding Ig-like lectin 7 (SIGLEC-7),CD328,Q9Y286,TATATGCTGA,TATATGCTGA -CD25,,Interleukin-2 receptor subunit alpha,IL-2Rα,P01589,AGAGACGAAT,AGAGACGAAT -PD-1,,Programmed cell death protein 1 (PD-1),CD279,Q15116,TACAGAGCCC,TACAGAGCCC -NKp46,,Natural cytotoxicity triggering receptor 1 (NKp46),CD335,O76036,ATTACCCGCG,ATTACCCGCG -mIgG2a,yes,,,,ATTTCCACTA,ATTTCCACTA -mIgG2b,yes,,,,CTAAATGGCT,CTAAATGGCT -CTLA-4,,Cytotoxic T-lymphocyte protein 4,CD152,P16410,TTTCTGCATT,TTTCTGCATT -CD86,,T-lymphocyte activation antigen CD86,B7-2,P42081,ACCATCACTT,ACCATCACTT -CD13,,Aminopeptidase N,Aminopeptidase N,P15144,GCATGGGTAG,GCATGGGTAG -ADAM10,,Disintegrin and metalloproteinase domain-containing protein 10,CD156c,O14672,ATAAGTTCCA,ATAAGTTCCA -KIR2DL1,,Killer cell immunoglobulin-like receptor 2DL1,CD158a,P43626,TGTTACGGTC,TGTTACGGTC -KIR2DL2/DL3,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158b,P43627,ACTGCATTGA,ACTGCATTGA -NKG2A,,NKG2-A/NKG2-B type II integral membrane protein,CD159a,P26715,CGTACACGGT,CGTACACGGT -NKG2C,,NKG2-C type II integral membrane protein,CD159c,P26717,CAACAGTCGA,CAACAGTCGA -CD163,,Scavenger receptor cysteine-rich type 1 protein M130,,Q86VB7,GACCGTGATT,GACCGTGATT -CD169,,Sialoadhesin,Siglec-1,Q9BZZ2,TAATCGCGGG,TAATCGCGGG -CD1a,,T cell surface glycoprotein CD1a,,P06126,CGACTAATCA,CGACTAATCA -CD1c,,T cell surface glycoprotein CD1c,,P29017,GTGCACTGTC,GTGCACTGTC -CD206,,Macrophage mannose receptor 1,Mannose receptor,P22897,TGCCTAATAG,TGCCTAATAG -DNAM-1,,CD226 antigen,CD226,Q15762,CGGTCATTAA,CGGTCATTAA -PD-L2,,Programmed cell death 1 ligand 2 (PDL2),CD273,Q9BQ51,ATCGCGAAGC,ATCGCGAAGC -CD28,,T cell-specific surface glycoprotein CD28,,P10747,CATAACAATC,CATAACAATC -SLAMF6,,SLAM family member 6,CD352;NTB-A,Q96DU3,TCGGAGACAC,TCGGAGACAC -CD45RO,,"Receptor-type tyrosine-protein phosphatase C. Isoform O",,P08575,TTGATGACTC,TTGATGACTC -CD49e,,Integrin α-5,Integrin α5,P08648,AACTCCTGAA,AACTCCTGAA -CD56,,Neural cell adhesion molecule 1,NCAM,P13591,GTGCGTAAGC,GTGCGTAAGC -CD79a,,B-cell antigen receptor complex-associated protein alpha chain,MB-1,P11912,AGATCGACAG,AGATCGACAG -CD80,,T-lymphocyte activation antigen CD80,B7-1,P33681,AAGACGCGGA,AAGACGCGGA -CD81,,CD81 antigen,Tetraspanin-28,P60033,TGGGTTATGT,TGGGTTATGT -LILRB1,,Leukocyte immunoglobulin-like receptor subfamily B member 1,CD85j;ILT-2,Q8NHL6,CCTAAGTCTA,CCTAAGTCTA -CD93,,Complement component C1q receptor,,Q9NPY3,GCAGCGAACA,GCAGCGAACA -IgD,,Immunoglobulin delta heavy chain,,P0DOX3,AGATGAGGCA,AGATGAGGCA -IgE,,Immunoglobulin epsilon heavy chain,,P0DOX4,CGACGGTAAG,CGACGGTAAG -IgM,,Immunoglobulin mu heavy chain,,P0DOX6,GTGGATCCAA,GTGGATCCAA -KLRG1,,Killer cell lectin-like receptor subfamily G member 1,,Q96E93,TATACAGACA,TATACAGACA -NKp80,,Killer cell lectin-like receptor subfamily F member 1,KLRF1,Q9NZS2,CCATCGGATC,CCATCGGATC -TCRgd,,T cell receptor gamma constant 1 /delta constant,,P0CF51;B7Z8K6,CTTATGACCA,CTTATGACCA -CD10,,Neprilysin,Neprilysin,P08473,CGCAGGTAGC,CGCAGGTAGC -CD103,,Integrin alpha-E,Integrin αE,P38570,CCTATGCGAA,CCTATGCGAA -CD1b,,T cell surface glycoprotein CD1b,,P29016,GACACCACCG,GACACCACCG -CD21,,Complement receptor type 2,CR2,P20023,GTGGCGTTAA,GTGGCGTTAA -TALLA,,Tetraspanin-7,CD231;Tetraspanin-7,P41732,CACGATACTT,CACGATACTT -CD277,,Butyrophilin subfamily 3 member A1,BTN3,O00481,GAGTGATACG,GAGTGATACG -LAIR1,,Leukocyte-associated immunoglobulin-like receptor 1,CD305,Q6GTX8,GCAATGTGTA,GCAATGTGTA -CD371,,C-type lectin domain family 12 member A,CLEC12A,Q5QGZ9,AAGGTCCCAT,AAGGTCCCAT -CD89,,Immunoglobulin alpha Fc receptor,FcαRI;FCAR,P24071,GTATCATAAG,GTATCATAAG -CD90,,Thy-1 membrane glycoprotein,Thy-1,P04216,TAGCCGATTA,TAGCCGATTA -CD70,,CD70 antigen,CD27L,P32970,CTCAGCATGC,CTCAGCATGC -GPR56,,Adhesion G-protein coupled receptor G1,TM7XN1,Q9Y653,GCGTCTCTCT,GCGTCTCTCT -HLA-DQ,,"HLA class II histocompatibility antigen, DQ",,P01906;P05538;P01920;P01909,ATACTTGAGC,ATACTTGAGC -TCRVd2,,T cell receptor delta variable 2,,,CCGACCATTC,CCGACCATTC -HLA-DR-DP-DQ,,HLA class II histocompatibility antigen,,P01903;P20036;P01909,AACAGAGGAA,AACAGAGGAA -Siglec-9,,Sialic acid-binding Ig-like lectin 9,,Q9Y336,TTAACAAGCA,TTAACAAGCA -TCRVa7.2,,T cell receptor alpha variable 7,,A0A075B6U4,TCCCAGGTCC,TCCCAGGTCC -Fas,,Tumor necrosis factor receptor superfamily member 6,CD95,P25445,TACTGTTGGG,TACTGTTGGG -TCRVg9,,T cell receptor gamma variable 9,,,TCGTTTGTCA,TCGTTTGTCA -CD127,,Interleukin-7 receptor subunit alpha,IL-7Rα,P16871,TGTTAGAGGA,TGTTAGAGGA -CD141,,Thrombomodulin,TM,P07204,AATTGTTCGT,AATTGTTCGT -CD31,,Platelet endothelial cell adhesion molecule,PECAM-1,P16284,GGCAAAGAGC,GGCAAAGAGC -CD6,,T cell differentiation antigen CD6,,P30203,CTAAGATCTC,CTAAGATCTC -CD57,,Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1,,Q9P2W7,ACGACGGGAC,ACGACGGGAC -CD73,,5’-nucleotidase,NT5E,P21589,ACCAAGGACG,ACCAAGGACG -TIM-3,,Hepatitis A virus cellular receptor 2,CD366;HAVCR2,Q8TDQ0,CGCCAAGTGG,CGCCAAGTGG -GITR,,Tumor necrosis factor receptor superfamily member 18,CD357,Q9Y5U5,TGAGTCACTC,TGAGTCACTC -CCR3,,C-C chemokine receptor type 3,CD193,P51677,CCGTGACCCA,CCGTGACCCA -SLAMF7,,SLAM family member 7,CD319;CRACC,Q9NQ25,AGGCGGAAAT,AGGCGGAAAT -TIGIT,,T cell immunoreceptor with Ig and ITIM domains,,Q495A1,ACTGAGTCGC,ACTGAGTCGC -OX40,,Tumor necrosis factor receptor superfamily member 4,CD134,P43489,CCACTTCCGT,CCACTTCCGT -ICAM-2,,Intercellular adhesion molecule 2,CD102,P13598,TATCTGGGAT,TATCTGGGAT -CD123,,Interleukin-3 receptor subunit alpha,IL-3Rα,P26951,TGACTGCTAC,TGACTGCTAC -CD150,,Signaling lymphocytic activation molecule,SLAMF1,Q13291,TCGAATGGAT,TCGAATGGAT -CD40L,,CD40 ligand,CD154,P29965,CTAGATTTGC,CTAGATTTGC -KIR,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158,Q8N743,TCCTCTCCTG,TCCTCTCCTG -CD161,,Killer cell lectin-like receptor subfamily B member 1,KLRB1,Q12918,ACTGAACTAC,ACTGAACTAC -CD180,,CD180 antigen,RP105,Q99467,TGAGCTCCAA,TGAGCTCCAA -CCR1,,C-C chemokine receptor type 1,CD191,P32246,CCGGTGGTTC,CCGGTGGTTC -CCR2,,C-C chemokine receptor type 2,CD192,P41597,GGTTCTCCAC,GGTTCTCCAC -CD1d,,Antigen-presenting glycoprotein CD1d,,P15813,CAACGTCCCA,CAACGTCCCA -CD200,,OX-2 membrane glycoprotein,,P41217,CGCACGGGTT,CGCACGGGTT -Ly9,,T-lymphocyte surface antigen Ly-9,CD229;SLAMF3,Q9HBG7,TCGACGAGTG,TCGACGAGTG -CD24,,Signal transducer CD24,HSA,P25063,TCTTGTTCCC,TCTTGTTCCC -2B4,,Natural killer cell receptor 2B4,CD244;SLAMF4,Q9BZW8,TCTCAATCAA,TCTCAATCAA -BAFF-R,,Tumor necrosis factor receptor superfamily member 13C (BAFFR),CD268,Q96RJ3,ACGTAACCGC,ACGTAACCGC -ICOS,,Inducible T cell co-stimulator,CD278,Q9Y6W8,CAGGCACCTG,CAGGCACCTG -CD32,,Low-affinity immunoglobulin gamma Fc region receptor II-b,FcγRII,P31994,GATTTCCAGC,GATTTCCAGC -CD33,,Myeloid cell surface antigen CD33,Siglec-3,P20138,GCGATATAGT,GCGATATAGT -NKp30,,Natural cytotoxicity triggering receptor 3 (NKp30),CD337,O14931,CTTATCTCTT,CTTATCTCTT -CD38,,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,,P28907,TCCGATCTGG,TCCGATCTGG -CD39,,Ectonucleoside triphosphate diphosphohydrolase 1,ENTPD1,P49961,TCAGCGCCTT,TCAGCGCCTT -CD40,,Tumor necrosis factor receptor superfamily member 5,,P25942,TCTGGCGTGG,TCTGGCGTGG -CD48,,CD48 antigen,SLAMF2;BLAST-1,P09326,AGTACGAAGA,AGTACGAAGA -ICAM-3,,Intercellular adhesion molecule 3,CD50,P32942,CTCCGCGTTG,CTCCGCGTTG -CD55,,Complement decay-accelerating factor (DAF),DAF,P08174,TTAGCTAAAC,TTAGCTAAAC -CD58,,Lymphocyte function-associated antigen 3 (LFA3),LFA-3,P19256,ATGTTATGTG,ATGTTATGTG -CD62P,,P-selectin,P-selectin,P16109,ACTTAGCGCT,ACTTAGCGCT -CD69,,Early activation antigen CD69,,Q07108,GAAGGGTCTC,GAAGGGTCTC -CD72,,B-cell differentiation antigen CD72,Lyb-2,P21854,GCGGTGACTT,GCGGTGACTT -CD84,,SLAM family member 5,SLAMF5,Q9UIB8,GCCATTGGAA,GCCATTGGAA -CD9,,CD9 antigen,Tetraspanin-29,P21926,GTCTGGTCAT,GTCTGGTCAT -CD94,,Natural killer cells antigen CD94,KLRD1,Q13241,CTACAACCTT,CTACAACCTT -TCRVb5,,T cell receptor beta variable 5,,,GGCCTCAAGT,GGCCTCAAGT -CD3e,,T cell surface glycoprotein CD3 epsilon chain,,P07766,TGTAGAATTC,TGTAGAATTC -CD4,,T cell surface glycoprotein CD4,,P01730,GACAACTTCT,GACAACTTCT -CD11a,,Integrin α-L (LFA-1 α),ITGAL;LFA-1 α,P20701,ACACACTTGA,ACACACTTGA -CD43,,Leukosialin,Leukosialin,P16150,GAGATTACTA,GAGATTACTA -CD7,,T cell antigen CD7,,P09564,CTGGGTCCGT,CTGGGTCCGT -CD53,,Leukocyte surface antigen CD53,Tetraspanin-25,P19397,CAACCCGCTT,CAACCCGCTT -CD302,,C-type lectin domain family 13 member A,CLEC13A,Q8IX05,TAGACATTGG,TAGACATTGG -VISTA,,V-type immunoglobulin domain-containing suppressor of T cell activation,VSIR,Q9H7M9,AATGTTAACG,AATGTTAACG -BCMA,,Tumor necrosis factor receptor superfamily member 17,CD269,Q02223,CTGGACTATG,CTGGACTATG -CD138,,Syndecan-1,Syndecan-1,P18827,CTGGGCTTAC,CTGGGCTTAC -4-1BB,,Tumor necrosis factor receptor superfamily member 9,CD137,Q07011,CCAGCTAGAA,CCAGCTAGAA -CD66b,,Cell adhesion molecule CEACAM8,CEACAM8,P31997,CTAGGCAGTT,CTAGGCAGTT -EpCAM,,Epithelial cell adhesion molecule,CD326,P16422,CGTTCTTACA,CGTTCTTACA -DC-SIGN,,CD209 antigen,CD209,Q9NNX6,TGGACGTGAA,TGGACGTGAA -CD34,,Hematopoietic progenitor cell antigen CD34,,P28906,CCGTCTAGCC,CCGTCTAGCC -Dectin-1,,C-type lectin domain family 7 member A,CD369;CLEC7A,Q9BXN2,CTGCCAAGAC,CTGCCAAGAC -ICAM-1,,Intercellular adhesion molecule 1,CD54,P05362,AGCAGCTGAT,AGCAGCTGAT -CD71,,Transferrin receptor protein 1,Transferrin receptor,P02786,TCAGGACAGA,TCAGGACAGA -CD47,,Leukocyte surface antigen CD47,Integrin associated protein,Q08722,AGCTACTATT,AGCTACTATT -c-Kit,,Mast/Stem cell growth factor receptor Kit,CD117,P10721,GCTATAATTG,GCTATAATTG -NKG2D,,NKG2-D type II integral membrane protein,CD314;KG2DN,P26718,TGGCGCACAC,TGGCGCACAC -CD98,,4F2 cell-surface antigen heavy chain,SLC3A2,P08195,CCAGAGCGGA,CCAGAGCGGA -CD298,,Na+/K+-ATPase β3,ATP1B3,P54709,AAGCCTGCCT,AAGCCTGCCT -B2M-1,,,,,TGAGTGGTGA,TGAGTGGTGA,yes -B2M-2,,,,,TAGAGGAGGC,TAGAGGAGGC,yes -B2M-3,,,,,CCCACTAAGC,CCCACTAAGC,yes -B2M-4,,,,,TGGTTTACAA,TGGTTTACAA,yes -B2M-5,,,,,CTAACTACGG,CTAACTACGG,yes -B2M-6,,,,,TATTGAACCT,TATTGAACCT,yes -B2M-7,,,,,ATCAACCCTA,ATCAACCCTA,yes -B2M-8,,,,,GTATCCCTAC,GTATCCCTAC,yes -CD298-1,,,,,GCTAGCAACG,GCTAGCAACG,yes -CD298-2,,,,,AAATAGTACG,AAATAGTACG,yes -CD298-3,,,,,GACGGCTTAG,GACGGCTTAG,yes -CD298-4,,,,,GTCAAGGTAA,GTCAAGGTAA,yes -CD298-5,,,,,GGTAAGCCCT,GGTAAGCCCT,yes -CD298-6,,,,,GCCGCCTATG,GCCGCCTATG,yes -CD298-7,,,,,GCTCCGCAAC,GCTCCGCAAC,yes -CD298-8,,,,,AGCCTCAGCA,AGCCTCAGCA,yes -CD98-1,,,,,CACTTGGCCA,CACTTGGCCA,yes -CD98-2,,,,,ATTGTGTGGG,ATTGTGTGGG,yes -CD98-3,,,,,CATAGACCAT,CATAGACCAT,yes -CD98-4,,,,,ATGTTCCTCT,ATGTTCCTCT,yes -CD98-5,,,,,TTCGTAACTA,TTCGTAACTA,yes -CD98-6,,,,,CTGACCGCTA,CTGACCGCTA,yes -CD98-7,,,,,CCCTCGGTCT,CCCTCGGTCT,yes -CD98-8,,,,,ATCGCACGTA,ATCGCACGTA,yes diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-155-v2.0.csv b/src/pixelator/pna/resources/panels/proxiome-v2-immuno-155-v2.0.csv index 8ec463c7b..80d2694d8 100644 --- a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-155-v2.0.csv +++ b/src/pixelator/pna/resources/panels/proxiome-v2-immuno-155-v2.0.csv @@ -2,8 +2,9 @@ # name: proxiome-v2-immuno-155-v2.0 # product: proxiome-v2-immuno-155 # description: >- -# Panel for the Proxiome Immuno Kit with 155 markers + 3 control markers + 3*8 hashing antibodies +# Panel for the Proxiome Immuno Kit with 155 markers + 3 control markers # version: 2.0.0 +# panel_type: base # --- marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG @@ -164,27 +165,3 @@ c-Kit,,Mast/Stem cell growth factor receptor Kit,CD117,P10721,GCTATAATTG,GCTATAA NKG2D,,NKG2-D type II integral membrane protein,CD314;KG2DN,P26718,TGGCGCACAC,TGGCGCACAC CD98,,4F2 cell-surface antigen heavy chain,SLC3A2,P08195,CCAGAGCGGA,CCAGAGCGGA CD298,,Na+/K+-ATPase β3,ATP1B3,P54709,AAGCCTGCCT,AAGCCTGCCT -B2M-1,,,,,GAGGGACGGT,GAGGGACGGT,yes -B2M-2,,,,,TAGAGGAGGC,TAGAGGAGGC,yes -B2M-3,,,,,CCCACTAAGC,CCCACTAAGC,yes -B2M-4,,,,,TGGTTTACAA,TGGTTTACAA,yes -B2M-5,,,,,CTAACTACGG,CTAACTACGG,yes -B2M-6,,,,,TATTGAACCT,TATTGAACCT,yes -B2M-7,,,,,ATCAACCCTA,ATCAACCCTA,yes -B2M-8,,,,,GTATCCCTAC,GTATCCCTAC,yes -CD298-1,,,,,AAAGTCTCTG,AAAGTCTCTG,yes -CD298-2,,,,,AAATAGTACG,AAATAGTACG,yes -CD298-3,,,,,GACGGCTTAG,GACGGCTTAG,yes -CD298-4,,,,,GTCAAGGTAA,GTCAAGGTAA,yes -CD298-5,,,,,GGTAAGCCCT,GGTAAGCCCT,yes -CD298-6,,,,,GCCGCCTATG,GCCGCCTATG,yes -CD298-7,,,,,GCTCCGCAAC,GCTCCGCAAC,yes -CD298-8,,,,,AGCCTCAGCA,AGCCTCAGCA,yes -CD98-1,,,,,TGGCTTAGCC,TGGCTTAGCC,yes -CD98-2,,,,,ATTGTGTGGG,ATTGTGTGGG,yes -CD98-3,,,,,CATAGACCAT,CATAGACCAT,yes -CD98-4,,,,,ATGTTCCTCT,ATGTTCCTCT,yes -CD98-5,,,,,TTCGTAACTA,TTCGTAACTA,yes -CD98-6,,,,,CTGACCGCTA,CTGACCGCTA,yes -CD98-7,,,,,CCCTCGGTCT,CCCTCGGTCT,yes -CD98-8,,,,,ATCGCACGTA,ATCGCACGTA,yes diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FLAG-prerelease.csv b/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FLAG-prerelease.csv deleted file mode 100644 index f7dc946a2..000000000 --- a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FLAG-prerelease.csv +++ /dev/null @@ -1,194 +0,0 @@ -# --- -# name: proxiome-v2-immuno-156-FLAG-prerelease -# product: proxiome-v2-immuno-156-FLAG -# aliases: -# - proxiome-v2-immuno-156-FLAG-v1.0 -# description: >- -# Panel for the Proxiome Immuno Kit with 155 markers + 3 control markers -# + 3*8 hashing antibodies + the FLAG marker -# version: 1.0.1 -# --- -marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing -HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG -B2M,,Beta-2-microglobulin,,P61769,CCAGGTTCCG,CCAGGTTCCG -CD11b,,Integrin α-M (ITGAM),ITGAM;Mac-1 α,P11215,CAGCTATGGT,CAGCTATGGT -CD11c,,Integrin α-X,Integrin αX,P20702,ATATGACGGT,ATATGACGGT -CD18,,Integrin beta 2,Integrin β2,P05107,GGGTAGGCTG,GGGTAGGCTG -CD82,,CD82 antigen,Tetraspanin-27,P27701,CCCGTCATGA,CCCGTCATGA -CD8,,T cell surface glycoprotein CD8 a/b chains,,P01732;P10966,CGGTGGATCA,CGGTGGATCA -TCRab,,T cell receptor alpha chain constant/beta constant 1,,P01848;P01850,CTGGTAGCAA,CTGGTAGCAA -HLA-DR,,"HLA class II histocompatibility antigen, DR",,P01903;P01911,TGTTGTCGAA,TGTTGTCGAA -CD45,,"Receptor-type tyrosine-protein phosphatase C. All 6 isoforms (ABC, AB, BC, B and O)",PTPRC,P08575,TGGAGGCTCT,TGGAGGCTCT -CD14,,Monocyte differentiation antigen CD14,,P08571,TGGCTATGTA,TGGCTATGTA -CD16,,Low-affinity immunoglobulin gamma Fc region receptor / III-A and -B,FcγRIII,P08637;O75015,ATAGGTTAGG,ATAGGTTAGG -CD19,,B-lymphocyte antigen CD19,,P15391,ACGGAATATT,ACGGAATATT -mIgG1,yes,,,,ATGCTAGTCG,ATGCTAGTCG -CD45RB,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, BC, and B)",,P08575,GAAGCAGTAT,GAAGCAGTAT -CD44,,CD44 antigen,,P16070,GTGAGTCAAT,GTGAGTCAAT -CD52,,CAMPATH-1 antigen,CAMPATH-1,P31358,CTTTAGCAGG,CTTTAGCAGG -CD59,,CD59 glycoprotein,Protectin;MAC-IP,P13987,GGTGTATGAG,GGTGTATGAG -CD45RA,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, and A)",,P08575,GGATTCGTGG,GGATTCGTGG -CD36,,Platelet glycoprotein 4,FAT;SCARB3,P16671,TACCCTGCGA,TACCCTGCGA -CD2,,T cell surface antigen CD2,,P06729,TGCCGATGCC,TGCCGATGCC -CD29,,Integrin beta-1,Integrin β1,P05556,TCCAGTGTCT,TCCAGTGTCT -CD5,,T cell surface glycoprotein CD5,,P06127,CACCCATCAA,CACCCATCAA -CD162,,P-selectin glycoprotein ligand 1,SELPLG;PSGL-1,Q14242,CTTCGTGGAC,CTTCGTGGAC -CD27,,CD27 antigen,,P26842,GGTTTGCAAA,GGTTTGCAAA -CR1,,Complement receptor type 1,CD35,P17927,CGCCACCTTT,CGCCACCTTT -CD26,,Dipeptidyl peptidase 4,DPP4,P27487,GATTCGCTGT,GATTCGCTGT -CD49d,,Integrin α-4,Integrin α4,P13612,AACTTAGGTT,AACTTAGGTT -CD37,,Leukocyte antigen CD37,Tetraspanin-26,P11049,AGAAGAAGAG,AGAAGAAGAG -CD41,,Integrin α-IIb,Integrin αIIb,P08514,TAAGGCATAA,TAAGGCATAA -CD20,,B-lymphocyte antigen CD20,,P11836,GCCACACCCA,GCCACACCCA -CD64,,High affinity immunoglobulin gamma Fc receptor I,FcγRI,P12314,CTTGTATATC,CTTGTATATC -CD22,,B-cell receptor CD22,,P20273,TGACCCGTTC,TGACCCGTTC -PD-L1,,Programmed cell death 1 ligand 1 (PDL1),CD274,Q9NZQ7,GCTTGAGATT,GCTTGAGATT -Siglec-7,,Sialic acid-binding Ig-like lectin 7 (SIGLEC-7),CD328,Q9Y286,TATATGCTGA,TATATGCTGA -CD25,,Interleukin-2 receptor subunit alpha,IL-2Rα,P01589,AGAGACGAAT,AGAGACGAAT -PD-1,,Programmed cell death protein 1 (PD-1),CD279,Q15116,TACAGAGCCC,TACAGAGCCC -NKp46,,Natural cytotoxicity triggering receptor 1 (NKp46),CD335,O76036,ATTACCCGCG,ATTACCCGCG -mIgG2a,yes,,,,ATTTCCACTA,ATTTCCACTA -mIgG2b,yes,,,,CTAAATGGCT,CTAAATGGCT -CTLA-4,,Cytotoxic T-lymphocyte protein 4,CD152,P16410,TTTCTGCATT,TTTCTGCATT -CD86,,T-lymphocyte activation antigen CD86,B7-2,P42081,ACCATCACTT,ACCATCACTT -CD13,,Aminopeptidase N,Aminopeptidase N,P15144,GCATGGGTAG,GCATGGGTAG -ADAM10,,Disintegrin and metalloproteinase domain-containing protein 10,CD156c,O14672,ATAAGTTCCA,ATAAGTTCCA -KIR2DL1,,Killer cell immunoglobulin-like receptor 2DL1,CD158a,P43626,TGTTACGGTC,TGTTACGGTC -KIR2DL2/DL3,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158b,P43627,ACTGCATTGA,ACTGCATTGA -NKG2A,,NKG2-A/NKG2-B type II integral membrane protein,CD159a,P26715,CGTACACGGT,CGTACACGGT -NKG2C,,NKG2-C type II integral membrane protein,CD159c,P26717,CAACAGTCGA,CAACAGTCGA -CD163,,Scavenger receptor cysteine-rich type 1 protein M130,,Q86VB7,GACCGTGATT,GACCGTGATT -CD169,,Sialoadhesin,Siglec-1,Q9BZZ2,TAATCGCGGG,TAATCGCGGG -CD1a,,T cell surface glycoprotein CD1a,,P06126,CGACTAATCA,CGACTAATCA -CD1c,,T cell surface glycoprotein CD1c,,P29017,GTGCACTGTC,GTGCACTGTC -CD206,,Macrophage mannose receptor 1,Mannose receptor,P22897,TGCCTAATAG,TGCCTAATAG -DNAM-1,,CD226 antigen,CD226,Q15762,CGGTCATTAA,CGGTCATTAA -PD-L2,,Programmed cell death 1 ligand 2 (PDL2),CD273,Q9BQ51,ATCGCGAAGC,ATCGCGAAGC -CD28,,T cell-specific surface glycoprotein CD28,,P10747,CATAACAATC,CATAACAATC -SLAMF6,,SLAM family member 6,CD352;NTB-A,Q96DU3,TCGGAGACAC,TCGGAGACAC -CD45RO,,"Receptor-type tyrosine-protein phosphatase C. Isoform O",,P08575,TTGATGACTC,TTGATGACTC -CD49e,,Integrin α-5,Integrin α5,P08648,AACTCCTGAA,AACTCCTGAA -CD56,,Neural cell adhesion molecule 1,NCAM,P13591,GTGCGTAAGC,GTGCGTAAGC -CD79a,,B-cell antigen receptor complex-associated protein alpha chain,MB-1,P11912,AGATCGACAG,AGATCGACAG -CD80,,T-lymphocyte activation antigen CD80,B7-1,P33681,AAGACGCGGA,AAGACGCGGA -CD81,,CD81 antigen,Tetraspanin-28,P60033,TGGGTTATGT,TGGGTTATGT -LILRB1,,Leukocyte immunoglobulin-like receptor subfamily B member 1,CD85j;ILT-2,Q8NHL6,CCTAAGTCTA,CCTAAGTCTA -CD93,,Complement component C1q receptor,,Q9NPY3,GCAGCGAACA,GCAGCGAACA -IgD,,Immunoglobulin delta heavy chain,,P0DOX3,AGATGAGGCA,AGATGAGGCA -IgE,,Immunoglobulin epsilon heavy chain,,P0DOX4,CGACGGTAAG,CGACGGTAAG -IgM,,Immunoglobulin mu heavy chain,,P0DOX6,GTGGATCCAA,GTGGATCCAA -KLRG1,,Killer cell lectin-like receptor subfamily G member 1,,Q96E93,TATACAGACA,TATACAGACA -NKp80,,Killer cell lectin-like receptor subfamily F member 1,KLRF1,Q9NZS2,CCATCGGATC,CCATCGGATC -TCRgd,,T cell receptor gamma constant 1 /delta constant,,P0CF51;B7Z8K6,CTTATGACCA,CTTATGACCA -CD10,,Neprilysin,Neprilysin,P08473,CGCAGGTAGC,CGCAGGTAGC -CD103,,Integrin alpha-E,Integrin αE,P38570,CCTATGCGAA,CCTATGCGAA -CD1b,,T cell surface glycoprotein CD1b,,P29016,GACACCACCG,GACACCACCG -CD21,,Complement receptor type 2,CR2,P20023,GTGGCGTTAA,GTGGCGTTAA -TALLA,,Tetraspanin-7,CD231;Tetraspanin-7,P41732,CACGATACTT,CACGATACTT -CD277,,Butyrophilin subfamily 3 member A1,BTN3,O00481,GAGTGATACG,GAGTGATACG -LAIR1,,Leukocyte-associated immunoglobulin-like receptor 1,CD305,Q6GTX8,GCAATGTGTA,GCAATGTGTA -CD371,,C-type lectin domain family 12 member A,CLEC12A,Q5QGZ9,AAGGTCCCAT,AAGGTCCCAT -CD89,,Immunoglobulin alpha Fc receptor,FcαRI;FCAR,P24071,GTATCATAAG,GTATCATAAG -CD90,,Thy-1 membrane glycoprotein,Thy-1,P04216,TAGCCGATTA,TAGCCGATTA -CD70,,CD70 antigen,CD27L,P32970,CTCAGCATGC,CTCAGCATGC -GPR56,,Adhesion G-protein coupled receptor G1,TM7XN1,Q9Y653,GCGTCTCTCT,GCGTCTCTCT -HLA-DQ,,"HLA class II histocompatibility antigen, DQ",,P01906;P05538;P01920;P01909,ATACTTGAGC,ATACTTGAGC -TCRVd2,,T cell receptor delta variable 2,,,CCGACCATTC,CCGACCATTC -HLA-DR-DP-DQ,,HLA class II histocompatibility antigen,,P01903;P20036;P01909,AACAGAGGAA,AACAGAGGAA -Siglec-9,,Sialic acid-binding Ig-like lectin 9,,Q9Y336,TTAACAAGCA,TTAACAAGCA -TCRVa7.2,,T cell receptor alpha variable 7,,A0A075B6U4,TCCCAGGTCC,TCCCAGGTCC -Fas,,Tumor necrosis factor receptor superfamily member 6,CD95,P25445,TACTGTTGGG,TACTGTTGGG -TCRVg9,,T cell receptor gamma variable 9,,,TCGTTTGTCA,TCGTTTGTCA -CD127,,Interleukin-7 receptor subunit alpha,IL-7Rα,P16871,TGTTAGAGGA,TGTTAGAGGA -CD141,,Thrombomodulin,TM,P07204,AATTGTTCGT,AATTGTTCGT -CD31,,Platelet endothelial cell adhesion molecule,PECAM-1,P16284,GGCAAAGAGC,GGCAAAGAGC -CD6,,T cell differentiation antigen CD6,,P30203,CTAAGATCTC,CTAAGATCTC -CD57,,Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1,,Q9P2W7,ACGACGGGAC,ACGACGGGAC -CD73,,5’-nucleotidase,NT5E,P21589,ACCAAGGACG,ACCAAGGACG -TIM-3,,Hepatitis A virus cellular receptor 2,CD366;HAVCR2,Q8TDQ0,CGCCAAGTGG,CGCCAAGTGG -GITR,,Tumor necrosis factor receptor superfamily member 18,CD357,Q9Y5U5,TGAGTCACTC,TGAGTCACTC -CCR3,,C-C chemokine receptor type 3,CD193,P51677,CCGTGACCCA,CCGTGACCCA -SLAMF7,,SLAM family member 7,CD319;CRACC,Q9NQ25,AGGCGGAAAT,AGGCGGAAAT -TIGIT,,T cell immunoreceptor with Ig and ITIM domains,,Q495A1,ACTGAGTCGC,ACTGAGTCGC -OX40,,Tumor necrosis factor receptor superfamily member 