Archive 4 checkpoints (1-4)

paper-releases/20260928/diffusion/data/cohorts/ji2025_chili/pairs.csv

@@ -0,0 +1,41 @@
+sample_id,bulk_gsm,sc_gsm,donor_id,row,bulk_title,sc_title,id_match,group,timepoint,outcome,sex_geo,age_geo,age_geo_bulk,regimen,cancer_type,steroid_bulk,steroid_sc,bulk_library,bulk_batch,library_key,round,PID_visit,bulk_subject_raw,seurat_orig_ident,metadata_notes,n_cells_library,n_cells_retained,bulk_XIST_cpm,bulk_Ysum_cpm,bulk_sex_score,bulk_sex_call,sc_XIST_cpm,sc_Ysum_cpm,sc_sex_score,sc_sex_call,sex_concordant,bulk_possible_mixture,expr_rho_own,expr_rho_best,expr_own_rank_among_sc,expr_best_is_own,expr_best_sc_gsm,expr_centred_own_rank_among_sc,expr_centred_best_is_own,expr_reverse_own_rank_among_bulk,expr_reverse_best_is_own,expr_resid_k0_own_rank_bulk_to_sc,expr_resid_k0_own_rank_sc_to_bulk,expr_resid_k0_patient_rank_bulk_to_sc,expr_resid_k0_patient_rank_sc_to_bulk,expr_resid_k0_best_sc_gsm,expr_resid_k0_best_sc_patient,expr_resid_k0_best_bulk_patient,expr_resid_k0_r_own,expr_resid_k0_r_best,expr_resid_k0_r_best_other_patient_sc,expr_resid_k0_own_tp_best_within_patient_sc,expr_resid_k0_own_tp_best_within_patient_bulk,expr_resid_k3_own_rank_bulk_to_sc,expr_resid_k3_own_rank_sc_to_bulk,expr_resid_k3_patient_rank_bulk_to_sc,expr_resid_k3_patient_rank_sc_to_bulk,expr_resid_k3_best_sc_gsm,expr_resid_k3_best_sc_patient,expr_resid_k3_best_bulk_patient,expr_resid_k3_r_own,expr_resid_k3_r_best,expr_resid_k3_r_best_other_patient_sc,expr_resid_k3_own_tp_best_within_patient_sc,expr_resid_k3_own_tp_best_within_patient_bulk,expr_resid_k5_own_rank_bulk_to_sc,expr_resid_k5_own_rank_sc_to_bulk,expr_resid_k5_patient_rank_bulk_to_sc,expr_resid_k5_patient_rank_sc_to_bulk,expr_resid_k5_best_sc_gsm,expr_resid_k5_best_sc_patient,expr_resid_k5_best_bulk_patient,expr_resid_k5_r_own,expr_resid_k5_r_best,expr_resid_k5_r_best_other_patient_sc,expr_resid_k5_own_tp_best_within_patient_sc,expr_resid_k5_own_tp_best_within_patient_bulk,expr_resid_k8_own_rank_bulk_to_sc,expr_resid_k8_own_rank_sc_to_bulk,expr_resid_k8_patient_rank_bulk_to_sc,expr_resid_k8_patient_rank_sc_to_bulk,expr_resid_k8_best_sc_gsm,expr_resid_k8_best_sc_patient,expr_resid_k8_best_bulk_patient,expr_resid_k8_r_own,expr_resid_k8_r_best,expr_resid_k8_r_best_other_patient_sc,expr_resid_k8_own_tp_best_within_patient_sc,expr_resid_k8_own_tp_best_within_patient_bulk,expr_resid_k10_own_rank_bulk_to_sc,expr_resid_k10_own_rank_sc_to_bulk,expr_resid_k10_patient_rank_bulk_to_sc,expr_resid_k10_patient_rank_sc_to_bulk,expr_resid_k10_best_sc_gsm,expr_resid_k10_best_sc_patient,expr_resid_k10_best_bulk_patient,expr_resid_k10_r_own,expr_resid_k10_r_best,expr_resid_k10_r_best_other_patient_sc,expr_resid_k10_own_tp_best_within_patient_sc,expr_resid_k10_own_tp_best_within_patient_bulk,identity_check,identity_pass,identity_notes
+N064_TOL,GSM8747285,GSM8747452,N064,0,N064_chili_TOL,N064V01_Rd3_GPEX,exact_subject_id,TOL,TOL,ChILI,Male,72,72,Ipilimumab + Nivolumab,Melanoma,y,y,itox010095,2,Rd3_N064V01,Rd3,N064V01,N064,N064V01PH,,2498,2498,0.37411610393992895,184.06512313844502,-7.07338531655642,male,0.0,1133.822246644405,-10.148250622735398,male,True,False,0.12282698770155277,0.21373901770945766,22,False,GSM8747446,1,True,56,False,1,4,1,3,GSM8747452,N064,N073,0.3222498547452296,0.3222498547452296,0.1877471081305456,True,True,2,1,1,1,GSM8747454,N064,N064,0.24718001529513,0.3022905125050749,0.17968979833648205,False,True,2,1,1,1,GSM8747454,N064,N064,0.25821429995723727,0.27144582319999794,0.12998688257950514,False,True,1,1,1,1,GSM8747452,N064,N064,0.2498770230356043,0.2498770230356043,0.1571328384794707,True,True,1,1,1,1,GSM8747452,N064,N064,0.1964667382294672,0.1964667382294672,0.09257149471362465,True,True,pass,True,bulk matches this patient's other sc time point slightly better (time point not resolvable)
+N064_FU1,GSM8747286,GSM8747454,N064,1,N064_chili_FU1,N064V02_Rd3_GPEX,exact_subject_id,FU1,FU1,ChILI,Male,72,72,Ipilimumab + Nivolumab,Melanoma,y,y,itox010096,2,Rd3_N064V02,Rd3,N064V02,N064,N064V02PH,,4659,4659,0.9538920384990827,169.79278285283672,-6.449752448436471,male,0.0,990.8213832985317,-9.953936519427574,male,True,False,0.18961438746610063,0.2447957545856874,11,False,GSM8747446,1,True,16,False,1,2,1,2,GSM8747454,N064,N022,0.4483183136381997,0.4483183136381997,0.22051613328055475,True,True,1,1,1,1,GSM8747454,N064,N064,0.36576914568330543,0.36576914568330543,0.23726109868129475,True,True,1,1,1,1,GSM8747454,N064,N064,0.33702355510810833,0.33702355510810833,0.1599590801254204,True,True,1,1,1,1,GSM8747454,N064,N064,0.26574677707404765,0.26574677707404765,0.11785146933780624,True,True,1,1,1,1,GSM8747454,N064,N064,0.25642658766511706,0.25642658766511706,0.12047458280125815,True,True,pass,True,
+N032_BC,GSM8747298,GSM8747458,N032,2,N032_control_BC,N032V01_Rd4a_GPEX,exact_subject_id,BC,BC,control,Female,55,55,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox010108,2,Rd4a_N032V01,Rd4a,N032V01,N032,N032V01,,1860,1780,520.3937514640181,0.0,9.026229483070344,female,51.76953285723392,0.0,5.721633307004046,female,True,False,0.0008510756626071974,0.1853201805056856,40,False,GSM8747446,32,False,100,False,24,46,6,15,GSM8747450,N012,N073,0.02870868631884434,0.16964976365899492,0.16964976365899492,False,False,3,9,1,8,GSM8747434,N032,N012,0.08282991328836802,0.19145952826676113,0.098639430208711,False,True,4,15,1,13,GSM8747434,N032,N012,0.07223052646753113,0.2056644573625683,0.08261025167816462,False,True,8,17,1,13,GSM8747434,N032,N012,0.04851056848387708,0.15206568293029457,0.07875899027728421,False,False,2,4,1,3,GSM8747434,N032,N111,0.07567497205045208,0.1592431826657,0.07364955681320517,False,False,borderline: own patient rank 1 (bulk->sc) and 13 (sc->bulk),False,bulk matches this patient's other sc time point slightly better (time point not resolvable)
