add G4S proxiome-v2 panel

CHANGELOG.md

@@ -9,7 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 - `annotate_cells` method to determine cell-types using another given set of pre-annotated cells.
-- `proxiome-v2-immuno-155-v2.0` panel
+- `proxiome-v2-immuno-155-v2.0` panels (including panels for FLAG, FMC63 and G4S add ons to the immuno-155 base panel)
 - Expose `coarsened_pmds_3d` (and other supported layout algorithms) on the `single-cell-pna layout` CLI, and make `coarsened_pmds_3d` the default.
 
 

src/pixelator/pna/resources/panels/proxiome-v2-immuno-156-G4S-v2.0.csv

@@ -0,0 +1,192 @@
+# ---
+# 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

tests/pna/config/test_config.py

@@ -321,6 +321,7 @@ def test_list_panel_names(pna_data_root):
             "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",
         ]
     )
 
@@ -337,6 +338,7 @@ def test_list_panel_names(pna_data_root):
         "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",
     ]