4,CD134,P43489,CCACTTCCGT,CCACTTCCGT -ICAM-2,,Intercellular adhesion molecule 2,CD102,P13598,TATCTGGGAT,TATCTGGGAT -CD123,,Interleukin-3 receptor subunit alpha,IL-3Rα,P26951,TGACTGCTAC,TGACTGCTAC -CD150,,Signaling lymphocytic activation molecule,SLAMF1,Q13291,TCGAATGGAT,TCGAATGGAT -CD40L,,CD40 ligand,CD154,P29965,CTAGATTTGC,CTAGATTTGC -KIR,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158,Q8N743,TCCTCTCCTG,TCCTCTCCTG -CD161,,Killer cell lectin-like receptor subfamily B member 1,KLRB1,Q12918,ACTGAACTAC,ACTGAACTAC -CD180,,CD180 antigen,RP105,Q99467,TGAGCTCCAA,TGAGCTCCAA -CCR1,,C-C chemokine receptor type 1,CD191,P32246,CCGGTGGTTC,CCGGTGGTTC -CCR2,,C-C chemokine receptor type 2,CD192,P41597,GGTTCTCCAC,GGTTCTCCAC -CD1d,,Antigen-presenting glycoprotein CD1d,,P15813,CAACGTCCCA,CAACGTCCCA -CD200,,OX-2 membrane glycoprotein,,P41217,CGCACGGGTT,CGCACGGGTT -Ly9,,T-lymphocyte surface antigen Ly-9,CD229;SLAMF3,Q9HBG7,TCGACGAGTG,TCGACGAGTG -CD24,,Signal transducer CD24,HSA,P25063,TCTTGTTCCC,TCTTGTTCCC -2B4,,Natural killer cell receptor 2B4,CD244;SLAMF4,Q9BZW8,TCTCAATCAA,TCTCAATCAA -BAFF-R,,Tumor necrosis factor receptor superfamily member 13C (BAFFR),CD268,Q96RJ3,ACGTAACCGC,ACGTAACCGC -ICOS,,Inducible T cell co-stimulator,CD278,Q9Y6W8,CAGGCACCTG,CAGGCACCTG -CD32,,Low-affinity immunoglobulin gamma Fc region receptor II-b,FcγRII,P31994,GATTTCCAGC,GATTTCCAGC -CD33,,Myeloid cell surface antigen CD33,Siglec-3,P20138,GCGATATAGT,GCGATATAGT -NKp30,,Natural cytotoxicity triggering receptor 3 (NKp30),CD337,O14931,CTTATCTCTT,CTTATCTCTT -CD38,,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,,P28907,TCCGATCTGG,TCCGATCTGG -CD39,,Ectonucleoside triphosphate diphosphohydrolase 1,ENTPD1,P49961,TCAGCGCCTT,TCAGCGCCTT -CD40,,Tumor necrosis factor receptor superfamily member 5,,P25942,TCTGGCGTGG,TCTGGCGTGG -CD48,,CD48 antigen,SLAMF2;BLAST-1,P09326,AGTACGAAGA,AGTACGAAGA -ICAM-3,,Intercellular adhesion molecule 3,CD50,P32942,CTCCGCGTTG,CTCCGCGTTG -CD55,,Complement decay-accelerating factor (DAF),DAF,P08174,TTAGCTAAAC,TTAGCTAAAC -CD58,,Lymphocyte function-associated antigen 3 (LFA3),LFA-3,P19256,ATGTTATGTG,ATGTTATGTG -CD62P,,P-selectin,P-selectin,P16109,ACTTAGCGCT,ACTTAGCGCT -CD69,,Early activation antigen CD69,,Q07108,GAAGGGTCTC,GAAGGGTCTC -CD72,,B-cell differentiation antigen CD72,Lyb-2,P21854,GCGGTGACTT,GCGGTGACTT -CD84,,SLAM family member 5,SLAMF5,Q9UIB8,GCCATTGGAA,GCCATTGGAA -CD9,,CD9 antigen,Tetraspanin-29,P21926,GTCTGGTCAT,GTCTGGTCAT -CD94,,Natural killer cells antigen CD94,KLRD1,Q13241,CTACAACCTT,CTACAACCTT -TCRVb5,,T cell receptor beta variable 5,,,GGCCTCAAGT,GGCCTCAAGT -CD3e,,T cell surface glycoprotein CD3 epsilon chain,,P07766,TGTAGAATTC,TGTAGAATTC -CD4,,T cell surface glycoprotein CD4,,P01730,GACAACTTCT,GACAACTTCT -CD11a,,Integrin α-L (LFA-1 α),ITGAL;LFA-1 α,P20701,ACACACTTGA,ACACACTTGA -CD43,,Leukosialin,Leukosialin,P16150,GAGATTACTA,GAGATTACTA -CD7,,T cell antigen CD7,,P09564,CTGGGTCCGT,CTGGGTCCGT -CD53,,Leukocyte surface antigen CD53,Tetraspanin-25,P19397,CAACCCGCTT,CAACCCGCTT -CD302,,C-type lectin domain family 13 member A,CLEC13A,Q8IX05,TAGACATTGG,TAGACATTGG -VISTA,,V-type immunoglobulin domain-containing suppressor of T cell activation,VSIR,Q9H7M9,AATGTTAACG,AATGTTAACG -BCMA,,Tumor necrosis factor receptor superfamily member 17,CD269,Q02223,CTGGACTATG,CTGGACTATG -CD138,,Syndecan-1,Syndecan-1,P18827,CTGGGCTTAC,CTGGGCTTAC -4-1BB,,Tumor necrosis factor receptor superfamily member 9,CD137,Q07011,CCAGCTAGAA,CCAGCTAGAA -CD66b,,Cell adhesion molecule CEACAM8,CEACAM8,P31997,CTAGGCAGTT,CTAGGCAGTT -EpCAM,,Epithelial cell adhesion molecule,CD326,P16422,CGTTCTTACA,CGTTCTTACA -DC-SIGN,,CD209 antigen,CD209,Q9NNX6,TGGACGTGAA,TGGACGTGAA -CD34,,Hematopoietic progenitor cell antigen CD34,,P28906,CCGTCTAGCC,CCGTCTAGCC -Dectin-1,,C-type lectin domain family 7 member A,CD369;CLEC7A,Q9BXN2,CTGCCAAGAC,CTGCCAAGAC -ICAM-1,,Intercellular adhesion molecule 1,CD54,P05362,AGCAGCTGAT,AGCAGCTGAT -CD71,,Transferrin receptor protein 1,Transferrin receptor,P02786,TCAGGACAGA,TCAGGACAGA -CD47,,Leukocyte surface antigen CD47,Integrin associated protein,Q08722,AGCTACTATT,AGCTACTATT -c-Kit,,Mast/Stem cell growth factor receptor Kit,CD117,P10721,GCTATAATTG,GCTATAATTG -NKG2D,,NKG2-D type II integral membrane protein,CD314;KG2DN,P26718,TGGCGCACAC,TGGCGCACAC -CD98,,4F2 cell-surface antigen heavy chain,SLC3A2,P08195,CCAGAGCGGA,CCAGAGCGGA -CD298,,Na+/K+-ATPase β3,ATP1B3,P54709,AAGCCTGCCT,AAGCCTGCCT -B2M-1,,,,,TGAGTGGTGA,TGAGTGGTGA,yes -B2M-2,,,,,TAGAGGAGGC,TAGAGGAGGC,yes -B2M-3,,,,,CCCACTAAGC,CCCACTAAGC,yes -B2M-4,,,,,TGGTTTACAA,TGGTTTACAA,yes -B2M-5,,,,,CTAACTACGG,CTAACTACGG,yes -B2M-6,,,,,TATTGAACCT,TATTGAACCT,yes -B2M-7,,,,,ATCAACCCTA,ATCAACCCTA,yes -B2M-8,,,,,GTATCCCTAC,GTATCCCTAC,yes -CD298-1,,,,,GCTAGCAACG,GCTAGCAACG,yes -CD298-2,,,,,AAATAGTACG,AAATAGTACG,yes -CD298-3,,,,,GACGGCTTAG,GACGGCTTAG,yes -CD298-4,,,,,GTCAAGGTAA,GTCAAGGTAA,yes -CD298-5,,,,,GGTAAGCCCT,GGTAAGCCCT,yes -CD298-6,,,,,GCCGCCTATG,GCCGCCTATG,yes -CD298-7,,,,,GCTCCGCAAC,GCTCCGCAAC,yes -CD298-8,,,,,AGCCTCAGCA,AGCCTCAGCA,yes -CD98-1,,,,,CACTTGGCCA,CACTTGGCCA,yes -CD98-2,,,,,ATTGTGTGGG,ATTGTGTGGG,yes -CD98-3,,,,,CATAGACCAT,CATAGACCAT,yes -CD98-4,,,,,ATGTTCCTCT,ATGTTCCTCT,yes -CD98-5,,,,,TTCGTAACTA,TTCGTAACTA,yes -CD98-6,,,,,CTGACCGCTA,CTGACCGCTA,yes -CD98-7,,,,,CCCTCGGTCT,CCCTCGGTCT,yes -CD98-8,,,,,ATCGCACGTA,ATCGCACGTA,yes -FLAG,,,,,CTTAACATCT,CTTAACATCT diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FLAG-v2.0.csv b/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FLAG-v2.0.csv deleted file mode 100644 index 3308e4399..000000000 --- a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FLAG-v2.0.csv +++ /dev/null @@ -1,192 +0,0 @@ -# --- -# name: proxiome-v2-immuno-156-FLAG-v2.0 -# product: proxiome-v2-immuno-156-FLAG -# description: >- -# Panel for the Proxiome Immuno Kit with 155 markers + 3 control markers -# + 3*8 hashing antibodies + the FLAG marker -# version: 2.0.0 -# --- -marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing -HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG -B2M,,Beta-2-microglobulin,,P61769,CCAGGTTCCG,CCAGGTTCCG -CD11b,,Integrin α-M (ITGAM),ITGAM;Mac-1 α,P11215,CAGCTATGGT,CAGCTATGGT -CD11c,,Integrin α-X,Integrin αX,P20702,ATATGACGGT,ATATGACGGT -CD18,,Integrin beta 2,Integrin β2,P05107,GGGTAGGCTG,GGGTAGGCTG -CD82,,CD82 antigen,Tetraspanin-27,P27701,CCCGTCATGA,CCCGTCATGA -CD8,,T cell surface glycoprotein CD8 a/b chains,,P01732;P10966,CGGTGGATCA,CGGTGGATCA -TCRab,,T cell receptor alpha chain constant/beta constant 1,,P01848;P01850,CTGGTAGCAA,CTGGTAGCAA -HLA-DR,,"HLA class II histocompatibility antigen, DR",,P01903;P01911,TGTTGTCGAA,TGTTGTCGAA -CD45,,"Receptor-type tyrosine-protein phosphatase C. All 6 isoforms (ABC, AB, BC, B and O)",PTPRC,P08575,TGGAGGCTCT,TGGAGGCTCT -CD14,,Monocyte differentiation antigen CD14,,P08571,TGGCTATGTA,TGGCTATGTA -CD16,,Low-affinity immunoglobulin gamma Fc region receptor / III-A and -B,FcγRIII,P08637;O75015,ATAGGTTAGG,ATAGGTTAGG -CD19,,B-lymphocyte antigen CD19,,P15391,ACGGAATATT,ACGGAATATT -mIgG1,yes,,,,ATGCTAGTCG,ATGCTAGTCG -CD45RB,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, BC, and B)",,P08575,GAAGCAGTAT,GAAGCAGTAT -CD44,,CD44 antigen,,P16070,GTGAGTCAAT,GTGAGTCAAT -CD52,,CAMPATH-1 antigen,CAMPATH-1,P31358,CTTTAGCAGG,CTTTAGCAGG -CD59,,CD59 glycoprotein,Protectin;MAC-IP,P13987,GGTGTATGAG,GGTGTATGAG -CD45RA,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, and A)",,P08575,GGATTCGTGG,GGATTCGTGG -CD36,,Platelet glycoprotein 4,FAT;SCARB3,P16671,TACCCTGCGA,TACCCTGCGA -CD2,,T cell surface antigen CD2,,P06729,TGCCGATGCC,TGCCGATGCC -CD29,,Integrin beta-1,Integrin β1,P05556,TCCAGTGTCT,TCCAGTGTCT -CD5,,T cell surface glycoprotein CD5,,P06127,CACCCATCAA,CACCCATCAA -CD162,,P-selectin glycoprotein ligand 1,SELPLG;PSGL-1,Q14242,CTTCGTGGAC,CTTCGTGGAC -CD27,,CD27 antigen,,P26842,GGTTTGCAAA,GGTTTGCAAA -CR1,,Complement receptor type 1,CD35,P17927,CGCCACCTTT,CGCCACCTTT -CD26,,Dipeptidyl peptidase 4,DPP4,P27487,GATTCGCTGT,GATTCGCTGT -CD49d,,Integrin α-4,Integrin α4,P13612,AACTTAGGTT,AACTTAGGTT -CD37,,Leukocyte antigen CD37,Tetraspanin-26,P11049,AGAAGAAGAG,AGAAGAAGAG -CD41,,Integrin α-IIb,Integrin αIIb,P08514,TAAGGCATAA,TAAGGCATAA -CD20,,B-lymphocyte antigen CD20,,P11836,GCCACACCCA,GCCACACCCA -CD64,,High affinity immunoglobulin gamma Fc receptor I,FcγRI,P12314,CTTGTATATC,CTTGTATATC -CD22,,B-cell receptor CD22,,P20273,TGACCCGTTC,TGACCCGTTC -PD-L1,,Programmed cell death 1 ligand 1 (PDL1),CD274,Q9NZQ7,GCTTGAGATT,GCTTGAGATT -Siglec-7,,Sialic acid-binding Ig-like lectin 7 (SIGLEC-7),CD328,Q9Y286,TATATGCTGA,TATATGCTGA -CD25,,Interleukin-2 receptor subunit alpha,IL-2Rα,P01589,AGAGACGAAT,AGAGACGAAT -PD-1,,Programmed cell death protein 1 (PD-1),CD279,Q15116,TACAGAGCCC,TACAGAGCCC -NKp46,,Natural cytotoxicity triggering receptor 1 (NKp46),CD335,O76036,ATTACCCGCG,ATTACCCGCG -mIgG2a,yes,,,,ATTTCCACTA,ATTTCCACTA -mIgG2b,yes,,,,CTAAATGGCT,CTAAATGGCT -CTLA-4,,Cytotoxic T-lymphocyte protein 4,CD152,P16410,TTTCTGCATT,TTTCTGCATT -CD86,,T-lymphocyte activation antigen CD86,B7-2,P42081,ACCATCACTT,ACCATCACTT -CD13,,Aminopeptidase N,Aminopeptidase N,P15144,GCATGGGTAG,GCATGGGTAG -ADAM10,,Disintegrin and metalloproteinase domain-containing protein 10,CD156c,O14672,ATAAGTTCCA,ATAAGTTCCA -KIR2DL1,,Killer cell immunoglobulin-like receptor 2DL1,CD158a,P43626,TGTTACGGTC,TGTTACGGTC -KIR2DL2/DL3,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158b,P43627,ACTGCATTGA,ACTGCATTGA -NKG2A,,NKG2-A/NKG2-B type II integral membrane protein,CD159a,P26715,CGTACACGGT,CGTACACGGT -NKG2C,,NKG2-C type II integral membrane protein,CD159c,P26717,CAACAGTCGA,CAACAGTCGA -CD163,,Scavenger receptor cysteine-rich type 1 protein M130,,Q86VB7,GACCGTGATT,GACCGTGATT -CD169,,Sialoadhesin,Siglec-1,Q9BZZ2,TAATCGCGGG,TAATCGCGGG -CD1a,,T cell surface glycoprotein CD1a,,P06126,CGACTAATCA,CGACTAATCA -CD1c,,T cell surface glycoprotein CD1c,,P29017,GTGCACTGTC,GTGCACTGTC -CD206,,Macrophage mannose receptor 1,Mannose receptor,P22897,TGCCTAATAG,TGCCTAATAG -DNAM-1,,CD226 antigen,CD226,Q15762,CGGTCATTAA,CGGTCATTAA -PD-L2,,Programmed cell death 1 ligand 2 (PDL2),CD273,Q9BQ51,ATCGCGAAGC,ATCGCGAAGC -CD28,,T cell-specific surface glycoprotein CD28,,P10747,CATAACAATC,CATAACAATC -SLAMF6,,SLAM family member 6,CD352;NTB-A,Q96DU3,TCGGAGACAC,TCGGAGACAC -CD45RO,,"Receptor-type tyrosine-protein phosphatase C. Isoform O",,P08575,TTGATGACTC,TTGATGACTC -CD49e,,Integrin α-5,Integrin α5,P08648,AACTCCTGAA,AACTCCTGAA -CD56,,Neural cell adhesion molecule 1,NCAM,P13591,GTGCGTAAGC,GTGCGTAAGC -CD79a,,B-cell antigen