+N032_AC,GSM8747299,GSM8747434,N032,3,N032_control_AC,N032V02_Rd2_GPEX,exact_subject_id,AC,AC,control,Female,55,55,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox010109,2,Rd2_N032V02,Rd2,N032V02,N032,N032V02JP,,8290,7350,582.9611248966088,1.3234077750206783,7.973486139986201,female,76.79504197727734,0.0,6.281606307390295,female,True,False,0.14027186403266007,0.2225231543605964,29,False,GSM8747446,10,False,25,False,1,1,1,1,GSM8747434,N032,N032,0.26426384531929964,0.26426384531929964,0.21424252254065868,True,True,1,1,1,1,GSM8747434,N032,N032,0.24946909430034417,0.24946909430034417,0.1452119396422286,True,True,1,1,1,1,GSM8747434,N032,N032,0.2354525904006715,0.2354525904006715,0.13921281458216794,True,True,1,1,1,1,GSM8747434,N032,N032,0.16475961443789328,0.16475961443789328,0.12141576349525128,True,True,1,1,1,1,GSM8747434,N032,N032,0.16805044607216788,0.16805044607216788,0.12699368024718974,True,True,pass,True,
+N038_BC,GSM8747300,GSM8747436,N038,4,N038_control_BC,N038V01_Rd2_GPEX,exact_subject_id,BC,BC,control,Male,54,54,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox010110,2,Rd2_N038V01,Rd2,N038V01,N038,N038V01MS,,2801,2801,1.6976562497347412,145.31937497729385,-5.761270483498894,male,0.0,1054.7106894293006,-10.043998812434712,male,True,False,0.0487877259417857,0.16194798036009278,29,False,GSM8747446,37,False,102,False,11,36,9,28,GSM8747444,N002,N029,0.07451838437857024,0.1924397059347268,0.1924397059347268,False,True,1,2,1,1,GSM8747436,N038,N038,0.2408519595477648,0.2408519595477648,0.11745059564073833,True,False,1,2,1,1,GSM8747436,N038,N038,0.23883829555457992,0.23883829555457992,0.13008564784793072,True,False,2,3,1,1,GSM8747438,N038,N038,0.13708348804086873,0.14877199241947311,0.10837123885759722,False,False,4,2,2,1,GSM8747448,N012,N038,0.09540316726978099,0.1240556530416798,0.1240556530416798,False,False,pass,True,
+N038_AC,GSM8747301,GSM8747438,N038,5,N038_control_AC,N038V02_Rd2_GPEX,exact_subject_id,AC,AC,control,Male,54,54,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox010111,2,Rd2_N038V02,Rd2,N038V02,N038,N038V02MS,,3976,3976,2.3955448341615644,109.85284168083746,-5.028858861995217,male,0.0,1178.8408648030418,-10.204376568790108,male,True,False,0.031797054883197146,0.17710634981862278,34,False,GSM8747446,35,False,104,False,18,21,14,18,GSM8747484,N138,N143,0.09980299532928708,0.26105270715170176,0.26105270715170176,True,True,1,1,1,1,GSM8747438,N038,N038,0.26488583566705204,0.26488583566705204,0.16423484214868989,True,True,1,1,1,1,GSM8747438,N038,N038,0.29381173884466877,0.29381173884466877,0.14583704522139104,True,True,1,2,1,2,GSM8747438,N038,N078,0.24458774891772353,0.24458774891772353,0.11405285916046516,True,True,1,1,1,1,GSM8747438,N038,N038,0.19828947437356356,0.19828947437356356,0.11428172752301836,True,True,pass,True,
+N055_AC,GSM8747305,GSM8747472,N055,6,N055_control_AC,N055V02_Rd4b_GPEX,exact_subject_id,AC,AC,control,Male,64,64,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox010115,2,Rd4b_N055V02,Rd4b,N055V02,N055,N055V02,,4308,4308,3.3303489706168863,89.91942220665592,-4.392033318375188,male,0.0,785.3808971248754,-9.619084465728463,male,True,False,-0.008658195419666899,0.10033090873978126,17,False,GSM8747446,15,False,126,False,5,1,4,1,GSM8747484,N138,N055,0.2824344262449397,0.36452739567278036,0.36452739567278036,,True,1,3,1,1,GSM8747472,N055,N055,0.22811184016791616,0.22811184016791616,0.09752808138686857,,False,1,2,1,2,GSM8747472,N055,N078,0.22934295757401033,0.22934295757401033,0.08828781620863113,,True,1,1,1,1,GSM8747472,N055,N055,0.2157891487250944,0.2157891487250944,0.06938875926627343,,True,1,2,1,1,GSM8747472,N055,N055,0.21887489691847264,0.21887489691847264,0.08942650129916646,,False,pass,True,
+N063_AC,GSM8747307,GSM8747474,N063,7,N063_control_AC,N063V02_Rd4b_GPEX,exact_subject_id,AC,AC,control,Male,73,73,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox010117,2,Rd4b_N063V02,Rd4b,N063V02,N063,N063V02,,3338,3338,1.8136230293852271,110.63100479249886,-5.310164923330354,male,0.0,1063.1496801292121,-10.055485374967812,male,True,False,0.1416663579255348,0.27342842161886116,37,False,GSM8747446,1,True,17,False,4,31,4,25,GSM8747490,N147,N015,0.11313005021430039,0.1735699982801594,0.1735699982801594,,True,5,14,5,12,GSM8747490,N147,N002,0.0891699252608342,0.15426178343765373,0.15426178343765373,,True,3,20,3,14,GSM8747470,N129,N078,0.06238786647787026,0.09719745208610968,0.09719745208610968,,True,1,3,1,3,GSM8747474,N063,N078,0.08853344358857974,0.08853344358857974,0.07948422667786753,,True,1,3,1,3,GSM8747474,N063,N078,0.07286987191292849,0.07286987191292849,0.07188216284439994,,True,borderline: own patient rank 3 (bulk->sc) and 14 (sc->bulk),False,
+N106_AC,GSM8747310,GSM8747478,N106,8,N106_control_AC,N106V02_Rd4b_GPEX,exact_subject_id,AC,AC,control,Female,49,49,Ipilimumab + Nivolumab,Renal,NA,NA,itox011662,3,Rd4b_N106V02,Rd4b,N106V02,N106,N106V02,,5030,5030,752.2440332103116,1.1744637520847954,8.436313869855486,female,49.87325365685242,0.0,5.668835461242344,female,True,False,0.14010533142068773,0.2258339379661543,15,False,GSM8747446,2,False,62,False,1,2,1,2,GSM8747478,N106,N111,0.3122171620664638,0.3122171620664638,0.2822906225642828,,True,1,1,1,1,GSM8747478,N106,N106,0.21583868568601516,0.21583868568601516,0.20151376220763628,,True,2,2,2,2,GSM8747446,N002,N078,0.1382054399810151,0.13981381026624984,0.13981381026624984,,True,1,1,1,1,GSM8747478,N106,N106,0.18295625989577446,0.18295625989577446,0.058645878226137566,,True,1,1,1,1,GSM8747478,N106,N106,0.2051395632744425,0.2051395632744425,0.06909963204458511,,True,borderline: own patient rank 2 (bulk->sc) and 2 (sc->bulk),False,
