diff --git a/CHANGELOG.md b/CHANGELOG.md index 34f494fc..5bb06b0f 100644 --- a/CHANGELOG.md +++ b/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. 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 new file mode 100644 index 00000000..74c28a02 --- /dev/null +++ b/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 diff --git a/tests/pna/config/test_config.py b/tests/pna/config/test_config.py index aa74e65d..81bf6ba1 100644 --- a/tests/pna/config/test_config.py +++ b/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", ]