receptor complex-associated protein alpha chain,MB-1,P11912,AGATCGACAG,AGATCGACAG -CD80,,T-lymphocyte activation antigen CD80,B7-1,P33681,AAGACGCGGA,AAGACGCGGA -CD81,,CD81 antigen,Tetraspanin-28,P60033,TGGGTTATGT,TGGGTTATGT -LILRB1,,Leukocyte immunoglobulin-like receptor subfamily B member 1,CD85j;ILT-2,Q8NHL6,CCTAAGTCTA,CCTAAGTCTA -CD93,,Complement component C1q receptor,,Q9NPY3,GCAGCGAACA,GCAGCGAACA -IgD,,Immunoglobulin delta heavy chain,,P0DOX3,AGATGAGGCA,AGATGAGGCA -IgE,,Immunoglobulin epsilon heavy chain,,P0DOX4,CGACGGTAAG,CGACGGTAAG -IgM,,Immunoglobulin mu heavy chain,,P0DOX6,GTGGATCCAA,GTGGATCCAA -KLRG1,,Killer cell lectin-like receptor subfamily G member 1,,Q96E93,TATACAGACA,TATACAGACA -NKp80,,Killer cell lectin-like receptor subfamily F member 1,KLRF1,Q9NZS2,CCATCGGATC,CCATCGGATC -TCRgd,,T cell receptor gamma constant 1 /delta constant,,P0CF51;B7Z8K6,CTTATGACCA,CTTATGACCA -CD10,,Neprilysin,Neprilysin,P08473,CGCAGGTAGC,CGCAGGTAGC -CD103,,Integrin alpha-E,Integrin αE,P38570,CCTATGCGAA,CCTATGCGAA -CD1b,,T cell surface glycoprotein CD1b,,P29016,GACACCACCG,GACACCACCG -CD21,,Complement receptor type 2,CR2,P20023,GTGGCGTTAA,GTGGCGTTAA -TALLA,,Tetraspanin-7,CD231;Tetraspanin-7,P41732,CACGATACTT,CACGATACTT -CD277,,Butyrophilin subfamily 3 member A1,BTN3,O00481,GAGTGATACG,GAGTGATACG -LAIR1,,Leukocyte-associated immunoglobulin-like receptor 1,CD305,Q6GTX8,GCAATGTGTA,GCAATGTGTA -CD371,,C-type lectin domain family 12 member A,CLEC12A,Q5QGZ9,AAGGTCCCAT,AAGGTCCCAT -CD89,,Immunoglobulin alpha Fc receptor,FcαRI;FCAR,P24071,GTATCATAAG,GTATCATAAG -CD90,,Thy-1 membrane glycoprotein,Thy-1,P04216,TAGCCGATTA,TAGCCGATTA -CD70,,CD70 antigen,CD27L,P32970,CTCAGCATGC,CTCAGCATGC -GPR56,,Adhesion G-protein coupled receptor G1,TM7XN1,Q9Y653,GCGTCTCTCT,GCGTCTCTCT -HLA-DQ,,"HLA class II histocompatibility antigen, DQ",,P01906;P05538;P01920;P01909,ATACTTGAGC,ATACTTGAGC -TCRVd2,,T cell receptor delta variable 2,,,CCGACCATTC,CCGACCATTC -HLA-DR-DP-DQ,,HLA class II histocompatibility antigen,,P01903;P20036;P01909,AACAGAGGAA,AACAGAGGAA -Siglec-9,,Sialic acid-binding Ig-like lectin 9,,Q9Y336,TTAACAAGCA,TTAACAAGCA -TCRVa7.2,,T cell receptor alpha variable 7,,A0A075B6U4,TCCCAGGTCC,TCCCAGGTCC -Fas,,Tumor necrosis factor receptor superfamily member 6,CD95,P25445,TACTGTTGGG,TACTGTTGGG -TCRVg9,,T cell receptor gamma variable 9,,,TCGTTTGTCA,TCGTTTGTCA -CD127,,Interleukin-7 receptor subunit alpha,IL-7Rα,P16871,TGTTAGAGGA,TGTTAGAGGA -CD141,,Thrombomodulin,TM,P07204,AATTGTTCGT,AATTGTTCGT -CD31,,Platelet endothelial cell adhesion molecule,PECAM-1,P16284,GGCAAAGAGC,GGCAAAGAGC -CD6,,T cell differentiation antigen CD6,,P30203,CTAAGATCTC,CTAAGATCTC -CD57,,Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1,,Q9P2W7,ACGACGGGAC,ACGACGGGAC -CD73,,5’-nucleotidase,NT5E,P21589,ACCAAGGACG,ACCAAGGACG -TIM-3,,Hepatitis A virus cellular receptor 2,CD366;HAVCR2,Q8TDQ0,CGCCAAGTGG,CGCCAAGTGG -GITR,,Tumor necrosis factor receptor superfamily member 18,CD357,Q9Y5U5,TGAGTCACTC,TGAGTCACTC -CCR3,,C-C chemokine receptor type 3,CD193,P51677,CCGTGACCCA,CCGTGACCCA -SLAMF7,,SLAM family member 7,CD319;CRACC,Q9NQ25,AGGCGGAAAT,AGGCGGAAAT -TIGIT,,T cell immunoreceptor with Ig and ITIM domains,,Q495A1,ACTGAGTCGC,ACTGAGTCGC -OX40,,Tumor necrosis factor receptor superfamily member 4,CD134,P43489,CCACTTCCGT,CCACTTCCGT -ICAM-2,,Intercellular adhesion molecule 2,CD102,P13598,TATCTGGGAT,TATCTGGGAT -CD123,,Interleukin-3 receptor subunit alpha,IL-3Rα,P26951,TGACTGCTAC,TGACTGCTAC -CD150,,Signaling lymphocytic activation molecule,SLAMF1,Q13291,TCGAATGGAT,TCGAATGGAT -CD40L,,CD40 ligand,CD154,P29965,CTAGATTTGC,CTAGATTTGC -KIR,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158,Q8N743,TCCTCTCCTG,TCCTCTCCTG -CD161,,Killer cell lectin-like receptor subfamily B member 1,KLRB1,Q12918,ACTGAACTAC,ACTGAACTAC -CD180,,CD180 antigen,RP105,Q99467,TGAGCTCCAA,TGAGCTCCAA -CCR1,,C-C chemokine receptor type 1,CD191,P32246,CCGGTGGTTC,CCGGTGGTTC -CCR2,,C-C chemokine receptor type 2,CD192,P41597,GGTTCTCCAC,GGTTCTCCAC -CD1d,,Antigen-presenting glycoprotein CD1d,,P15813,CAACGTCCCA,CAACGTCCCA -CD200,,OX-2 membrane glycoprotein,,P41217,CGCACGGGTT,CGCACGGGTT -Ly9,,T-lymphocyte surface antigen Ly-9,CD229;SLAMF3,Q9HBG7,TCGACGAGTG,TCGACGAGTG -CD24,,Signal transducer CD24,HSA,P25063,TCTTGTTCCC,TCTTGTTCCC -2B4,,Natural killer cell receptor 2B4,CD244;SLAMF4,Q9BZW8,TCTCAATCAA,TCTCAATCAA -BAFF-R,,Tumor necrosis factor receptor superfamily member 13C (BAFFR),CD268,Q96RJ3,ACGTAACCGC,ACGTAACCGC -ICOS,,Inducible T cell co-stimulator,CD278,Q9Y6W8,CAGGCACCTG,CAGGCACCTG -CD32,,Low-affinity immunoglobulin gamma Fc region receptor II-b,FcγRII,P31994,GATTTCCAGC,GATTTCCAGC -CD33,,Myeloid cell surface antigen CD33,Siglec-3,P20138,GCGATATAGT,GCGATATAGT -NKp30,,Natural cytotoxicity triggering receptor 3 (NKp30),CD337,O14931,CTTATCTCTT,CTTATCTCTT -CD38,,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,,P28907,TCCGATCTGG,TCCGATCTGG -CD39,,Ectonucleoside triphosphate diphosphohydrolase 1,ENTPD1,P49961,TCAGCGCCTT,TCAGCGCCTT -CD40,,Tumor necrosis factor receptor superfamily member 5,,P25942,TCTGGCGTGG,TCTGGCGTGG -CD48,,CD48 antigen,SLAMF2;BLAST-1,P09326,AGTACGAAGA,AGTACGAAGA -ICAM-3,,Intercellular adhesion molecule 3,CD50,P32942,CTCCGCGTTG,CTCCGCGTTG -CD55,,Complement decay-accelerating factor (DAF),DAF,P08174,TTAGCTAAAC,TTAGCTAAAC -CD58,,Lymphocyte function-associated antigen 3 (LFA3),LFA-3,P19256,ATGTTATGTG,ATGTTATGTG -CD62P,,P-selectin,P-selectin,P16109,ACTTAGCGCT,ACTTAGCGCT -CD69,,Early activation antigen CD69,,Q07108,GAAGGGTCTC,GAAGGGTCTC -CD72,,B-cell differentiation antigen CD72,Lyb-2,P21854,GCGGTGACTT,GCGGTGACTT -CD84,,SLAM family member 5,SLAMF5,Q9UIB8,GCCATTGGAA,GCCATTGGAA -CD9,,CD9 antigen,Tetraspanin-29,P21926,GTCTGGTCAT,GTCTGGTCAT -CD94,,Natural killer cells antigen CD94,KLRD1,Q13241,CTACAACCTT,CTACAACCTT -TCRVb5,,T cell receptor beta variable 5,,,GGCCTCAAGT,GGCCTCAAGT -CD3e,,T cell surface glycoprotein CD3 epsilon chain,,P07766,TGTAGAATTC,TGTAGAATTC -CD4,,T cell surface glycoprotein CD4,,P01730,GACAACTTCT,GACAACTTCT -CD11a,,Integrin α-L (LFA-1 α),ITGAL;LFA-1 α,P20701,ACACACTTGA,ACACACTTGA -CD43,,Leukosialin,Leukosialin,P16150,GAGATTACTA,GAGATTACTA -CD7,,T cell antigen CD7,,P09564,CTGGGTCCGT,CTGGGTCCGT -CD53,,Leukocyte surface antigen CD53,Tetraspanin-25,P19397,CAACCCGCTT,CAACCCGCTT -CD302,,C-type lectin domain family 13 member A,CLEC13A,Q8IX05,TAGACATTGG,TAGACATTGG -VISTA,,V-type immunoglobulin domain-containing suppressor of T cell activation,VSIR,Q9H7M9,AATGTTAACG,AATGTTAACG -BCMA,,Tumor necrosis factor receptor superfamily member 17,CD269,Q02223,CTGGACTATG,CTGGACTATG -CD138,,Syndecan-1,Syndecan-1,P18827,CTGGGCTTAC,CTGGGCTTAC -4-1BB,,Tumor necrosis factor receptor superfamily member 9,CD137,Q07011,CCAGCTAGAA,CCAGCTAGAA -CD66b,,Cell adhesion molecule CEACAM8,CEACAM8,P31997,CTAGGCAGTT,CTAGGCAGTT -EpCAM,,Epithelial cell adhesion molecule,CD326,P16422,CGTTCTTACA,CGTTCTTACA -DC-SIGN,,CD209 antigen,CD209,Q9NNX6,TGGACGTGAA,TGGACGTGAA -CD34,,Hematopoietic progenitor cell antigen CD34,,P28906,CCGTCTAGCC,CCGTCTAGCC -Dectin-1,,C-type lectin domain family 7 member A,CD369;CLEC7A,Q9BXN2,CTGCCAAGAC,CTGCCAAGAC -ICAM-1,,Intercellular adhesion molecule 1,CD54,P05362,AGCAGCTGAT,AGCAGCTGAT -CD71,,Transferrin receptor protein 1,Transferrin receptor,P02786,TCAGGACAGA,TCAGGACAGA -CD47,,Leukocyte surface antigen CD47,Integrin associated protein,Q08722,AGCTACTATT,AGCTACTATT -c-Kit,,Mast/Stem cell growth factor receptor Kit,CD117,P10721,GCTATAATTG,GCTATAATTG -NKG2D,,NKG2-D type II integral membrane protein,CD314;KG2DN,P26718,TGGCGCACAC,TGGCGCACAC -CD98,,4F2 cell-surface antigen heavy chain,SLC3A2,P08195,CCAGAGCGGA,CCAGAGCGGA -CD298,,Na+/K+-ATPase β3,ATP1B3,P54709,AAGCCTGCCT,AAGCCTGCCT -B2M-1,,,,,GAGGGACGGT,GAGGGACGGT,yes -B2M-2,,,,,TAGAGGAGGC,TAGAGGAGGC,yes -B2M-3,,,,,CCCACTAAGC,CCCACTAAGC,yes -B2M-4,,,,,TGGTTTACAA,TGGTTTACAA,yes -B2M-5,,,,,CTAACTACGG,CTAACTACGG,yes -B2M-6,,,,,TATTGAACCT,TATTGAACCT,yes -B2M-7,,,,,ATCAACCCTA,ATCAACCCTA,yes -B2M-8,,,,,GTATCCCTAC,GTATCCCTAC,yes -CD298-1,,,,,AAAGTCTCTG,AAAGTCTCTG,yes -CD298-2,,,,,AAATAGTACG,AAATAGTACG,yes -CD298-3,,,,,GACGGCTTAG,GACGGCTTAG,yes -CD298-4,,,,,GTCAAGGTAA,GTCAAGGTAA,yes -CD298-5,,,,,GGTAAGCCCT,GGTAAGCCCT,yes -CD298-6,,,,,GCCGCCTATG,GCCGCCTATG,yes -CD298-7,,,,,GCTCCGCAAC,GCTCCGCAAC,yes -CD298-8,,,,,AGCCTCAGCA,AGCCTCAGCA,yes -CD98-1,,,,,TGGCTTAGCC,TGGCTTAGCC,yes -CD98-2,,,,,ATTGTGTGGG,ATTGTGTGGG,yes -CD98-3,,,,,CATAGACCAT,CATAGACCAT,yes -CD98-4,,,,,ATGTTCCTCT,ATGTTCCTCT,yes -CD98-5,,,,,TTCGTAACTA,TTCGTAACTA,yes -CD98-6,,,,,CTGACCGCTA,CTGACCGCTA,yes -CD98-7,,,,,CCCTCGGTCT,CCCTCGGTCT,yes -CD98-8,,,,,ATCGCACGTA,ATCGCACGTA,yes -FLAG,,,,,CTTAACATCT,CTTAACATCT diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FMC63-prerelease.csv b/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FMC63-prerelease.csv deleted file mode 100644 index 2dbe4a14e..000000000 --- a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FMC63-prerelease.csv +++ /dev/null @@ -1,194 +0,0 @@ -# --- -# name: proxiome-v2-immuno-156-FMC63-prerelease -# product: proxiome-v2-immuno-156-FMC63 -# aliases: -# - proxiome-v2-immuno-156-FMC63-v1.0 -# description: >- -# Panel for the Proxiome Immuno Kit with 155 markers + 3 control markers -# + 3*8 hashing antibodies + the FMC63 marker -# version: 1.0.0 -# --- -marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing -HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG -B2M,,Beta-2-microglobulin,,P61769,CCAGGTTCCG,CCAGGTTCCG -CD11b,,Integrin α-M (ITGAM),ITGAM;Mac-1 α,P11215,CAGCTATGGT,CAGCTATGGT -CD11c,,Integrin α-X,Integrin αX,P20702,ATATGACGGT,ATATGACGGT -CD18,,Integrin beta 2,Integrin β2,P05107,GGGTAGGCTG,GGGTAGGCTG -CD82,,CD82 antigen,Tetraspanin-27,P27701,CCCGTCATGA,CCCGTCATGA -CD8,,T cell surface glycoprotein CD8 a/b chains,,P01732;P10966,CGGTGGATCA,CGGTGGATCA -TCRab,,T cell receptor alpha chain constant/beta constant 1,,P01848;P01850,CTGGTAGCAA,CTGGTAGCAA -HLA-DR,,"HLA class II histocompatibility antigen, DR",,P01903;P01911,TGTTGTCGAA,TGTTGTCGAA -CD45,,"Receptor-type tyrosine-protein phosphatase C. All 6 isoforms (ABC, AB, BC, B and O)",PTPRC,P08575,TGGAGGCTCT,TGGAGGCTCT -CD14,,Monocyte differentiation antigen CD14,,P08571,TGGCTATGTA,TGGCTATGTA -CD16,,Low-affinity immunoglobulin gamma Fc region receptor / III-A and -B,FcγRIII,P08637;O75015,ATAGGTTAGG,ATAGGTTAGG -CD19,,B-lymphocyte antigen CD19,,P15391,ACGGAATATT,ACGGAATATT -mIgG1,yes,,,,ATGCTAGTCG,ATGCTAGTCG -CD45RB,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, BC, and B)",,P08575,GAAGCAGTAT,GAAGCAGTAT -CD44,,CD44 