+N087_AC,GSM8747315,GSM8747476,N087,9,N87_control_AC,N087V02_Rd4b_GPEX,zero_padding_difference,AC,AC,control,Male,63,63,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox011667,3,Rd4b_N087V02,Rd4b,N087V02,N87,N087V02,,8987,8987,0.3569974353304246,212.97446999140757,-7.300876869781118,male,0.15926362868640553,895.380120474972,-9.594758155908265,male,True,False,0.19960582036237995,0.2431818488227612,21,False,GSM8747498,29,False,16,False,27,88,17,52,GSM8747470,N129,N111,-0.05153897273137417,0.2760933710934987,0.2760933710934987,,True,19,48,16,35,GSM8747486,N138,N096,0.024032541556127197,0.1279216192129387,0.1279216192129387,,True,8,13,8,13,GSM8747414,N016,N096,0.07848107989514805,0.1293445613324191,0.1293445613324191,,True,1,11,1,10,GSM8747476,N087,N096,0.08094870741307268,0.08094870741307268,0.07999308826423217,,True,1,5,1,5,GSM8747476,N087,N096,0.09545032726569502,0.09545032726569502,0.09463814486162363,,True,fail: expression: own patient rank 8 (bulk->28 sc patients) and 13 (sc->61 bulk patients); bulk best sc = Rd1_N016V01,False,
+N136_TOL,GSM8747331,GSM8747480,N136,10,N136_chili_TOL,N136V01_Rd4b_GPEX,exact_subject_id,TOL,TOL,ChILI,Female,69,69,Ipilimumab + Nivolumab,Melanoma,y,y,itox012831,4,Rd4b_N136V01,Rd4b,N136V01,N136,N136V01,,759,759,394.49949687692725,3.825590184231149,6.356826650066324,female,56.38402760660586,0.0,5.842577324830083,female,True,False,0.15980168235341172,0.2546861915546285,22,False,GSM8747486,5,False,24,False,1,1,1,1,GSM8747480,N136,N136,0.2674227742742407,0.2674227742742407,0.24363504681083234,True,True,1,1,1,1,GSM8747480,N136,N136,0.2550442435086539,0.2550442435086539,0.16338609411503774,True,True,1,1,1,1,GSM8747480,N136,N136,0.21530479780458645,0.21530479780458645,0.11229421498675843,True,True,1,2,1,2,GSM8747480,N136,N064,0.14804014489359404,0.14804014489359404,0.08921521963013565,True,True,1,2,1,2,GSM8747480,N136,N132,0.10948270718921044,0.10948270718921044,0.06577942393955458,True,True,pass,True,
+N136_FU1,GSM8747332,GSM8747482,N136,11,N136_chili_FU1,N136V02_Rd4b_GPEX,exact_subject_id,FU1,FU1,ChILI,Female,69,69,Ipilimumab + Nivolumab,Melanoma,y,y,itox012832,4,Rd4b_N136V02,Rd4b,N136V02,N136,N136V02,,2927,2927,533.0688976872138,3.4417665251358285,6.90974849716139,female,40.29243602710777,0.0,5.367805627001824,female,True,False,0.12145794903387686,0.20995248224976462,20,False,GSM8747498,9,False,58,False,1,26,1,6,GSM8747482,N136,N112,0.16819974148227848,0.16819974148227848,0.15438683296690708,True,False,1,2,1,2,GSM8747482,N136,N019,0.22838066204943824,0.22838066204943824,0.14256698369741178,True,True,1,1,1,1,GSM8747482,N136,N136,0.21565368361090603,0.21565368361090603,0.12236387699392817,True,True,1,1,1,1,GSM8747482,N136,N136,0.16348760044151817,0.16348760044151817,0.07829027295190451,True,True,1,1,1,1,GSM8747482,N136,N136,0.14727620228868285,0.14727620228868285,0.08589008232770465,True,True,pass,True,
+N138_TOL,GSM8747333,GSM8747484,N138,12,N138_chili_TOL,N138V01_Rd4b_GPEX,exact_subject_id,TOL,TOL,ChILI,Male,67,67,Ipilimumab + Nivolumab,Renal,y,y,itox012833,4,Rd4b_N138V01,Rd4b,N138V01,N138,N138V01,,5129,5129,2.1610778267607076,81.44562059604418,-4.704954401205152,male,0.0,809.5029129904431,-9.66267356064933,male,True,False,0.17445824949573666,0.18044804369820683,4,False,GSM8747446,1,True,55,False,1,2,1,1,GSM8747484,N138,N138,0.48458080633132666,0.48458080633132666,0.35788144006240424,True,False,2,2,2,1,GSM8747448,N012,N138,0.2026354784854129,0.20532044027081642,0.20532044027081642,True,False,1,8,1,1,GSM8747484,N138,N138,0.12124593809686109,0.12124593809686109,0.060327662166194895,True,False,2,5,1,1,GSM8747486,N138,N138,0.10219475682135247,0.10884042590760146,0.07554042039852983,False,False,1,2,1,1,GSM8747484,N138,N138,0.11598351591029302,0.11598351591029302,0.08999056620254757,True,False,pass,True,
+N138_FU1,GSM8747334,GSM8747486,N138,13,N138_chili_FU1,N138V02_Rd4b_GPEX,exact_subject_id,FU1,FU1,ChILI,Male,67,67,Ipilimumab + Nivolumab,Renal,y,y,itox012834,4,Rd4b_N138V02,Rd4b,N138V02,N138,N138V02,,2107,2107,1.8376846643377076,106.35599994854482,-5.241544733195261,male,0.0,772.278488552409,-9.594844269768773,male,True,False,0.17883630127414601,0.19878733384380476,6,False,GSM8747446,5,False,67,False,2,1,1,1,GSM8747484,N138,N138,0.5069641281131348,0.5780832011799766,0.46896200422858936,False,True,2,2,1,1,GSM8747484,N138,N138,0.1973827767608485,0.21184305324700656,0.19046029989615168,False,False,2,5,1,4,GSM8747484,N138,N005,0.0942179472318257,0.17093264835134947,0.08701014166581114,False,False,2,3,1,1,GSM8747484,N138,N138,0.10449725992979844,0.14176001696174997,0.1021184737525835,False,False,3,3,1,1,GSM8747484,N138,N138,0.0876928260249128,0.12706027439880177,0.08914950486033588,False,False,pass,True,bulk matches this patient's other sc time point slightly better (time point not resolvable)
+N128_BC,GSM8747343,GSM8747464,N128,14,N128_control_BC,N128V01_Rd4a_GPEX,exact_subject_id,BC,BC,control,Male,61,61,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox012843,4,Rd4a_N128V01,Rd4a,N128V01,N128,N128V01,,3902,3902,4.641300828672902,164.20169688467107,-4.872056823065231,male,0.1085533882389134,1030.9315281049608,-9.86245327878391,male,True,False,0.08614018898702551,0.2079575743337697,23,False,GSM8747446,17,False,77,False,6,1,3,1,GSM8747498,N158,N128,0.2641489490919229,0.32549477859770215,0.32549477859770215,False,True,5,1,1,1,GSM8747466,N128,N128,0.11913717433122151,0.2852667307392922,0.1597388003413714,False,True,4,1,1,1,GSM8747466,N128,N128,0.1307351816843094,0.23906662586262023,0.14851383919477917,False,True,2,1,1,1,GSM8747466,N128,N128,0.12234176358660416,0.18664795562866263,0.06294240934315619,False,True,2,2,1,2,GSM8747466,N128,N001,0.10631664181202463,0.18302609464484246,0.08920063474860138,False,True,pass,True,bulk matches this patient's other sc time point slightly better (time point not resolvable)
+N128_AC,GSM8747344,GSM8747466,N128,15,N128_control_AC,N128V02_Rd4a_GPEX,exact_subject_id,AC,AC,control,Male,62,61,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox012844,4,Rd4a_N128V02,Rd4a,N128V02,N128,N128V02,age bulk 61 vs sc 62,2713,2713,0.7898061747949381,146.2269717906057,-6.362094824461741,male,0.0,965.3578721563654,-9.916413752306239,male,True,False,0.09661391322378042,0.2137575381188218,21,False,GSM8747446,9,False,78,False,3,2,2,1,GSM8747444,N002,N128,0.2767898017264951,0.34367763423217507,0.34367763423217507,True,False,1,2,1,1,GSM8747466,N128,N128,0.22718524034063683,0.22718524034063683,0.20071050138424257,True,False,1,2,1,1,GSM8747466,N128,N128,0.2214164125487261,0.2214164125487261,0.157463833511703,True,False,1,2,1,1,GSM8747466,N128,N128,0.1588235136521684,0.1588235136521684,0.06277577300820814,True,False,1,2,1,1,GSM8747466,N128,N128,0.15227611339951727,0.15227611339951727,0.06404736520801675,True,False,pass,True,
+N129_BC,GSM8747345,GSM8747468,N129,16,N129_control_BC,N129V01_Rd4a_GPEX,exact_subject_id,BC,BC,control,Male,50,50,Ipilimumab + Nivolumab,Renal,NA,NA,itox012845,4,Rd4a_N129V01,Rd4a,N129V01,N129,N129V01,,3087,3087,0.7178606603743787,187.24198891431712,-6.77583163774649,male,0.0,1138.1476501695029,-10.153739038171553,male,True,False,0.09069570039601352,0.2405554956109284,36,False,GSM8747446,17,False,53,False,16,52,13,39,GSM8747496,N158,N073,0.06487912462727731,0.19360349734623966,0.19360349734623966,True,True,1,1,1,1,GSM8747468,N129,N129,0.19886563508590685,0.19886563508590685,0.121061265353855,True,True,1,1,1,1,GSM8747468,N129,N129,0.1890590195805968,0.1890590195805968,0.10316201076231059,True,True,1,1,1,1,GSM8747468,N129,N129,0.17472400348025757,0.17472400348025757,0.09380071475008199,True,True,1,1,1,1,GSM8747468,N129,N129,0.16126760373709242,0.16126760373709242,0.07955479273488879,True,True,pass,True,
+N129_AC,GSM8747346,GSM8747470,N129,17,N129_control_AC,N129V02_Rd4a_GPEX,exact_subject_id,AC,AC,control,Male,51,50,Ipilimumab + Nivolumab,Renal,NA,NA,itox012846,4,Rd4a_N129V02,Rd4a,N129V02,N129,N129V02,age bulk 50 vs sc 51,2798,2798,1.4620673925343914,158.67731407211485,-6.019145295936081,male,0.20158677010218232,1234.3157933356622,-10.0057233474515,male,True,False,0.05289595469948181,0.2258886857556305,41,False,GSM8747446,43,False,70,False,17,55,13,39,GSM8747444,N002,N073,0.02946378091958672,0.16437007646714924,0.16437007646714924,False,True,1,1,1,1,GSM8747470,N129,N129,0.13716516529653566,0.13716516529653566,0.1053357726334241,True,True,2,2,1,2,GSM8747468,N129,N002,0.12122896681948195,0.14359116700219415,0.07213296223327124,False,True,2,1,1,1,GSM8747468,N129,N129,0.12279309303688836,0.13622318996134497,0.09542838330488851,False,True,2,1,1,1,GSM8747468,N129,N129,0.1311858084517422,0.15532333994117295,0.08776418931375528,False,True,pass,True,bulk matches this patient's other sc time point slightly better (time point not resolvable)
+N147_TOL,GSM8747347,GSM8747490,N147,18,N147_chili_TOL,N147V01_Rd5_GPEX,exact_subject_id,TOL,TOL,ChILI,Male,60,60,Ipilimumab + Nivolumab,Renal,NA,NA,itox014973,5,Rd5_N147V01,Rd5,N147V01,N147,PBMCN147DEV01TOL,,3210,3210,0.0,332.7255134056504,-8.382518174936788,male,0.0,736.3661854615967,-9.526237447831855,male,True,False,0.28456527103339,0.28456527103339,1,True,GSM8747490,1,True,10,False,1,5,1,5,GSM8747490,N147,N132,0.26458062064493665,0.26458062064493665,0.1205750762589527,,,1,5,1,5,GSM8747490,N147,N111,0.19553688404646238,0.19553688404646238,0.10621361696676634,,,1,2,1,2,GSM8747490,N147,N111,0.1502215460057778,0.1502215460057778,0.0981072458092032,,,1,3,1,3,GSM8747490,N147,N012,0.12228927518855227,0.12228927518855227,0.09632773572093367,,,1,2,1,2,GSM8747490,N147,N111,0.12350899797778066,0.12350899797778066,0.07683778855307768,,,pass,True,
+N150_BC,GSM8747363,GSM8747492,N150,19,N150_control_BC,N150V01_Rd5_GPEX,exact_subject_id,BC,BC,control,Male,57,57,Ipilimumab + Nivolumab,Renal,NA,NA,itox014989,5,Rd5_N150V01,Rd5,N150V01,N150,PBMCN150JGV01CTLBC,,2433,2433,8.57409113294289,143.40167419846986,-3.9148081200470246,male,0.0,1024.5974142274831,-10.002248814362142,male,True,False,0.06309797194698023,0.20194321433362672,35,False,GSM8747446,35,False,74,False,20,56,7,36,GSM8747482,N136,N096,-0.00010117792535294445,0.13960204294812228,0.13960204294812228,False,True,1,5,1,3,GSM8747492,N150,N005,0.11716758327421077,0.11716758327421077,0.060533703947127704,True,True,1,7,1,5,GSM8747492,N150,N022,0.11038869155156378,0.11038869155156378,0.05767963735360276,True,True,2,6,1,5,GSM8747494,N150,N078,0.07910790560052795,0.08407951748322856,0.06731106982417737,False,True,1,13,1,8,GSM8747492,N150,N028,0.044340525813876444,0.044340525813876444,0.038596920036541096,True,True,pass,True,
+N150_AC,GSM8747364,GSM8747494,N150,20,N150_control_AC,N150V02_Rd5_GPEX,exact_subject_id,AC,AC,control,Male,57,57,Ipilimumab + Nivolumab,Renal,NA,NA,itox014990,5,Rd5_N150V02,Rd5,N150V02,N150,PBMCN150JGV02AC,,4316,4316,0.0,198.6324825281981,-7.641202672822707,male,0.0,862.2379885829506,-9.7536145447933,male,True,False,0.1682537862228449,0.21051598632778978,10,False,GSM8747446,9,False,50,False,2,28,2,23,GSM8747490,N147,N111,0.11147607000132347,0.11456148368898597,0.11456148368898597,True,True,1,8,1,5,GSM8747494,N150,N064,0.10902055133025132,0.10902055133025132,0.0657565417439651,True,False,1,11,1,8,GSM8747494,N150,N022,0.10395031953294692,0.10395031953294692,0.04730292117259629,True,False,1,10,1,7,GSM8747494,N150,N078,0.08109638547400037,0.08109638547400037,0.06009233422693504,True,False,6,27,3,15,GSM8747428,N005,N078,0.02764055932210892,0.0506960687609957,0.0506960687609957,False,False,borderline: own patient rank 1 (bulk->sc) and 8 (sc->bulk),False,