antigen,,P16070,GTGAGTCAAT,GTGAGTCAAT -CD52,,CAMPATH-1 antigen,CAMPATH-1,P31358,CTTTAGCAGG,CTTTAGCAGG -CD59,,CD59 glycoprotein,Protectin;MAC-IP,P13987,GGTGTATGAG,GGTGTATGAG -CD45RA,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, and A)",,P08575,GGATTCGTGG,GGATTCGTGG -CD36,,Platelet glycoprotein 4,FAT;SCARB3,P16671,TACCCTGCGA,TACCCTGCGA -CD2,,T cell surface antigen CD2,,P06729,TGCCGATGCC,TGCCGATGCC -CD29,,Integrin beta-1,Integrin β1,P05556,TCCAGTGTCT,TCCAGTGTCT -CD5,,T cell surface glycoprotein CD5,,P06127,CACCCATCAA,CACCCATCAA -CD162,,P-selectin glycoprotein ligand 1,SELPLG;PSGL-1,Q14242,CTTCGTGGAC,CTTCGTGGAC -CD27,,CD27 antigen,,P26842,GGTTTGCAAA,GGTTTGCAAA -CR1,,Complement receptor type 1,CD35,P17927,CGCCACCTTT,CGCCACCTTT -CD26,,Dipeptidyl peptidase 4,DPP4,P27487,GATTCGCTGT,GATTCGCTGT -CD49d,,Integrin α-4,Integrin α4,P13612,AACTTAGGTT,AACTTAGGTT -CD37,,Leukocyte antigen CD37,Tetraspanin-26,P11049,AGAAGAAGAG,AGAAGAAGAG -CD41,,Integrin α-IIb,Integrin αIIb,P08514,TAAGGCATAA,TAAGGCATAA -CD20,,B-lymphocyte antigen CD20,,P11836,GCCACACCCA,GCCACACCCA -CD64,,High affinity immunoglobulin gamma Fc receptor I,FcγRI,P12314,CTTGTATATC,CTTGTATATC -CD22,,B-cell receptor CD22,,P20273,TGACCCGTTC,TGACCCGTTC -PD-L1,,Programmed cell death 1 ligand 1 (PDL1),CD274,Q9NZQ7,GCTTGAGATT,GCTTGAGATT -Siglec-7,,Sialic acid-binding Ig-like lectin 7 (SIGLEC-7),CD328,Q9Y286,TATATGCTGA,TATATGCTGA -CD25,,Interleukin-2 receptor subunit alpha,IL-2Rα,P01589,AGAGACGAAT,AGAGACGAAT -PD-1,,Programmed cell death protein 1 (PD-1),CD279,Q15116,TACAGAGCCC,TACAGAGCCC -NKp46,,Natural cytotoxicity triggering receptor 1 (NKp46),CD335,O76036,ATTACCCGCG,ATTACCCGCG -mIgG2a,yes,,,,ATTTCCACTA,ATTTCCACTA -mIgG2b,yes,,,,CTAAATGGCT,CTAAATGGCT -CTLA-4,,Cytotoxic T-lymphocyte protein 4,CD152,P16410,TTTCTGCATT,TTTCTGCATT -CD86,,T-lymphocyte activation antigen CD86,B7-2,P42081,ACCATCACTT,ACCATCACTT -CD13,,Aminopeptidase N,Aminopeptidase N,P15144,GCATGGGTAG,GCATGGGTAG -ADAM10,,Disintegrin and metalloproteinase domain-containing protein 10,CD156c,O14672,ATAAGTTCCA,ATAAGTTCCA -KIR2DL1,,Killer cell immunoglobulin-like receptor 2DL1,CD158a,P43626,TGTTACGGTC,TGTTACGGTC -KIR2DL2/DL3,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158b,P43627,ACTGCATTGA,ACTGCATTGA -NKG2A,,NKG2-A/NKG2-B type II integral membrane protein,CD159a,P26715,CGTACACGGT,CGTACACGGT -NKG2C,,NKG2-C type II integral membrane protein,CD159c,P26717,CAACAGTCGA,CAACAGTCGA -CD163,,Scavenger receptor cysteine-rich type 1 protein M130,,Q86VB7,GACCGTGATT,GACCGTGATT -CD169,,Sialoadhesin,Siglec-1,Q9BZZ2,TAATCGCGGG,TAATCGCGGG -CD1a,,T cell surface glycoprotein CD1a,,P06126,CGACTAATCA,CGACTAATCA -CD1c,,T cell surface glycoprotein CD1c,,P29017,GTGCACTGTC,GTGCACTGTC -CD206,,Macrophage mannose receptor 1,Mannose receptor,P22897,TGCCTAATAG,TGCCTAATAG -DNAM-1,,CD226 antigen,CD226,Q15762,CGGTCATTAA,CGGTCATTAA -PD-L2,,Programmed cell death 1 ligand 2 (PDL2),CD273,Q9BQ51,ATCGCGAAGC,ATCGCGAAGC -CD28,,T cell-specific surface glycoprotein CD28,,P10747,CATAACAATC,CATAACAATC -SLAMF6,,SLAM family member 6,CD352;NTB-A,Q96DU3,TCGGAGACAC,TCGGAGACAC -CD45RO,,"Receptor-type tyrosine-protein phosphatase C. Isoform O",,P08575,TTGATGACTC,TTGATGACTC -CD49e,,Integrin α-5,Integrin α5,P08648,AACTCCTGAA,AACTCCTGAA -CD56,,Neural cell adhesion molecule 1,NCAM,P13591,GTGCGTAAGC,GTGCGTAAGC -CD79a,,B-cell antigen receptor complex-associated protein alpha chain,MB-1,P11912,AGATCGACAG,AGATCGACAG -CD80,,T-lymphocyte activation antigen CD80,B7-1,P33681,AAGACGCGGA,AAGACGCGGA -CD81,,CD81 antigen,Tetraspanin-28,P60033,TGGGTTATGT,TGGGTTATGT -LILRB1,,Leukocyte immunoglobulin-like receptor subfamily B member 1,CD85j;ILT-2,Q8NHL6,CCTAAGTCTA,CCTAAGTCTA -CD93,,Complement component C1q receptor,,Q9NPY3,GCAGCGAACA,GCAGCGAACA -IgD,,Immunoglobulin delta heavy chain,,P0DOX3,AGATGAGGCA,AGATGAGGCA -IgE,,Immunoglobulin epsilon heavy chain,,P0DOX4,CGACGGTAAG,CGACGGTAAG -IgM,,Immunoglobulin mu heavy chain,,P0DOX6,GTGGATCCAA,GTGGATCCAA -KLRG1,,Killer cell lectin-like receptor subfamily G member 1,,Q96E93,TATACAGACA,TATACAGACA -NKp80,,Killer cell lectin-like receptor subfamily F member 1,KLRF1,Q9NZS2,CCATCGGATC,CCATCGGATC -TCRgd,,T cell receptor gamma constant 1 /delta constant,,P0CF51;B7Z8K6,CTTATGACCA,CTTATGACCA -CD10,,Neprilysin,Neprilysin,P08473,CGCAGGTAGC,CGCAGGTAGC -CD103,,Integrin alpha-E,Integrin αE,P38570,CCTATGCGAA,CCTATGCGAA -CD1b,,T cell surface glycoprotein CD1b,,P29016,GACACCACCG,GACACCACCG -CD21,,Complement receptor type 2,CR2,P20023,GTGGCGTTAA,GTGGCGTTAA -TALLA,,Tetraspanin-7,CD231;Tetraspanin-7,P41732,CACGATACTT,CACGATACTT -CD277,,Butyrophilin subfamily 3 member A1,BTN3,O00481,GAGTGATACG,GAGTGATACG -LAIR1,,Leukocyte-associated immunoglobulin-like receptor 1,CD305,Q6GTX8,GCAATGTGTA,GCAATGTGTA -CD371,,C-type lectin domain family 12 member A,CLEC12A,Q5QGZ9,AAGGTCCCAT,AAGGTCCCAT -CD89,,Immunoglobulin alpha Fc receptor,FcαRI;FCAR,P24071,GTATCATAAG,GTATCATAAG -CD90,,Thy-1 membrane glycoprotein,Thy-1,P04216,TAGCCGATTA,TAGCCGATTA -CD70,,CD70 antigen,CD27L,P32970,CTCAGCATGC,CTCAGCATGC -GPR56,,Adhesion G-protein coupled receptor G1,TM7XN1,Q9Y653,GCGTCTCTCT,GCGTCTCTCT -HLA-DQ,,"HLA class II histocompatibility antigen, DQ",,P01906;P05538;P01920;P01909,ATACTTGAGC,ATACTTGAGC -TCRVd2,,T cell receptor delta variable 2,,,CCGACCATTC,CCGACCATTC -HLA-DR-DP-DQ,,HLA class II histocompatibility antigen,,P01903;P20036;P01909,AACAGAGGAA,AACAGAGGAA -Siglec-9,,Sialic acid-binding Ig-like lectin 9,,Q9Y336,TTAACAAGCA,TTAACAAGCA -TCRVa7.2,,T cell receptor alpha variable 7,,A0A075B6U4,TCCCAGGTCC,TCCCAGGTCC -Fas,,Tumor necrosis factor receptor superfamily member 6,CD95,P25445,TACTGTTGGG,TACTGTTGGG -TCRVg9,,T cell receptor gamma variable 9,,,TCGTTTGTCA,TCGTTTGTCA -CD127,,Interleukin-7 receptor subunit alpha,IL-7Rα,P16871,TGTTAGAGGA,TGTTAGAGGA -CD141,,Thrombomodulin,TM,P07204,AATTGTTCGT,AATTGTTCGT -CD31,,Platelet endothelial cell adhesion molecule,PECAM-1,P16284,GGCAAAGAGC,GGCAAAGAGC -CD6,,T cell differentiation antigen CD6,,P30203,CTAAGATCTC,CTAAGATCTC -CD57,,Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1,,Q9P2W7,ACGACGGGAC,ACGACGGGAC -CD73,,5’-nucleotidase,NT5E,P21589,ACCAAGGACG,ACCAAGGACG -TIM-3,,Hepatitis A virus cellular receptor 2,CD366;HAVCR2,Q8TDQ0,CGCCAAGTGG,CGCCAAGTGG -GITR,,Tumor necrosis factor receptor superfamily member 18,CD357,Q9Y5U5,TGAGTCACTC,TGAGTCACTC -CCR3,,C-C chemokine receptor type 3,CD193,P51677,CCGTGACCCA,CCGTGACCCA -SLAMF7,,SLAM family member 7,CD319;CRACC,Q9NQ25,AGGCGGAAAT,AGGCGGAAAT -TIGIT,,T cell immunoreceptor with Ig and ITIM domains,,Q495A1,ACTGAGTCGC,ACTGAGTCGC -OX40,,Tumor necrosis factor receptor superfamily member 4,CD134,P43489,CCACTTCCGT,CCACTTCCGT -ICAM-2,,Intercellular adhesion molecule 2,CD102,P13598,TATCTGGGAT,TATCTGGGAT -CD123,,Interleukin-3 receptor subunit alpha,IL-3Rα,P26951,TGACTGCTAC,TGACTGCTAC -CD150,,Signaling lymphocytic activation molecule,SLAMF1,Q13291,TCGAATGGAT,TCGAATGGAT -CD40L,,CD40 ligand,CD154,P29965,CTAGATTTGC,CTAGATTTGC -KIR,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158,Q8N743,TCCTCTCCTG,TCCTCTCCTG -CD161,,Killer cell lectin-like receptor subfamily B member 1,KLRB1,Q12918,ACTGAACTAC,ACTGAACTAC -CD180,,CD180 antigen,RP105,Q99467,TGAGCTCCAA,TGAGCTCCAA -CCR1,,C-C chemokine receptor type 1,CD191,P32246,CCGGTGGTTC,CCGGTGGTTC -CCR2,,C-C chemokine receptor type 2,CD192,P41597,GGTTCTCCAC,GGTTCTCCAC -CD1d,,Antigen-presenting glycoprotein CD1d,,P15813,CAACGTCCCA,CAACGTCCCA -CD200,,OX-2 membrane glycoprotein,,P41217,CGCACGGGTT,CGCACGGGTT -Ly9,,T-lymphocyte surface antigen Ly-9,CD229;SLAMF3,Q9HBG7,TCGACGAGTG,TCGACGAGTG -CD24,,Signal transducer CD24,HSA,P25063,TCTTGTTCCC,TCTTGTTCCC -2B4,,Natural killer cell receptor 2B4,CD244;SLAMF4,Q9BZW8,TCTCAATCAA,TCTCAATCAA -BAFF-R,,Tumor necrosis factor receptor superfamily member 13C (BAFFR),CD268,Q96RJ3,ACGTAACCGC,ACGTAACCGC -ICOS,,Inducible T cell co-stimulator,CD278,Q9Y6W8,CAGGCACCTG,CAGGCACCTG -CD32,,Low-affinity immunoglobulin gamma Fc region receptor II-b,FcγRII,P31994,GATTTCCAGC,GATTTCCAGC -CD33,,Myeloid cell surface antigen CD33,Siglec-3,P20138,GCGATATAGT,GCGATATAGT -NKp30,,Natural cytotoxicity triggering receptor 3 (NKp30),CD337,O14931,CTTATCTCTT,CTTATCTCTT -CD38,,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,,P28907,TCCGATCTGG,TCCGATCTGG -CD39,,Ectonucleoside triphosphate diphosphohydrolase 1,ENTPD1,P49961,TCAGCGCCTT,TCAGCGCCTT -CD40,,Tumor necrosis factor receptor superfamily member 5,,P25942,TCTGGCGTGG,TCTGGCGTGG -CD48,,CD48 antigen,SLAMF2;BLAST-1,P09326,AGTACGAAGA,AGTACGAAGA -ICAM-3,,Intercellular adhesion molecule 3,CD50,P32942,CTCCGCGTTG,CTCCGCGTTG -CD55,,Complement decay-accelerating factor (DAF),DAF,P08174,TTAGCTAAAC,TTAGCTAAAC -CD58,,Lymphocyte function-associated antigen 3 (LFA3),LFA-3,P19256,ATGTTATGTG,ATGTTATGTG -CD62P,,P-selectin,P-selectin,P16109,ACTTAGCGCT,ACTTAGCGCT -CD69,,Early activation antigen CD69,,Q07108,GAAGGGTCTC,GAAGGGTCTC -CD72,,B-cell differentiation antigen CD72,Lyb-2,P21854,GCGGTGACTT,GCGGTGACTT -CD84,,SLAM family member 5,SLAMF5,Q9UIB8,GCCATTGGAA,GCCATTGGAA -CD9,,CD9 antigen,Tetraspanin-29,P21926,GTCTGGTCAT,GTCTGGTCAT -CD94,,Natural killer cells antigen CD94,KLRD1,Q13241,CTACAACCTT,CTACAACCTT -TCRVb5,,T cell receptor beta variable 5,,,GGCCTCAAGT,GGCCTCAAGT -CD3e,,T cell surface glycoprotein CD3 epsilon chain,,P07766,TGTAGAATTC,TGTAGAATTC -CD4,,T cell surface glycoprotein CD4,,P01730,GACAACTTCT,GACAACTTCT -CD11a,,Integrin α-L (LFA-1 α),ITGAL;LFA-1 α,P20701,ACACACTTGA,ACACACTTGA -CD43,,Leukosialin,Leukosialin,P16150,GAGATTACTA,GAGATTACTA -CD7,,T cell antigen CD7,,P09564,CTGGGTCCGT,CTGGGTCCGT -CD53,,Leukocyte surface antigen CD53,Tetraspanin-25,P19397,CAACCCGCTT,CAACCCGCTT -CD302,,C-type lectin domain family 13 member A,CLEC13A,Q8IX05,TAGACATTGG,TAGACATTGG -VISTA,,V-type immunoglobulin domain-containing suppressor of T cell activation,VSIR,Q9H7M9,AATGTTAACG,AATGTTAACG -BCMA,,Tumor necrosis factor receptor superfamily member 17,CD269,Q02223,CTGGACTATG,CTGGACTATG -CD138,,Syndecan-1,Syndecan-1,P18827,CTGGGCTTAC,CTGGGCTTAC -4-1BB,,Tumor necrosis factor receptor superfamily member 9,CD137,Q07011,CCAGCTAGAA,CCAGCTAGAA -CD66b,,Cell adhesion molecule CEACAM8,CEACAM8,P31997,CTAGGCAGTT,CTAGGCAGTT -EpCAM,,Epithelial cell adhesion molecule,CD326,P16422,CGTTCTTACA,CGTTCTTACA -DC-SIGN,,CD209 antigen,CD209,Q9NNX6,TGGACGTGAA,TGGACGTGAA -CD34,,Hematopoietic progenitor cell antigen CD34,,P28906,CCGTCTAGCC,CCGTCTAGCC -Dectin-1,,C-type lectin domain family 7 member A,CD369;CLEC7A,Q9BXN2,CTGCCAAGAC,CTGCCAAGAC -ICAM-1,,Intercellular adhesion molecule 1,CD54,P05362,AGCAGCTGAT,AGCAGCTGAT -CD71,,Transferrin receptor protein 1,Transferrin receptor,P02786,TCAGGACAGA,TCAGGACAGA -CD47,,Leukocyte surface antigen CD47,Integrin associated protein,Q08722,AGCTACTATT,AGCTACTATT -c-Kit,,Mast/Stem cell growth factor receptor Kit,CD117,P10721,GCTATAATTG,GCTATAATTG -NKG2D,,NKG2-D type II integral membrane protein,CD314;KG2DN,P26718,TGGCGCACAC,TGGCGCACAC -CD98,,4F2 cell-surface antigen heavy chain,SLC3A2,P08195,CCAGAGCGGA,CCAGAGCGGA -CD298,,Na+/K+-ATPase β3,ATP1B3,P54709,AAGCCTGCCT,AAGCCTGCCT -B2M-1,,,,,TGAGTGGTGA,TGAGTGGTGA,yes -B2M-2,,,,,TAGAGGAGGC,TAGAGGAGGC,yes -B2M-3,,,,,CCCACTAAGC,CCCACTAAGC,yes -B2M-4,,,,,TGGTTTACAA,TGGTTTACAA,yes -B2M-5,,,,,CTAACTACGG,CTAACTACGG,yes -B2M-6,,,,,TATTGAACCT,TATTGAACCT,yes -B2M-7,,,,,ATCAACCCTA,ATCAACCCTA,yes -B2M-8,,,,,GTATCCCTAC,GTATCCCTAC,yes -CD298-1,,,,,GCTAGCAACG,GCTAGCAACG,yes -CD298-2,,,,,AAATAGTACG,AAATAGTACG,yes -CD298-3,,,,,GACGGCTTAG,GACGGCTTAG,yes -CD298-4,,,,,GTCAAGGTAA,GTCAAGGTAA,yes -CD298-5,,,,,GGTAAGCCCT,GGTAAGCCCT,yes -CD298-6,,,,,GCCGCCTATG,GCCGCCTATG,yes -CD298-7,,,,,GCTCCGCAAC,GCTCCGCAAC,yes -CD298-8,,,,,AGCCTCAGCA,AGCCTCAGCA,yes -CD98-1,,,,,CACTTGGCCA,CACTTGGCCA,yes -CD98-2,,,,,ATTGTGTGGG,ATTGTGTGGG,yes -CD98-3,,,,,CATAGACCAT,CATAGACCAT,yes -CD98-4,,,,,ATGTTCCTCT,ATGTTCCTCT,yes -CD98-5,,,,,TTCGTAACTA,TTCGTAACTA,yes -CD98-6,,,,,CTGACCGCTA,CTGACCGCTA,yes -CD98-7,,,,,CCCTCGGTCT,CCCTCGGTCT,yes -CD98-8,,,,,ATCGCACGTA,ATCGCACGTA,yes -FMC63,,,,,CGATTGGCAC,CGATTGGCAC diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FMC63-v2.0.csv b/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FMC63-v2.0.csv deleted file mode 100644 index b3e9766ee..000000000 --- a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-FMC63-v2.0.csv +++ /dev/null @@ -1,192 +0,0 @@ -# --- -# name: proxiome-v2-immuno-156-FMC63-v2.0 -# product: proxiome-v2-immuno-156-FMC63 -# description: >- -# Panel for the Proxiome Immuno Kit with 155 markers + 3 control markers -# + 3*8 hashing antibodies + the FMC63 marker -# version: 2.0.0 -# --- -marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing -HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG -B2M,,Beta-2-microglobulin,,P61769,CCAGGTTCCG,CCAGGTTCCG -CD11b,,Integrin α-M (ITGAM),ITGAM;Mac-1 α,P11215,CAGCTATGGT,CAGCTATGGT -CD11c,,Integrin α-X,Integrin αX,P20702,ATATGACGGT,ATATGACGGT -CD18,,Integrin beta 2,Integrin β2,P05107,GGGTAGGCTG,GGGTAGGCTG -CD82,,CD82 antigen,Tetraspanin-27,P27701,CCCGTCATGA,CCCGTCATGA -CD8,,T cell surface glycoprotein CD8 a/b chains,,P01732;P10966,CGGTGGATCA,CGGTGGATCA -TCRab,,T cell receptor alpha chain constant/beta constant 1,,P01848;P01850,CTGGTAGCAA,CTGGTAGCAA -HLA-DR,,"HLA class II histocompatibility antigen, DR",,P01903;P01911,TGTTGTCGAA,TGTTGTCGAA -CD45,,"Receptor-type tyrosine-protein phosphatase C. All 6 isoforms (ABC, AB, BC, B and O)",PTPRC,P08575,TGGAGGCTCT,TGGAGGCTCT -CD14,,Monocyte differentiation antigen CD14,,P08571,TGGCTATGTA,TGGCTATGTA -CD16,,Low-affinity immunoglobulin gamma Fc region receptor / III-A and -B,FcγRIII,P08637;O75015,ATAGGTTAGG,ATAGGTTAGG -CD19,,B-lymphocyte antigen CD19,,P15391,ACGGAATATT,ACGGAATATT -mIgG1,yes,,,,ATGCTAGTCG,ATGCTAGTCG -CD45RB,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, BC, and B)",,P08575,GAAGCAGTAT,GAAGCAGTAT -CD44,,CD44 antigen,,P16070,GTGAGTCAAT,GTGAGTCAAT -CD52,,CAMPATH-1 antigen,CAMPATH-1,P31358,CTTTAGCAGG,CTTTAGCAGG -CD59,,CD59 glycoprotein,Protectin;MAC-IP,P13987,GGTGTATGAG,GGTGTATGAG -CD45RA,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, and A)",,P08575,GGATTCGTGG,GGATTCGTGG -CD36,,Platelet glycoprotein 4,FAT;SCARB3,P16671,TACCCTGCGA,TACCCTGCGA -CD2,,T cell surface antigen CD2,,P06729,TGCCGATGCC,TGCCGATGCC -CD29,,Integrin beta-1,Integrin β1,P05556,TCCAGTGTCT,TCCAGTGTCT -CD5,,T cell surface glycoprotein CD5,,P06127,CACCCATCAA,CACCCATCAA -CD162,,P-selectin glycoprotein ligand 1,SELPLG;PSGL-1,Q14242,CTTCGTGGAC,CTTCGTGGAC -CD27,,CD27 antigen,,P26842,GGTTTGCAAA,GGTTTGCAAA -CR1,,Complement receptor type 1,CD35,P17927,CGCCACCTTT,CGCCACCTTT -CD26,,Dipeptidyl peptidase 4,DPP4,P27487,GATTCGCTGT,GATTCGCTGT -CD49d,,Integrin α-4,Integrin α4,P13612,AACTTAGGTT,AACTTAGGTT -CD37,,Leukocyte antigen CD37,Tetraspanin-26,P11049,AGAAGAAGAG,AGAAGAAGAG -CD41,,Integrin α-IIb,Integrin αIIb,P08514,TAAGGCATAA,TAAGGCATAA -CD20,,B-lymphocyte antigen CD20,,P11836,GCCACACCCA,GCCACACCCA -CD64,,High affinity immunoglobulin gamma Fc receptor I,FcγRI,P12314,CTTGTATATC,CTTGTATATC -CD22,,B-cell receptor CD22,,P20273,TGACCCGTTC,TGACCCGTTC -PD-L1,,Programmed cell death 1 ligand 1 (PDL1),CD274,Q9NZQ7,GCTTGAGATT,GCTTGAGATT -Siglec-7,,Sialic acid-binding Ig-like lectin 7 (SIGLEC-7),CD328,Q9Y286,TATATGCTGA,TATATGCTGA -CD25,,Interleukin-2 receptor subunit alpha,IL-2Rα,P01589,AGAGACGAAT,AGAGACGAAT -PD-1,,Programmed cell death protein 1 (PD-1),CD279,Q15116,TACAGAGCCC,TACAGAGCCC -NKp46,,Natural cytotoxicity triggering receptor 1 (NKp46),CD335,O76036,ATTACCCGCG,ATTACCCGCG -mIgG2a,yes,,,,ATTTCCACTA,ATTTCCACTA -mIgG2b,yes,,,,CTAAATGGCT,CTAAATGGCT -CTLA-4,,Cytotoxic T-lymphocyte protein 4,CD152,P16410,TTTCTGCATT,TTTCTGCATT -CD86,,T-lymphocyte activation antigen CD86,B7-2,P42081,ACCATCACTT,ACCATCACTT -CD13,,Aminopeptidase N,Aminopeptidase N,P15144,GCATGGGTAG,GCATGGGTAG -ADAM10,,Disintegrin and metalloproteinase domain-containing protein 10,CD156c,O14672,ATAAGTTCCA,ATAAGTTCCA -KIR2DL1,,Killer cell immunoglobulin-like receptor 2DL1,CD158a,P43626,TGTTACGGTC,TGTTACGGTC -KIR2DL2/DL3,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158b,P43627,ACTGCATTGA,ACTGCATTGA -NKG2A,,NKG2-A/NKG2-B type II integral membrane protein,CD159a,P26715,CGTACACGGT,CGTACACGGT -NKG2C,,NKG2-C type II integral membrane protein,CD159c,P26717,CAACAGTCGA,CAACAGTCGA -CD163,,Scavenger receptor cysteine-rich type 1 protein M130,,Q86VB7,GACCGTGATT,GACCGTGATT -CD169,,Sialoadhesin,Siglec-1,Q9BZZ2,TAATCGCGGG,TAATCGCGGG -CD1a,,T cell surface glycoprotein CD1a,,P06126,CGACTAATCA,CGACTAATCA -CD1c,,T cell surface glycoprotein CD1c,,P29017,GTGCACTGTC,GTGCACTGTC -CD206,,Macrophage mannose receptor 1,Mannose receptor,P22897,TGCCTAATAG,TGCCTAATAG -DNAM-1,,CD226 antigen,CD226,Q15762,CGGTCATTAA,CGGTCATTAA -PD-L2,,Programmed cell death 1 ligand 2 (PDL2),CD273,Q9BQ51,ATCGCGAAGC,ATCGCGAAGC -CD28,,T cell-specific surface glycoprotein CD28,,P10747,CATAACAATC,CATAACAATC -SLAMF6,,SLAM family member 6,CD352;NTB-A,Q96DU3,TCGGAGACAC,TCGGAGACAC -CD45RO,,"Receptor-type tyrosine-protein phosphatase C. Isoform O",,P08575,TTGATGACTC,TTGATGACTC -CD49e,,Integrin α-5,Integrin α5,P08648,AACTCCTGAA,AACTCCTGAA -CD56,,Neural cell adhesion molecule 1,NCAM,P13591,GTGCGTAAGC,GTGCGTAAGC -CD79a,,B-cell antigen receptor complex-associated protein alpha chain,MB-1,P11912,AGATCGACAG,AGATCGACAG -CD80,,T-lymphocyte activation antigen CD80,B7-1,P33681,AAGACGCGGA,AAGACGCGGA -CD81,,CD81 antigen,Tetraspanin-28,P60033,TGGGTTATGT,TGGGTTATGT -LILRB1,,Leukocyte immunoglobulin-like receptor subfamily B member 1,CD85j;ILT-2,Q8NHL6,CCTAAGTCTA,CCTAAGTCTA -CD93,,Complement component C1q receptor,,Q9NPY3,GCAGCGAACA,GCAGCGAACA -IgD,,Immunoglobulin delta heavy chain,,P0DOX3,AGATGAGGCA,AGATGAGGCA -IgE,,Immunoglobulin epsilon heavy chain,,P0DOX4,CGACGGTAAG,CGACGGTAAG -IgM,,Immunoglobulin mu heavy chain,,P0DOX6,GTGGATCCAA,GTGGATCCAA -KLRG1,,Killer cell lectin-like receptor subfamily G member 1,,Q96E93,TATACAGACA,TATACAGACA -NKp80,,Killer cell lectin-like receptor subfamily F member 1,KLRF1,Q9NZS2,CCATCGGATC,CCATCGGATC -TCRgd,,T cell receptor gamma constant 1 /delta constant,,P0CF51;B7Z8K6,CTTATGACCA,CTTATGACCA -CD10,,Neprilysin,Neprilysin,P08473,CGCAGGTAGC,CGCAGGTAGC -CD103,,Integrin alpha-E,Integrin αE,P38570,CCTATGCGAA,CCTATGCGAA -CD1b,,T cell surface glycoprotein CD1b,,P29016,GACACCACCG,GACACCACCG -CD21,,Complement receptor type 2,CR2,P20023,GTGGCGTTAA,GTGGCGTTAA -TALLA,,Tetraspanin-7,CD231;Tetraspanin-7,P41732,CACGATACTT,CACGATACTT -CD277,,Butyrophilin subfamily 3 member A1,BTN3,O00481,GAGTGATACG,GAGTGATACG -LAIR1,,Leukocyte-associated immunoglobulin-like receptor 1,CD305,Q6GTX8,GCAATGTGTA,GCAATGTGTA -CD371,,C-type lectin domain family 12 member A,CLEC12A,Q5QGZ9,AAGGTCCCAT,AAGGTCCCAT -CD89,,Immunoglobulin alpha Fc receptor,FcαRI;FCAR,P24071,GTATCATAAG,GTATCATAAG -CD90,,Thy-1 membrane glycoprotein,Thy-1,P04216,TAGCCGATTA,TAGCCGATTA -CD70,,CD70 antigen,CD27L,P32970,CTCAGCATGC,CTCAGCATGC -GPR56,,Adhesion G-protein coupled receptor G1,TM7XN1,Q9Y653,GCGTCTCTCT,GCGTCTCTCT -HLA-DQ,,"HLA class II histocompatibility antigen, DQ",,P01906;P05538;P01920;P01909,ATACTTGAGC,ATACTTGAGC -TCRVd2,,T cell receptor delta variable 2,,,CCGACCATTC,CCGACCATTC -HLA-DR-DP-DQ,,HLA class II histocompatibility antigen,,P01903;P20036;P01909,AACAGAGGAA,AACAGAGGAA -Siglec-9,,Sialic acid-binding Ig-like lectin 9,,Q9Y336,TTAACAAGCA,TTAACAAGCA -TCRVa7.2,,T cell receptor alpha variable 7,,A0A075B6U4,TCCCAGGTCC,TCCCAGGTCC -Fas,,Tumor necrosis factor receptor superfamily member 6,CD95,P25445,TACTGTTGGG,TACTGTTGGG -TCRVg9,,T cell receptor gamma variable 9,,,TCGTTTGTCA,TCGTTTGTCA -CD127,,Interleukin-7 receptor subunit alpha,IL-7Rα,P16871,TGTTAGAGGA,TGTTAGAGGA -CD141,,Thrombomodulin,TM,P07204,AATTGTTCGT,AATTGTTCGT -CD31,,Platelet endothelial cell adhesion molecule,PECAM-1,P16284,GGCAAAGAGC,GGCAAAGAGC -CD6,,T cell differentiation antigen CD6,,P30203,CTAAGATCTC,CTAAGATCTC -CD57,,Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1,,Q9P2W7,ACGACGGGAC,ACGACGGGAC -CD73,,5’-nucleotidase,NT5E,P21589,ACCAAGGACG,ACCAAGGACG -TIM-3,,Hepatitis A virus cellular receptor 2,CD366;HAVCR2,Q8TDQ0,CGCCAAGTGG,CGCCAAGTGG -GITR,,Tumor necrosis factor receptor superfamily member 18,CD357,Q9Y5U5,TGAGTCACTC,TGAGTCACTC -CCR3,,C-C chemokine receptor type 3,CD193,P51677,CCGTGACCCA,CCGTGACCCA -SLAMF7,,SLAM family member 7,CD319;CRACC,Q9NQ25,AGGCGGAAAT,AGGCGGAAAT -TIGIT,,T cell immunoreceptor with Ig and ITIM domains,,Q495A1,ACTGAGTCGC,ACTGAGTCGC -OX40,,Tumor necrosis factor receptor superfamily member 4,CD134,P43489,CCACTTCCGT,CCACTTCCGT -ICAM-2,,Intercellular adhesion molecule 2,CD102,P13598,TATCTGGGAT,TATCTGGGAT -CD123,,Interleukin-3 receptor subunit alpha,IL-3Rα,P26951,TGACTGCTAC,TGACTGCTAC -CD150,,Signaling lymphocytic activation molecule,SLAMF1,Q13291,TCGAATGGAT,TCGAATGGAT -CD40L,,CD40 ligand,CD154,P29965,CTAGATTTGC,CTAGATTTGC -KIR,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158,Q8N743,TCCTCTCCTG,TCCTCTCCTG -CD161,,Killer cell lectin-like receptor subfamily B member 1,KLRB1,Q12918,ACTGAACTAC,ACTGAACTAC -CD180,,CD180 antigen,RP105,Q99467,TGAGCTCCAA,TGAGCTCCAA -CCR1,,C-C chemokine receptor type 1,CD191,P32246,CCGGTGGTTC,CCGGTGGTTC -CCR2,,C-C chemokine receptor type 2,CD192,P41597,GGTTCTCCAC,GGTTCTCCAC -CD1d,,Antigen-presenting glycoprotein CD1d,,P15813,CAACGTCCCA,CAACGTCCCA -CD200,,OX-2 membrane glycoprotein,,P41217,CGCACGGGTT,CGCACGGGTT -Ly9,,T-lymphocyte surface antigen Ly-9,CD229;SLAMF3,Q9HBG7,TCGACGAGTG,TCGACGAGTG -CD24,,Signal transducer CD24,HSA,P25063,TCTTGTTCCC,TCTTGTTCCC -2B4,,Natural killer cell receptor 2B4,CD244;SLAMF4,Q9BZW8,TCTCAATCAA,TCTCAATCAA -BAFF-R,,Tumor necrosis factor receptor superfamily member 13C (BAFFR),CD268,Q96RJ3,ACGTAACCGC,ACGTAACCGC -ICOS,,Inducible T cell co-stimulator,CD278,Q9Y6W8,CAGGCACCTG,CAGGCACCTG -CD32,,Low-affinity immunoglobulin gamma Fc region receptor II-b,FcγRII,P31994,GATTTCCAGC,GATTTCCAGC -CD33,,Myeloid cell surface antigen CD33,Siglec-3,P20138,GCGATATAGT,GCGATATAGT -NKp30,,Natural cytotoxicity triggering receptor 3 (NKp30),CD337,O14931,CTTATCTCTT,CTTATCTCTT -CD38,,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,,P28907,TCCGATCTGG,TCCGATCTGG -CD39,,Ectonucleoside triphosphate diphosphohydrolase 1,ENTPD1,P49961,TCAGCGCCTT,TCAGCGCCTT -CD40,,Tumor necrosis factor receptor superfamily member 5,,P25942,TCTGGCGTGG,TCTGGCGTGG -CD48,,CD48 antigen,SLAMF2;BLAST-1,P09326,AGTACGAAGA,AGTACGAAGA -ICAM-3,,Intercellular adhesion molecule 3,CD50,P32942,CTCCGCGTTG,CTCCGCGTTG -CD55,,Complement decay-accelerating factor (DAF),DAF,P08174,TTAGCTAAAC,TTAGCTAAAC -CD58,,Lymphocyte function-associated antigen 3 (LFA3),LFA-3,P19256,ATGTTATGTG,ATGTTATGTG -CD62P,,P-selectin,P-selectin,P16109,ACTTAGCGCT,ACTTAGCGCT -CD69,,Early activation antigen CD69,,Q07108,GAAGGGTCTC,GAAGGGTCTC -CD72,,B-cell differentiation antigen CD72,Lyb-2,P21854,GCGGTGACTT,GCGGTGACTT -CD84,,SLAM family member 5,SLAMF5,Q9UIB8,GCCATTGGAA,GCCATTGGAA -CD9,,CD9 antigen,Tetraspanin-29,P21926,GTCTGGTCAT,GTCTGGTCAT -CD94,,Natural killer cells antigen CD94,KLRD1,Q13241,CTACAACCTT,CTACAACCTT -TCRVb5,,T cell receptor beta variable 5,,,GGCCTCAAGT,GGCCTCAAGT -CD3e,,T cell surface glycoprotein CD3 epsilon chain,,P07766,TGTAGAATTC,TGTAGAATTC -CD4,,T cell surface glycoprotein CD4,,P01730,GACAACTTCT,GACAACTTCT -CD11a,,Integrin α-L (LFA-1 α),ITGAL;LFA-1 α,P20701,ACACACTTGA,ACACACTTGA -CD43,,Leukosialin,Leukosialin,P16150,GAGATTACTA,GAGATTACTA -CD7,,T cell antigen CD7,,P09564,CTGGGTCCGT,CTGGGTCCGT -CD53,,Leukocyte surface antigen CD53,Tetraspanin-25,P19397,CAACCCGCTT,CAACCCGCTT -CD302,,C-type lectin domain family 13 member A,CLEC13A,Q8IX05,TAGACATTGG,TAGACATTGG -VISTA,,V-type immunoglobulin domain-containing suppressor of T cell activation,VSIR,Q9H7M9,AATGTTAACG,AATGTTAACG -BCMA,,Tumor necrosis factor receptor superfamily member 17,CD269,Q02223,CTGGACTATG,CTGGACTATG -CD138,,Syndecan-1,Syndecan-1,P18827,CTGGGCTTAC,CTGGGCTTAC -4-1BB,,Tumor necrosis factor receptor superfamily member 9,CD137,Q07011,CCAGCTAGAA,CCAGCTAGAA -CD66b,,Cell adhesion molecule CEACAM8,CEACAM8,P31997,CTAGGCAGTT,CTAGGCAGTT -EpCAM,,Epithelial cell adhesion molecule,CD326,P16422,CGTTCTTACA,CGTTCTTACA -DC-SIGN,,CD209 antigen,CD209,Q9NNX6,TGGACGTGAA,TGGACGTGAA -CD34,,Hematopoietic progenitor cell antigen CD34,,P28906,CCGTCTAGCC,CCGTCTAGCC -Dectin-1,,C-type lectin domain family 7 member A,CD369;CLEC7A,Q9BXN2,CTGCCAAGAC,CTGCCAAGAC -ICAM-1,,Intercellular adhesion molecule 1,CD54,P05362,AGCAGCTGAT,AGCAGCTGAT -CD71,,Transferrin receptor protein 1,Transferrin receptor,P02786,TCAGGACAGA,TCAGGACAGA -CD47,,Leukocyte surface antigen CD47,Integrin associated protein,Q08722,AGCTACTATT,AGCTACTATT -c-Kit,,Mast/Stem cell growth factor receptor Kit,CD117,P10721,GCTATAATTG,GCTATAATTG -NKG2D,,NKG2-D type II integral membrane protein,CD314;KG2DN,P26718,TGGCGCACAC,TGGCGCACAC -CD98,,4F2 cell-surface antigen heavy chain,SLC3A2,P08195,CCAGAGCGGA,CCAGAGCGGA -CD298,,Na+/K+-ATPase β3,ATP1B3,P54709,AAGCCTGCCT,AAGCCTGCCT -B2M-1,,,,,GAGGGACGGT,GAGGGACGGT,yes -B2M-2,,,,,TAGAGGAGGC,TAGAGGAGGC,yes -B2M-3,,,,,CCCACTAAGC,CCCACTAAGC,yes -B2M-4,,,,,TGGTTTACAA,TGGTTTACAA,yes -B2M-5,,,,,CTAACTACGG,CTAACTACGG,yes -B2M-6,,,,,TATTGAACCT,TATTGAACCT,yes -B2M-7,,,,,ATCAACCCTA,ATCAACCCTA,yes -B2M-8,,,,,GTATCCCTAC,GTATCCCTAC,yes -CD298-1,,,,,AAAGTCTCTG,AAAGTCTCTG,yes -CD298-2,,,,,AAATAGTACG,AAATAGTACG,yes -CD298-3,,,,,GACGGCTTAG,GACGGCTTAG,yes -CD298-4,,,,,GTCAAGGTAA,GTCAAGGTAA,yes -CD298-5,,,,,GGTAAGCCCT,GGTAAGCCCT,yes -CD298-6,,,,,GCCGCCTATG,GCCGCCTATG,yes -CD298-7,,,,,GCTCCGCAAC,GCTCCGCAAC,yes -CD298-8,,,,,AGCCTCAGCA,AGCCTCAGCA,yes -CD98-1,,,,,TGGCTTAGCC,TGGCTTAGCC,yes -CD98-2,,,,,ATTGTGTGGG,ATTGTGTGGG,yes -CD98-3,,,,,CATAGACCAT,CATAGACCAT,yes -CD98-4,,,,,ATGTTCCTCT,ATGTTCCTCT,yes -CD98-5,,,,,TTCGTAACTA,TTCGTAACTA,yes -CD98-6,,,,,CTGACCGCTA,CTGACCGCTA,yes -CD98-7,,,,,CCCTCGGTCT,CCCTCGGTCT,yes -CD98-8,,,,,ATCGCACGTA,ATCGCACGTA,yes -FMC63,,,,,CGATTGGCAC,CGATTGGCAC diff --git a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-G4S-v2.0.csv b/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-G4S-v2.0.csv deleted file mode 100644 index 74c28a02c..000000000 --- a/src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-G4S-v2.0.csv +++ /dev/null @@ -1,192 +0,0 @@ -# --- -# name: proxiome-v2-immuno-156-G4S-v2.0 -# product: proxiome-v2-immuno-156-G4S -# description: >- -# Panel for the Proxiome Immuno Kit with 155 markers + 3 control markers -# + 3*8 hashing antibodies + the G4S marker -# version: 2.0.0 -# --- -marker_id,control,full_name,alt_id,uniprot_id,sequence_1,sequence_2,sample_hashing -HLA-ABC,,HLA class I histocompatibility antigen,,P04439;P01889;P10321,ACTTCCTAGG,ACTTCCTAGG -B2M,,Beta-2-microglobulin,,P61769,CCAGGTTCCG,CCAGGTTCCG -CD11b,,Integrin α-M (ITGAM),ITGAM;Mac-1 α,P11215,CAGCTATGGT,CAGCTATGGT -CD11c,,Integrin α-X,Integrin αX,P20702,ATATGACGGT,ATATGACGGT -CD18,,Integrin beta 2,Integrin β2,P05107,GGGTAGGCTG,GGGTAGGCTG -CD82,,CD82 antigen,Tetraspanin-27,P27701,CCCGTCATGA,CCCGTCATGA -CD8,,T cell surface glycoprotein CD8 a/b chains,,P01732;P10966,CGGTGGATCA,CGGTGGATCA -TCRab,,T cell receptor alpha chain constant/beta constant 1,,P01848;P01850,CTGGTAGCAA,CTGGTAGCAA -HLA-DR,,"HLA class II histocompatibility antigen, DR",,P01903;P01911,TGTTGTCGAA,TGTTGTCGAA -CD45,,"Receptor-type tyrosine-protein phosphatase C. All 6 isoforms (ABC, AB, BC, B and O)",PTPRC,P08575,TGGAGGCTCT,TGGAGGCTCT -CD14,,Monocyte differentiation antigen CD14,,P08571,TGGCTATGTA,TGGCTATGTA -CD16,,Low-affinity immunoglobulin gamma Fc region receptor / III-A and -B,FcγRIII,P08637;O75015,ATAGGTTAGG,ATAGGTTAGG -CD19,,B-lymphocyte antigen CD19,,P15391,ACGGAATATT,ACGGAATATT -mIgG1,yes,,,,ATGCTAGTCG,ATGCTAGTCG -CD45RB,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, BC, and B)",,P08575,GAAGCAGTAT,GAAGCAGTAT -CD44,,CD44 antigen,,P16070,GTGAGTCAAT,GTGAGTCAAT -CD52,,CAMPATH-1 antigen,CAMPATH-1,P31358,CTTTAGCAGG,CTTTAGCAGG -CD59,,CD59 glycoprotein,Protectin;MAC-IP,P13987,GGTGTATGAG,GGTGTATGAG -CD45RA,,"Receptor-type tyrosine-protein phosphatase C. Isoform (ABC, AB, and A)",,P08575,GGATTCGTGG,GGATTCGTGG -CD36,,Platelet glycoprotein 4,FAT;SCARB3,P16671,TACCCTGCGA,TACCCTGCGA -CD2,,T cell surface antigen CD2,,P06729,TGCCGATGCC,TGCCGATGCC -CD29,,Integrin beta-1,Integrin β1,P05556,TCCAGTGTCT,TCCAGTGTCT -CD5,,T cell surface glycoprotein CD5,,P06127,CACCCATCAA,CACCCATCAA -CD162,,P-selectin glycoprotein ligand 1,SELPLG;PSGL-1,Q14242,CTTCGTGGAC,CTTCGTGGAC -CD27,,CD27 antigen,,P26842,GGTTTGCAAA,GGTTTGCAAA -CR1,,Complement receptor type 1,CD35,P17927,CGCCACCTTT,CGCCACCTTT -CD26,,Dipeptidyl peptidase 4,DPP4,P27487,GATTCGCTGT,GATTCGCTGT -CD49d,,Integrin α-4,Integrin α4,P13612,AACTTAGGTT,AACTTAGGTT -CD37,,Leukocyte antigen CD37,Tetraspanin-26,P11049,AGAAGAAGAG,AGAAGAAGAG -CD41,,Integrin α-IIb,Integrin αIIb,P08514,TAAGGCATAA,TAAGGCATAA -CD20,,B-lymphocyte antigen CD20,,P11836,GCCACACCCA,GCCACACCCA -CD64,,High affinity immunoglobulin gamma Fc receptor I,FcγRI,P12314,CTTGTATATC,CTTGTATATC -CD22,,B-cell receptor CD22,,P20273,TGACCCGTTC,TGACCCGTTC -PD-L1,,Programmed cell death 1 ligand 1 (PDL1),CD274,Q9NZQ7,GCTTGAGATT,GCTTGAGATT -Siglec-7,,Sialic acid-binding Ig-like lectin 7 (SIGLEC-7),CD328,Q9Y286,TATATGCTGA,TATATGCTGA -CD25,,Interleukin-2 receptor subunit alpha,IL-2Rα,P01589,AGAGACGAAT,AGAGACGAAT -PD-1,,Programmed cell death protein 1 (PD-1),CD279,Q15116,TACAGAGCCC,TACAGAGCCC -NKp46,,Natural cytotoxicity triggering receptor 1 (NKp46),CD335,O76036,ATTACCCGCG,ATTACCCGCG -mIgG2a,yes,,,,ATTTCCACTA,ATTTCCACTA -mIgG2b,yes,,,,CTAAATGGCT,CTAAATGGCT -CTLA-4,,Cytotoxic T-lymphocyte protein 4,CD152,P16410,TTTCTGCATT,TTTCTGCATT -CD86,,T-lymphocyte activation antigen CD86,B7-2,P42081,ACCATCACTT,ACCATCACTT -CD13,,Aminopeptidase N,Aminopeptidase N,P15144,GCATGGGTAG,GCATGGGTAG -ADAM10,,Disintegrin and metalloproteinase domain-containing protein 10,CD156c,O14672,ATAAGTTCCA,ATAAGTTCCA -KIR2DL1,,Killer cell immunoglobulin-like receptor 2DL1,CD158a,P43626,TGTTACGGTC,TGTTACGGTC -KIR2DL2/DL3,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158b,P43627,ACTGCATTGA,ACTGCATTGA -NKG2A,,NKG2-A/NKG2-B type II integral membrane protein,CD159a,P26715,CGTACACGGT,CGTACACGGT -NKG2C,,NKG2-C type II integral membrane protein,CD159c,P26717,CAACAGTCGA,CAACAGTCGA -CD163,,Scavenger receptor cysteine-rich type 1 protein M130,,Q86VB7,GACCGTGATT,GACCGTGATT -CD169,,Sialoadhesin,Siglec-1,Q9BZZ2,TAATCGCGGG,TAATCGCGGG -CD1a,,T cell surface glycoprotein CD1a,,P06126,CGACTAATCA,CGACTAATCA -CD1c,,T cell surface glycoprotein CD1c,,P29017,GTGCACTGTC,GTGCACTGTC -CD206,,Macrophage mannose receptor 1,Mannose receptor,P22897,TGCCTAATAG,TGCCTAATAG -DNAM-1,,CD226 antigen,CD226,Q15762,CGGTCATTAA,CGGTCATTAA -PD-L2,,Programmed cell death 1 ligand 2 (PDL2),CD273,Q9BQ51,ATCGCGAAGC,ATCGCGAAGC -CD28,,T cell-specific surface glycoprotein CD28,,P10747,CATAACAATC,CATAACAATC -SLAMF6,,SLAM family member 6,CD352;NTB-A,Q96DU3,TCGGAGACAC,TCGGAGACAC -CD45RO,,"Receptor-type tyrosine-protein phosphatase C. Isoform O",,P08575,TTGATGACTC,TTGATGACTC -CD49e,,Integrin α-5,Integrin α5,P08648,AACTCCTGAA,AACTCCTGAA -CD56,,Neural cell adhesion molecule 1,NCAM,P13591,GTGCGTAAGC,GTGCGTAAGC -CD79a,,B-cell antigen receptor complex-associated protein alpha chain,MB-1,P11912,AGATCGACAG,AGATCGACAG -CD80,,T-lymphocyte activation antigen CD80,B7-1,P33681,AAGACGCGGA,AAGACGCGGA -CD81,,CD81 antigen,Tetraspanin-28,P60033,TGGGTTATGT,TGGGTTATGT -LILRB1,,Leukocyte immunoglobulin-like receptor subfamily B member 1,CD85j;ILT-2,Q8NHL6,CCTAAGTCTA,CCTAAGTCTA -CD93,,Complement component C1q receptor,,Q9NPY3,GCAGCGAACA,GCAGCGAACA -IgD,,Immunoglobulin delta heavy chain,,P0DOX3,AGATGAGGCA,AGATGAGGCA -IgE,,Immunoglobulin epsilon heavy chain,,P0DOX4,CGACGGTAAG,CGACGGTAAG -IgM,,Immunoglobulin mu