+N158_BC,GSM8747365,GSM8747496,N158,21,N158_control_BC,N158V01_Rd5_GPEX,exact_subject_id,BC,BC,control,Male,55,55,Ipilimumab + Nivolumab,Renal,NA,NA,itox014991,5,Rd5_N158V01,Rd5,N158V01,N158,PBMCN158CSV01CTLBC,,5274,5274,0.32690544603224236,132.5601583660743,-6.653280329582674,male,0.0748845187115819,998.0608653879636,-9.860247092444114,male,True,False,0.19337818006130794,0.22330291665596833,10,False,GSM8747446,20,False,32,False,1,35,1,18,GSM8747496,N158,N100,0.09968108464627569,0.09968108464627569,0.0832236095901469,True,False,1,21,1,13,GSM8747496,N158,N013,0.07058167776942528,0.07058167776942528,0.04843783338739485,True,False,14,47,11,18,GSM8747500,N159,N013,0.012839293164737909,0.046753198863746646,0.046753198863746646,True,False,14,42,13,11,GSM8747430,N018,N078,0.015374743964453376,0.07614089110114029,0.07614089110114029,True,False,28,79,22,6,GSM8747454,N064,N032,-0.013925205019359238,0.08199632746388277,0.08199632746388277,True,False,fail: expression: own patient rank 11 (bulk->28 sc patients) and 18 (sc->61 bulk patients); bulk best sc = Rd5_N159V01,False,
+N158_AC,GSM8747366,GSM8747498,N158,22,N158_control_AC,N158V02_Rd5_GPEX,exact_subject_id,AC,AC,control,Male,55,55,Ipilimumab + Nivolumab,Renal,NA,NA,itox014992,5,Rd5_N158V02,Rd5,N158V02,N158,PBMCN158CSV02AC,,3749,3749,0.14035812656709848,331.1048205717853,-8.186007883537403,male,0.0,812.8184120326998,-9.668563110451503,male,True,False,0.3114410885375346,0.31502147161729677,3,False,GSM8747446,20,False,6,False,2,35,1,26,GSM8747496,N158,N138,0.12008634429351436,0.14731072003431775,0.11193325426367882,False,True,3,8,1,7,GSM8747496,N158,N043,0.05981270867101658,0.08121948175251066,0.06876914756212059,False,True,1,2,1,2,GSM8747498,N158,N043,0.06517165692090422,0.06517165692090422,0.050584793551747005,True,True,1,6,1,6,GSM8747498,N158,N078,0.06874867278790613,0.06874867278790613,0.04698728780993677,True,True,1,2,1,2,GSM8747498,N158,N032,0.09499929085018684,0.09499929085018684,0.03741494885045178,True,True,pass,True,
+N159_BC,GSM8747367,GSM8747500,N159,23,N159_control_BC,N159V01_Rd5_GPEX,exact_subject_id,BC,BC,control,Female,56,56,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox014993,5,Rd5_N159V01,Rd5,N159V01,N159,PBMCN159NEV01CTLBC,,3779,3779,1345.8528881502114,5.254617523098515,7.750454899064719,female,52.12867570173004,0.0,5.731418847179655,female,True,False,0.32503524291606634,0.35337468692894597,8,False,GSM8747490,1,True,3,False,1,2,1,2,GSM8747500,N159,N119,0.32707217661795057,0.32707217661795057,0.23454272391238087,True,True,1,1,1,1,GSM8747500,N159,N159,0.11943186836825359,0.11943186836825359,0.06468375758365265,True,True,1,2,1,2,GSM8747500,N159,N035,0.11733423164537617,0.11733423164537617,0.08398186229324046,True,True,2,1,2,1,GSM8747444,N002,N159,0.09176409087442954,0.0924825012448631,0.0924825012448631,True,True,1,1,1,1,GSM8747500,N159,N159,0.09635622226487525,0.09635622226487525,0.09105958598921511,True,True,pass,True,
+N159_AC,GSM8747368,GSM8747502,N159,24,N159_control_AC,N159V02_Rd5_GPEX,exact_subject_id,AC,AC,control,Female,56,56,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox014994,5,Rd5_N159V02,Rd5,N159V02,N159,PBMCN159NEV02AC,,1632,1632,1778.7078921115647,0.7310759934696114,10.005755692386238,female,52.64094451418383,0.32295057984161857,5.341503566157684,female,True,False,0.1606448562282,0.24835719854157257,44,False,GSM8747446,3,False,14,False,3,33,1,8,GSM8747500,N159,N015,0.10578531271813783,0.14161797223294884,0.11061140604075237,False,False,9,45,7,11,GSM8747466,N128,N013,0.027895110292859356,0.08662534388932344,0.08662534388932344,True,False,30,81,9,3,GSM8747466,N128,N035,-0.017892516139488876,0.06865704088272673,0.06865704088272673,False,False,34,91,4,25,GSM8747464,N128,N078,-0.024697837074688162,0.06430591316246838,0.06430591316246838,False,False,27,70,14,18,GSM8747446,N002,N078,-0.011996344585463807,0.09559191122665431,0.09559191122665431,False,False,borderline: own patient rank 9 (bulk->sc) and 3 (sc->bulk),False,bulk matches this patient's other sc time point slightly better (time point not resolvable)
+N001_TOL,GSM8747369,GSM8747440,N001,25,N001_chili_TOL,N001V01_Rd3_GPEX,exact_subject_id,TOL,TOL,ChILI,Female,78,78,Ipilimumab + Nivolumab,Melanoma,y,y,itox009594,1,Rd3_N001V01,Rd3,N001V01,N001,N001V01SA,,5658,5658,611.0852233936745,0.0,9.25758872963299,female,89.24122869899091,0.0,6.495714806084541,female,True,False,0.19227171555591827,0.23053492155944597,9,False,GSM8747446,21,False,30,False,3,5,3,1,GSM8747424,N043,N001,0.19082548426967116,0.2384142026552179,0.2384142026552179,True,False,1,2,1,1,GSM8747440,N001,N001,0.20775259964725284,0.20775259964725284,0.16397625915296285,True,False,1,2,1,1,GSM8747440,N001,N001,0.12791129416066319,0.12791129416066319,0.10464597844241,True,False,1,1,1,1,GSM8747440,N001,N001,0.12156486520588719,0.12156486520588719,0.10695311800682177,True,True,2,1,2,1,GSM8747464,N128,N001,0.11771907348163728,0.11851235247227083,0.11851235247227083,True,True,pass,True,
+N001_FU1,GSM8747370,GSM8747442,N001,26,N001_chili_FU1,N001V02_Rd3_GPEX,exact_subject_id,FU1,FU1,ChILI,Female,78,78,Ipilimumab + Nivolumab,Melanoma,y,y,itox009595,1,Rd3_N001V02,Rd3,N001V02,N001,N001V02SA,,4547,4547,424.33663420822927,1.3260519819007166,7.514577971210999,female,92.86569009364925,0.0,6.552526013394067,female,True,False,0.21415004108556895,0.21415004108556895,1,True,GSM8747442,1,True,33,False,1,3,1,3,GSM8747442,N001,N138,0.36081959214313286,0.36081959214313286,0.26542739115662606,True,True,1,1,1,1,GSM8747442,N001,N001,0.24009379505270265,0.24009379505270265,0.10538427612599466,True,True,1,1,1,1,GSM8747442,N001,N001,0.20610211496458347,0.20610211496458347,0.08069687708643088,True,True,1,1,1,1,GSM8747442,N001,N001,0.1726089751959583,0.1726089751959583,0.07410199950931436,True,True,1,1,1,1,GSM8747442,N001,N001,0.1611686476949857,0.1611686476949857,0.061960794759648316,True,True,pass,True,
+N002_TOL,GSM8747371,GSM8747444,N002,27,N002_chili_TOL,N002V01_Rd3_GPEX,exact_subject_id,TOL,TOL,ChILI,Male,30,30,Ipilimumab + Nivolumab,Melanoma,n,n,itox009596,1,Rd3_N002V01,Rd3,N002V01,N002,N002V01KP,,6318,6318,0.0,166.6123643941417,-7.388984767166159,male,0.0,891.0127558752612,-9.800920530757075,male,True,False,0.18927809927676165,0.2261711890949129,2,False,GSM8747446,4,False,49,False,1,1,1,1,GSM8747444,N002,N002,0.34453216786375696,0.34453216786375696,0.1704172260356415,True,True,2,1,1,1,GSM8747446,N002,N002,0.1959349747391309,0.3322753984802663,0.17686293729604943,False,True,6,2,1,2,GSM8747446,N002,N136,0.11689394673149683,0.2711735155001521,0.1393259772229394,False,True,6,22,3,12,GSM8747426,N043,N101,0.05690080667789015,0.1038092735636719,0.1038092735636719,False,False,4,22,2,11,GSM8747426,N043,N101,0.05207552617469731,0.08531181242443715,0.08531181242443715,False,False,pass,True,bulk matches this patient's other sc time point slightly better (time point not resolvable)
+N002_FU1,GSM8747372,GSM8747446,N002,28,N002_chili_FU1,N002V02_Rd3_GPEX,exact_subject_id,FU1,FU1,ChILI,Male,30,30,Ipilimumab + Nivolumab,Melanoma,n,n,itox009597,1,Rd3_N002V02,Rd3,N002V02,N002,N002V02KP,,4975,4975,1.0640746753419494,129.10772727482316,-5.978067671595918,male,0.0,737.1392211154648,-9.527749139759699,male,True,False,0.287842317695265,0.287842317695265,1,True,GSM8747446,1,True,11,False,1,1,1,1,GSM8747446,N002,N002,0.5027054348900664,0.5027054348900664,0.23501992990416337,True,True,1,1,1,1,GSM8747446,N002,N002,0.5022834543640496,0.5022834543640496,0.27429265888200366,True,True,1,1,1,1,GSM8747446,N002,N002,0.40340474847261276,0.40340474847261276,0.22640560700663212,True,True,1,1,1,1,GSM8747446,N002,N002,0.20605829586601326,0.20605829586601326,0.17055767713227513,True,True,1,4,1,2,GSM8747446,N002,N022,0.13000634377032422,0.13000634377032422,0.11815534695756898,True,True,pass,True,
+N005_BC,GSM8747375,GSM8747428,N005,29,N005_control_BC,N005V01_Rd2_GPEX,exact_subject_id,BC,BC,control,Male,69,69,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox009600,1,Rd2_N005V01,Rd2,N005V01,N005,N005V01KG,,6359,6359,0.0,104.10760923482842,-6.715723306343844,male,0.17024882973082553,1195.317033540126,-9.997568728210238,male,True,False,0.027518855713107263,0.18363000278710312,37,False,GSM8747446,26,False,87,False,5,15,5,1,GSM8747414,N016,N005,0.1407697833775361,0.1961780485880878,0.1961780485880878,True,False,2,2,1,1,GSM8747456,N005,N005,0.23496802562404084,0.28674578693496217,0.12367924407449248,False,False,2,2,1,1,GSM8747456,N005,N005,0.26232873271645285,0.2672738171805538,0.11140165467726354,False,False,1,1,1,1,GSM8747428,N005,N005,0.2751058441047056,0.2751058441047056,0.11057544580654124,True,True,1,1,1,1,GSM8747428,N005,N005,0.2482574776119229,0.2482574776119229,0.10879767607599586,True,True,pass,True,bulk matches this patient's other sc time point slightly better (time point not resolvable)
+N005_AC,GSM8747376,GSM8747456,N005,30,N005_control_AC,N005V02_Rd4a_GPEX,exact_subject_id,AC,AC,control,Male,69,69,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox009601,1,Rd4a_N005V02,Rd4a,N005V02,N005,N005V02,,3433,3433,0.30730359228680276,200.0546385787086,-7.26484959706086,male,0.10632271410417585,1067.799017748238,-9.91600259091155,male,True,False,0.17175568769225943,0.19828050861402585,9,False,GSM8747446,1,True,17,False,1,1,1,1,GSM8747456,N005,N005,0.5956613744620003,0.5956613744620003,0.3685888841933803,True,True,1,1,1,1,GSM8747456,N005,N005,0.34274493119167904,0.34274493119167904,0.17756867647812422,True,True,1,1,1,1,GSM8747456,N005,N005,0.317082424746586,0.317082424746586,0.14775221050564194,True,True,1,1,1,1,GSM8747456,N005,N005,0.23512374456372345,0.23512374456372345,0.11933692307626918,True,True,1,1,1,1,GSM8747456,N005,N005,0.22646787472897223,0.22646787472897223,0.13080115907207965,True,True,pass,True,
+N012_TOL,GSM8747381,GSM8747448,N012,31,N012_chili_TOL,N012V01_Rd3_GPEX,exact_subject_id,TOL,TOL,ChILI,Male,68,68,Ipilimumab + Nivolumab,Renal,y,y,itox009606,1,Rd3_N012V01,Rd3,N012V01,N012,N012V01DH,,6709,6709,1.6761919065409032,104.92961334946054,-5.306780577141732,male,0.0,898.9223750583458,-9.813656753496838,male,True,False,0.10417677427103297,0.15077336670853994,9,False,GSM8747442,3,False,110,False,1,1,1,1,GSM8747448,N012,N012,0.37893672502117076,0.37893672502117076,0.3320116642491748,True,True,1,1,1,1,GSM8747448,N012,N012,0.30352691507807716,0.30352691507807716,0.15018624292362046,True,True,1,1,1,1,GSM8747448,N012,N012,0.19190037900819243,0.19190037900819243,0.1059048415720141,True,True,1,1,1,1,GSM8747448,N012,N012,0.16702266543210753,0.16702266543210753,0.13189021787964636,True,True,1,1,1,1,GSM8747448,N012,N012,0.18233083675790823,0.18233083675790823,0.11868623360775048,True,True,pass,True,