heavy chain,,P0DOX6,GTGGATCCAA,GTGGATCCAA -KLRG1,,Killer cell lectin-like receptor subfamily G member 1,,Q96E93,TATACAGACA,TATACAGACA -NKp80,,Killer cell lectin-like receptor subfamily F member 1,KLRF1,Q9NZS2,CCATCGGATC,CCATCGGATC -TCRgd,,T cell receptor gamma constant 1 /delta constant,,P0CF51;B7Z8K6,CTTATGACCA,CTTATGACCA -CD10,,Neprilysin,Neprilysin,P08473,CGCAGGTAGC,CGCAGGTAGC -CD103,,Integrin alpha-E,Integrin αE,P38570,CCTATGCGAA,CCTATGCGAA -CD1b,,T cell surface glycoprotein CD1b,,P29016,GACACCACCG,GACACCACCG -CD21,,Complement receptor type 2,CR2,P20023,GTGGCGTTAA,GTGGCGTTAA -TALLA,,Tetraspanin-7,CD231;Tetraspanin-7,P41732,CACGATACTT,CACGATACTT -CD277,,Butyrophilin subfamily 3 member A1,BTN3,O00481,GAGTGATACG,GAGTGATACG -LAIR1,,Leukocyte-associated immunoglobulin-like receptor 1,CD305,Q6GTX8,GCAATGTGTA,GCAATGTGTA -CD371,,C-type lectin domain family 12 member A,CLEC12A,Q5QGZ9,AAGGTCCCAT,AAGGTCCCAT -CD89,,Immunoglobulin alpha Fc receptor,FcαRI;FCAR,P24071,GTATCATAAG,GTATCATAAG -CD90,,Thy-1 membrane glycoprotein,Thy-1,P04216,TAGCCGATTA,TAGCCGATTA -CD70,,CD70 antigen,CD27L,P32970,CTCAGCATGC,CTCAGCATGC -GPR56,,Adhesion G-protein coupled receptor G1,TM7XN1,Q9Y653,GCGTCTCTCT,GCGTCTCTCT -HLA-DQ,,"HLA class II histocompatibility antigen, DQ",,P01906;P05538;P01920;P01909,ATACTTGAGC,ATACTTGAGC -TCRVd2,,T cell receptor delta variable 2,,,CCGACCATTC,CCGACCATTC -HLA-DR-DP-DQ,,HLA class II histocompatibility antigen,,P01903;P20036;P01909,AACAGAGGAA,AACAGAGGAA -Siglec-9,,Sialic acid-binding Ig-like lectin 9,,Q9Y336,TTAACAAGCA,TTAACAAGCA -TCRVa7.2,,T cell receptor alpha variable 7,,A0A075B6U4,TCCCAGGTCC,TCCCAGGTCC -Fas,,Tumor necrosis factor receptor superfamily member 6,CD95,P25445,TACTGTTGGG,TACTGTTGGG -TCRVg9,,T cell receptor gamma variable 9,,,TCGTTTGTCA,TCGTTTGTCA -CD127,,Interleukin-7 receptor subunit alpha,IL-7Rα,P16871,TGTTAGAGGA,TGTTAGAGGA -CD141,,Thrombomodulin,TM,P07204,AATTGTTCGT,AATTGTTCGT -CD31,,Platelet endothelial cell adhesion molecule,PECAM-1,P16284,GGCAAAGAGC,GGCAAAGAGC -CD6,,T cell differentiation antigen CD6,,P30203,CTAAGATCTC,CTAAGATCTC -CD57,,Galactosylgalactosylxylosylprotein 3-beta-glucuronosyltransferase 1,,Q9P2W7,ACGACGGGAC,ACGACGGGAC -CD73,,5’-nucleotidase,NT5E,P21589,ACCAAGGACG,ACCAAGGACG -TIM-3,,Hepatitis A virus cellular receptor 2,CD366;HAVCR2,Q8TDQ0,CGCCAAGTGG,CGCCAAGTGG -GITR,,Tumor necrosis factor receptor superfamily member 18,CD357,Q9Y5U5,TGAGTCACTC,TGAGTCACTC -CCR3,,C-C chemokine receptor type 3,CD193,P51677,CCGTGACCCA,CCGTGACCCA -SLAMF7,,SLAM family member 7,CD319;CRACC,Q9NQ25,AGGCGGAAAT,AGGCGGAAAT -TIGIT,,T cell immunoreceptor with Ig and ITIM domains,,Q495A1,ACTGAGTCGC,ACTGAGTCGC -OX40,,Tumor necrosis factor receptor superfamily member 4,CD134,P43489,CCACTTCCGT,CCACTTCCGT -ICAM-2,,Intercellular adhesion molecule 2,CD102,P13598,TATCTGGGAT,TATCTGGGAT -CD123,,Interleukin-3 receptor subunit alpha,IL-3Rα,P26951,TGACTGCTAC,TGACTGCTAC -CD150,,Signaling lymphocytic activation molecule,SLAMF1,Q13291,TCGAATGGAT,TCGAATGGAT -CD40L,,CD40 ligand,CD154,P29965,CTAGATTTGC,CTAGATTTGC -KIR,,Killer cell immunoglobulin-like receptor 2D (p50.3),CD158,Q8N743,TCCTCTCCTG,TCCTCTCCTG -CD161,,Killer cell lectin-like receptor subfamily B member 1,KLRB1,Q12918,ACTGAACTAC,ACTGAACTAC -CD180,,CD180 antigen,RP105,Q99467,TGAGCTCCAA,TGAGCTCCAA -CCR1,,C-C chemokine receptor type 1,CD191,P32246,CCGGTGGTTC,CCGGTGGTTC -CCR2,,C-C chemokine receptor type 2,CD192,P41597,GGTTCTCCAC,GGTTCTCCAC -CD1d,,Antigen-presenting glycoprotein CD1d,,P15813,CAACGTCCCA,CAACGTCCCA -CD200,,OX-2 membrane glycoprotein,,P41217,CGCACGGGTT,CGCACGGGTT -Ly9,,T-lymphocyte surface antigen Ly-9,CD229;SLAMF3,Q9HBG7,TCGACGAGTG,TCGACGAGTG -CD24,,Signal transducer CD24,HSA,P25063,TCTTGTTCCC,TCTTGTTCCC -2B4,,Natural killer cell receptor 2B4,CD244;SLAMF4,Q9BZW8,TCTCAATCAA,TCTCAATCAA -BAFF-R,,Tumor necrosis factor receptor superfamily member 13C (BAFFR),CD268,Q96RJ3,ACGTAACCGC,ACGTAACCGC -ICOS,,Inducible T cell co-stimulator,CD278,Q9Y6W8,CAGGCACCTG,CAGGCACCTG -CD32,,Low-affinity immunoglobulin gamma Fc region receptor II-b,FcγRII,P31994,GATTTCCAGC,GATTTCCAGC -CD33,,Myeloid cell surface antigen CD33,Siglec-3,P20138,GCGATATAGT,GCGATATAGT -NKp30,,Natural cytotoxicity triggering receptor 3 (NKp30),CD337,O14931,CTTATCTCTT,CTTATCTCTT -CD38,,ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 1,,P28907,TCCGATCTGG,TCCGATCTGG -CD39,,Ectonucleoside triphosphate diphosphohydrolase 1,ENTPD1,P49961,TCAGCGCCTT,TCAGCGCCTT -CD40,,Tumor necrosis factor receptor superfamily member 5,,P25942,TCTGGCGTGG,TCTGGCGTGG -CD48,,CD48 antigen,SLAMF2;BLAST-1,P09326,AGTACGAAGA,AGTACGAAGA -ICAM-3,,Intercellular adhesion molecule 3,CD50,P32942,CTCCGCGTTG,CTCCGCGTTG -CD55,,Complement decay-accelerating factor (DAF),DAF,P08174,TTAGCTAAAC,TTAGCTAAAC -CD58,,Lymphocyte function-associated antigen 3 (LFA3),LFA-3,P19256,ATGTTATGTG,ATGTTATGTG -CD62P,,P-selectin,P-selectin,P16109,ACTTAGCGCT,ACTTAGCGCT -CD69,,Early activation antigen CD69,,Q07108,GAAGGGTCTC,GAAGGGTCTC -CD72,,B-cell differentiation antigen CD72,Lyb-2,P21854,GCGGTGACTT,GCGGTGACTT -CD84,,SLAM family member 5,SLAMF5,Q9UIB8,GCCATTGGAA,GCCATTGGAA -CD9,,CD9 antigen,Tetraspanin-29,P21926,GTCTGGTCAT,GTCTGGTCAT -CD94,,Natural killer cells antigen CD94,KLRD1,Q13241,CTACAACCTT,CTACAACCTT -TCRVb5,,T cell receptor beta variable 5,,,GGCCTCAAGT,GGCCTCAAGT -CD3e,,T cell surface glycoprotein CD3 epsilon chain,,P07766,TGTAGAATTC,TGTAGAATTC -CD4,,T cell surface glycoprotein CD4,,P01730,GACAACTTCT,GACAACTTCT -CD11a,,Integrin α-L (LFA-1 α),ITGAL;LFA-1 α,P20701,ACACACTTGA,ACACACTTGA -CD43,,Leukosialin,Leukosialin,P16150,GAGATTACTA,GAGATTACTA -CD7,,T cell antigen CD7,,P09564,CTGGGTCCGT,CTGGGTCCGT -CD53,,Leukocyte surface antigen CD53,Tetraspanin-25,P19397,CAACCCGCTT,CAACCCGCTT -CD302,,C-type lectin domain family 13 member A,CLEC13A,Q8IX05,TAGACATTGG,TAGACATTGG -VISTA,,V-type immunoglobulin domain-containing suppressor of T cell activation,VSIR,Q9H7M9,AATGTTAACG,AATGTTAACG -BCMA,,Tumor necrosis factor receptor superfamily member 17,CD269,Q02223,CTGGACTATG,CTGGACTATG -CD138,,Syndecan-1,Syndecan-1,P18827,CTGGGCTTAC,CTGGGCTTAC -4-1BB,,Tumor necrosis factor receptor superfamily member 9,CD137,Q07011,CCAGCTAGAA,CCAGCTAGAA -CD66b,,Cell adhesion molecule CEACAM8,CEACAM8,P31997,CTAGGCAGTT,CTAGGCAGTT -EpCAM,,Epithelial cell adhesion molecule,CD326,P16422,CGTTCTTACA,CGTTCTTACA -DC-SIGN,,CD209 antigen,CD209,Q9NNX6,TGGACGTGAA,TGGACGTGAA -CD34,,Hematopoietic progenitor cell antigen CD34,,P28906,CCGTCTAGCC,CCGTCTAGCC -Dectin-1,,C-type lectin domain family 7 member A,CD369;CLEC7A,Q9BXN2,CTGCCAAGAC,CTGCCAAGAC -ICAM-1,,Intercellular adhesion molecule 1,CD54,P05362,AGCAGCTGAT,AGCAGCTGAT -CD71,,Transferrin receptor protein 1,Transferrin receptor,P02786,TCAGGACAGA,TCAGGACAGA -CD47,,Leukocyte surface antigen CD47,Integrin associated protein,Q08722,AGCTACTATT,AGCTACTATT -c-Kit,,Mast/Stem cell growth factor receptor Kit,CD117,P10721,GCTATAATTG,GCTATAATTG -NKG2D,,NKG2-D type II integral membrane protein,CD314;KG2DN,P26718,TGGCGCACAC,TGGCGCACAC -CD98,,4F2 cell-surface antigen heavy chain,SLC3A2,P08195,CCAGAGCGGA,CCAGAGCGGA -CD298,,Na+/K+-ATPase β3,ATP1B3,P54709,AAGCCTGCCT,AAGCCTGCCT -B2M-1,,,,,GAGGGACGGT,GAGGGACGGT,yes -B2M-2,,,,,TAGAGGAGGC,TAGAGGAGGC,yes -B2M-3,,,,,CCCACTAAGC,CCCACTAAGC,yes -B2M-4,,,,,TGGTTTACAA,TGGTTTACAA,yes -B2M-5,,,,,CTAACTACGG,CTAACTACGG,yes -B2M-6,,,,,TATTGAACCT,TATTGAACCT,yes -B2M-7,,,,,ATCAACCCTA,ATCAACCCTA,yes -B2M-8,,,,,GTATCCCTAC,GTATCCCTAC,yes -CD298-1,,,,,AAAGTCTCTG,AAAGTCTCTG,yes -CD298-2,,,,,AAATAGTACG,AAATAGTACG,yes -CD298-3,,,,,GACGGCTTAG,GACGGCTTAG,yes -CD298-4,,,,,GTCAAGGTAA,GTCAAGGTAA,yes -CD298-5,,,,,GGTAAGCCCT,GGTAAGCCCT,yes -CD298-6,,,,,GCCGCCTATG,GCCGCCTATG,yes -CD298-7,,,,,GCTCCGCAAC,GCTCCGCAAC,yes -CD298-8,,,,,AGCCTCAGCA,AGCCTCAGCA,yes -CD98-1,,,,,TGGCTTAGCC,TGGCTTAGCC,yes -CD98-2,,,,,ATTGTGTGGG,ATTGTGTGGG,yes -CD98-3,,,,,CATAGACCAT,CATAGACCAT,yes -CD98-4,,,,,ATGTTCCTCT,ATGTTCCTCT,yes -CD98-5,,,,,TTCGTAACTA,TTCGTAACTA,yes -CD98-6,,,,,CTGACCGCTA,CTGACCGCTA,yes -CD98-7,,,,,CCCTCGGTCT,CCCTCGGTCT,yes -CD98-8,,,,,ATCGCACGTA,ATCGCACGTA,yes -G4S,,,,,TTCTTTGATG,TTCTTTGATG diff --git a/tests/pna/config/test_config.py b/tests/pna/config/test_config.py index 4bd96a6d1..538b0abdd 100644 --- a/tests/pna/config/test_config.py +++ b/tests/pna/config/test_config.py @@ -172,12 +172,6 @@ def test_loading_multiple_major_version(config_with_multiple_versions): "panel_alias,panel_name,panel_version", [ ("test-pna==1.1.0", "test-pna-panel", "1.1.0"), - ( - # this test input ascertains alias lookup can resolve this specific version bump made to align product and panel versions - "proxiome-v2-immuno-155-v1.0", - "proxiome-v2-immuno-155-prerelease", - "1.0.1", # bump this version string when doing patch updates to proxiome-v2-immuno-155-prerelease - ), ], ) def test_loading_panel_from_config_alias( @@ -341,39 +335,30 @@ def test_list_panel_names(pna_data_root): """ assert sorted(pna_config.list_panel_names(include_aliases=True)) == sorted( [ + "proxiome-v1-FLAG-v1.0", + "proxiome-v1-FMC63-v1.0", "proxiome-v1-immuno-155-v1.0", "proxiome-v1-immuno-155-v1.1", - "proxiome-v1-immuno-156-FLAG-v1.0", - "proxiome-v1-immuno-156-FLAG-v1.1", - "proxiome-v1-immuno-156-FMC63-v1.0", - "proxiome-v1-immuno-156-FMC63-v1.1", - "proxiome-v2-immuno-155-v1.0", - "proxiome-v2-immuno-155-prerelease", + "proxiome-v2-FLAG-v2.0", + "proxiome-v2-FMC63-v2.0", + "proxiome-v2-G4S-v2.0", + "proxiome-v2-hashing-prerelease", + "proxiome-v2-hashing-v2.0", "proxiome-v2-immuno-155-v2.0", - "proxiome-v2-immuno-156-FLAG-v1.0", - "proxiome-v2-immuno-156-FLAG-prerelease", - "proxiome-v2-immuno-156-FLAG-v2.0", - "proxiome-v2-immuno-156-FMC63-v1.0", - "proxiome-v2-immuno-156-FMC63-prerelease", - "proxiome-v2-immuno-156-FMC63-v2.0", - "proxiome-v2-immuno-156-G4S-v2.0", ] ) assert sorted(pna_config.list_panel_names(include_aliases=False)) == [ + "proxiome-v1-FLAG-v1.0", + "proxiome-v1-FMC63-v1.0", "proxiome-v1-immuno-155-v1.0", "proxiome-v1-immuno-155-v1.1", - "proxiome-v1-immuno-156-FLAG-v1.0", - "proxiome-v1-immuno-156-FLAG-v1.1", - "proxiome-v1-immuno-156-FMC63-v1.0", - "proxiome-v1-immuno-156-FMC63-v1.1", - "proxiome-v2-immuno-155-prerelease", + "proxiome-v2-FLAG-v2.0", + "proxiome-v2-FMC63-v2.0", + "proxiome-v2-G4S-v2.0", + "proxiome-v2-hashing-prerelease", + "proxiome-v2-hashing-v2.0", "proxiome-v2-immuno-155-v2.0", - "proxiome-v2-immuno-156-FLAG-prerelease", - "proxiome-v2-immuno-156-FLAG-v2.0", - "proxiome-v2-immuno-156-FMC63-prerelease", - "proxiome-v2-immuno-156-FMC63-v2.0", - "proxiome-v2-immuno-156-G4S-v2.0", ]