+N012_FU1,GSM8747382,GSM8747450,N012,32,N012_chili_FU1,N012V02_Rd3_GPEX,exact_subject_id,FU1,FU1,ChILI,Male,68,68,Ipilimumab + Nivolumab,Renal,y,y,itox009607,1,Rd3_N012V02,Rd3,N012V02,N012,N012V02DH,,4369,4369,0.5685009539446008,83.5696402298563,-5.752681529506712,male,0.0,893.761599425652,-9.805359531210902,male,True,False,0.04158031227742669,0.12342962153423374,10,False,GSM8747446,7,False,126,False,4,2,4,2,GSM8747426,N043,N072,0.2920802258575945,0.34643390853663086,0.34643390853663086,True,True,1,1,1,1,GSM8747450,N012,N012,0.2514256931757175,0.2514256931757175,0.1787465960401585,True,True,1,1,1,1,GSM8747450,N012,N012,0.2649357723456042,0.2649357723456042,0.13574152603367032,True,True,1,1,1,1,GSM8747450,N012,N012,0.23263758058267597,0.23263758058267597,0.16221830391887276,True,True,1,1,1,1,GSM8747450,N012,N012,0.18717896289691757,0.18717896289691757,0.11918060271056774,True,True,pass,True,
+N018_BC,GSM8747389,GSM8747430,N018,33,N018_control_BC,N018V01_Rd2_GPEX,exact_subject_id,BC,BC,control,Female,36,36,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox009614,1,Rd2_N018V01,Rd2,N018V01,N018,N018V01TJ,,3045,3045,765.1164666143216,2.0060735883962284,7.993539593365751,female,73.75052142307904,0.0,6.224011737768228,female,True,False,0.07817425483718077,0.15355528900882792,17,False,GSM8747446,10,False,110,False,2,6,2,6,GSM8747422,N037,N131,0.16548719851568824,0.20808640454528068,0.20808640454528068,True,True,1,1,1,1,GSM8747430,N018,N018,0.21184781742927455,0.21184781742927455,0.08136953569767054,True,True,1,1,1,1,GSM8747430,N018,N018,0.2072869277784147,0.2072869277784147,0.06898271821957994,True,True,1,1,1,1,GSM8747430,N018,N018,0.17526403306090585,0.17526403306090585,0.1053229340840784,True,True,1,1,1,1,GSM8747430,N018,N018,0.174515146515006,0.174515146515006,0.08697574671307697,True,True,pass,True,
+N018_AC,GSM8747390,GSM8747432,N018,34,N018_control_AC,N018V02_Rd2_GPEX,exact_subject_id,AC,AC,control,Female,36,36,Ipilimumab + Nivolumab,Melanoma,NA,NA,itox009615,1,Rd2_N018V02,Rd2,N018V02,N018,N018V02TJ,,3520,3520,523.3601293242898,4.289837125608933,6.631190879205106,female,70.62242611574516,0.0,6.162339483775792,female,True,False,0.11756280149620574,0.17326930356036555,27,False,GSM8747446,2,False,54,False,1,2,1,2,GSM8747432,N018,N015,0.24656461221136639,0.24656461221136639,0.24241193786134158,True,True,1,1,1,1,GSM8747432,N018,N018,0.1835934733773603,0.1835934733773603,0.09805024416572215,True,True,1,2,1,1,GSM8747432,N018,N018,0.15101802675175224,0.15101802675175224,0.08192387888029992,True,False,1,1,1,1,GSM8747432,N018,N018,0.14664395336003738,0.14664395336003738,0.08205732330092806,True,True,1,4,1,1,GSM8747432,N018,N018,0.11603202563769321,0.11603202563769321,0.05598280903754514,True,False,pass,True,
+N022_TOL,GSM8747393,GSM8747416,N022,35,N022_chili_TOL,N022V01_Rd1_GPEX,exact_subject_id,TOL,TOL,ChILI,Male,67,67,Ipilimumab + Nivolumab,Melanoma,y,y,itox009618,1,Rd1_N022V01,Rd1,N022V01,N022,PBMCN022V01,,3651,3651,0.6117500670631011,134.27913972035068,-6.391167536628583,male,0.0,962.917288057818,-9.912765546574025,male,True,False,0.07183087361181487,0.2060373138876992,33,False,GSM8747442,23,False,70,False,5,13,1,1,GSM8747418,N022,N022,0.19656123339030307,0.3105957045848581,0.21458714429151762,False,False,2,1,1,1,GSM8747418,N022,N022,0.2712749213620788,0.31539010582839044,0.22255126393723762,False,True,4,2,2,1,GSM8747492,N150,N022,0.1580507331873571,0.19057008702018488,0.19057008702018488,False,False,5,3,2,1,GSM8747476,N087,N022,0.10687001668714202,0.1457823525944012,0.1457823525944012,False,False,1,2,1,1,GSM8747416,N022,N022,0.123256181308789,0.123256181308789,0.0906540151506616,True,False,pass,True,bulk matches this patient's other sc time point slightly better (time point not resolvable)
+N022_FU1,GSM8747394,GSM8747418,N022,36,N022_chili_FU1,N022V02_Rd1_GPEX,exact_subject_id,FU1,FU1,ChILI,Male,67,67,Ipilimumab + Nivolumab,Melanoma,y,y,itox009619,1,Rd1_N022V02,Rd1,N022V02,N022,PBMCN022V02,,2463,2463,0.2549461464507545,170.30402582910398,-7.092789791402241,male,0.11381401697012519,852.4669871062376,-9.581683185638598,male,True,False,0.1521064412003767,0.2198695088023125,19,False,GSM8747446,2,False,20,False,1,1,1,1,GSM8747418,N022,N022,0.5200298242031843,0.5200298242031843,0.4628587322899629,True,True,1,1,1,1,GSM8747418,N022,N022,0.3892824700049134,0.3892824700049134,0.20241024162178076,True,True,1,1,1,1,GSM8747418,N022,N022,0.32197003636672855,0.32197003636672855,0.21799799384232557,True,True,1,1,1,1,GSM8747418,N022,N022,0.20626752149432376,0.20626752149432376,0.1276879166337134,True,True,1,1,1,1,GSM8747418,N022,N022,0.19175274147258647,0.19175274147258647,0.15514140122371325,True,True,pass,True,
+N035_TOL,GSM8747407,GSM8747420,N035,37,N035_chili_TOL,N035V01_Rd1_GPEX,exact_subject_id,TOL,TOL,ChILI,Female,53,53,Ipilimumab + Nivolumab,Renal,n,n,itox009632,1,Rd1_N035V01,Rd1,N035V01,N035,PBMCN035V01,,1598,1598,451.64632192577034,2.91619901162725,6.852786340265424,female,109.31479369694334,0.0,6.7854824654009525,female,True,False,0.15726728085252417,0.20690746321733428,10,False,GSM8747446,2,False,67,False,1,1,1,1,GSM8747420,N035,N035,0.2504308990872504,0.2504308990872504,0.23106969698549776,,True,1,2,1,1,GSM8747420,N035,N035,0.23739697086333938,0.23739697086333938,0.20203946415472737,,False,1,2,1,1,GSM8747420,N035,N035,0.20829060290326848,0.20829060290326848,0.12208369856999457,,False,1,3,1,2,GSM8747420,N035,N078,0.1424776748874126,0.1424776748874126,0.07812116204224201,,False,1,3,1,2,GSM8747420,N035,N078,0.14353276536021992,0.14353276536021992,0.06883757893072823,,False,pass,True,
+N043_TOL,GSM8747410,GSM8747424,N043,38,N043_chili_TOL,N043V01_Rd1_GPEX,exact_subject_id,TOL,TOL,ChILI,Male,60,60,Ipilimumab + Nivolumab,Melanoma,n,y,itox009635,1,Rd1_N043V01,Rd1,N043V01,N043,PBMCN043V01,steroid bulk n vs sc y,2074,2074,1.1309155364422454,78.03317201451492,-5.212912997274723,male,0.0,837.5877966096106,-9.71181802556492,male,True,False,0.08726389959468457,0.1839448895090164,16,False,GSM8747446,1,True,68,False,1,2,1,2,GSM8747424,N043,N035,0.34867253412424004,0.34867253412424004,0.228242432503008,True,True,1,1,1,1,GSM8747424,N043,N043,0.3129443584880827,0.3129443584880827,0.3089180417654304,True,True,3,1,1,1,GSM8747426,N043,N043,0.1553089234308829,0.2027518933056039,0.19694011881366497,False,True,1,1,1,1,GSM8747424,N043,N043,0.16797408422635618,0.16797408422635618,0.09040296370475477,True,True,1,1,1,1,GSM8747424,N043,N043,0.14981585998641253,0.14981585998641253,0.053181246893831954,True,True,pass,True,bulk matches this patient's other sc time point slightly better (time point not resolvable)
+N043_FU1,GSM8747411,GSM8747426,N043,39,N043_chili_FU1,N043V02_Rd1_GPEX,exact_subject_id,FU1,FU1,ChILI,Male,60,60,Ipilimumab + Nivolumab,Melanoma,y,y,itox009636,1,Rd1_N043V02,Rd1,N043V02,N043,PBMCN043V02,,3437,3437,1.2772203597865892,129.31856142839217,-5.838624869590964,male,0.1684078210949826,706.3866055829045,-9.241811171103704,male,True,False,0.25753574765058324,0.25753574765058324,1,True,GSM8747426,1,True,13,False,1,9,1,7,GSM8747426,N043,N138,0.28075478185177066,0.28075478185177066,0.18329203648721218,True,False,1,1,1,1,GSM8747426,N043,N043,0.2035525741058322,0.2035525741058322,0.12960581376275973,True,True,1,4,1,2,GSM8747426,N043,N002,0.18700040174697488,0.18700040174697488,0.0704368200890784,True,False,1,1,1,1,GSM8747426,N043,N043,0.1825683141165709,0.1825683141165709,0.07956916984119393,True,True,1,1,1,1,GSM8747426,N043,N043,0.17095546052731608,0.17095546052731608,0.09456959484928222,True,True,pass,True,

paper-releases/20260928/diffusion/data/cohorts/ji2025_chili/samples.csv

@@ -0,0 +1,41 @@
+row,sample_id,donor_id,group,n_cells
+0,N064_TOL,N064,TOL,2498
+1,N064_FU1,N064,FU1,4659
+2,N032_BC,N032,BC,1780
+3,N032_AC,N032,AC,7350
+4,N038_BC,N038,BC,2801
+5,N038_AC,N038,AC,3976
+6,N055_AC,N055,AC,4308
+7,N063_AC,N063,AC,3338
+8,N106_AC,N106,AC,5030
+9,N087_AC,N087,AC,8987
+10,N136_TOL,N136,TOL,759
+11,N136_FU1,N136,FU1,2927
+12,N138_TOL,N138,TOL,5129
+13,N138_FU1,N138,FU1,2107
+14,N128_BC,N128,BC,3902
+15,N128_AC,N128,AC,2713
+16,N129_BC,N129,BC,3087
+17,N129_AC,N129,AC,2798
+18,N147_TOL,N147,TOL,3210
+19,N150_BC,N150,BC,2433
+20,N150_AC,N150,AC,4316
+21,N158_BC,N158,BC,5274
+22,N158_AC,N158,AC,3749
+23,N159_BC,N159,BC,3779
+24,N159_AC,N159,AC,1632
+25,N001_TOL,N001,TOL,5658
+26,N001_FU1,N001,FU1,4547
+27,N002_TOL,N002,TOL,6318
+28,N002_FU1,N002,FU1,4975
+29,N005_BC,N005,BC,6359
+30,N005_AC,N005,AC,3433
+31,N012_TOL,N012,TOL,6709
+32,N012_FU1,N012,FU1,4369
+33,N018_BC,N018,BC,3045
+34,N018_AC,N018,AC,3520
+35,N022_TOL,N022,TOL,3651
+36,N022_FU1,N022,FU1,2463
+37,N035_TOL,N035,TOL,1598
+38,N043_TOL,N043,TOL,2074
+39,N043_FU1,N043,FU1,3437

paper-releases/20260928/diffusion/data/cohorts/ye2026_sepsis/MANIFEST.json

@@ -0,0 +1,1190 @@
+{
+ "schema": "ye2026_sepsis_paired_ft_v1",
+ "written_utc": "2026-09-27T06:13:49.762772+00:00",
+ "started_utc": "2026-09-27T06:12:07.689644+00:00",
+ "study": "Ye Q et al., Nat Immunol 2026 (doi 10.1038/s41590-025-02345-x); bulk GSE279448, scRNA GSE279452",
+ "rows": 85,
+ "row_order": "bulk GSM ascending",
+ "pairs_by_group": {
+  "adult_sepsis": 48,
+  "ped_sepsis": 16,
+  "adult_HC": 7,
+  "adult_ICU_ctrl": 6,
+  "ped_HC": 4,
+  "ped_ICU_ctrl": 4
+ },
+ "pairs_by_id_match": {
+  "exact_title": 80,
+  "case_only_title_difference": 4,
+  "missing_S_letter_in_sc_title": 1
+ },
+ "cells": {
+  "n_cells": 610713,
+  "nnz": 255556515,
+  "per_row_min": 2107,
+  "per_row_median": 7172.0,
+  "per_row_max": 15576
+ },
+ "retained_cells_rule": "flag_conservative_review_pass = genes>=200 & UMIs>=500 & mito<=20% (qc_core, ImMicro definition); MAD flags are review-only columns",
+ "features_semantics": {
+  "bulk_raw": "htseq-count raw gene counts on the canonical axis; 0 where bulk_valid is False (ImMicro file uses NaN there)",
+  "pseudo_raw_sum": "sum of retained cells' UMI counts on the canonical axis; storage 0 where sc_valid is False",
+  "bulk_valid": "harmonization_valid from qc_bulk.harmonize (gene in the htseq table, unique mapping)",
+  "sc_valid": "harmonization_valid from qc_singlecell.canonical_export (gene in the 10x features table)",
+  "pair_valid": "bulk_valid & sc_valid",
+  "donor_ids": "= sample_ids (one sample per donor; no time points)",
+  "groups": "GEO 'group' field: adult_sepsis, ped_sepsis, adult_HC, adult_ICU_ctrl, ped_HC, ped_ICU_ctrl",
+  "extra_keys": "bulk_gsm, sc_gsm, sc_title_sample_id, id_match, sex_geo, age_geo, infection_source, collection_site, identity_pass, identity_check, sex_bulk_expr, sex_sc_expr",
+  "timepoints": "not included: GEO has no visit/time field and each sample ID occurs once per series"
+ },
+ "identity": {
+  "sex_rule": "CPM on the source axis (bulk: htseq assigned genes; sc: retained cells, all RNA features); score=log2(XIST+1)-log2(RPS4Y1+DDX3Y+UTY+KDM5D+1); female>2, male<-2, else ambiguous; opposite-sex signal flag: female call with Y CPM>20 or male call with XIST CPM>50 (bulk)",
+  "expression_rule": "log2(CPM+1) over the 19864 canonical genes measured in all 207 bulks and all 133 sc libraries; top 2000 by the mean of the bulk-mean and sc-mean log CPM; Spearman of each paired bulk vs all 133 sc pseudobulks (retained cells); sensitivity: same after subtracting each modality's per-gene mean; reverse: each paired sc vs all 207 bulks",
+  "expression_residualised_rule": "within each modality: centre log2(CPM+1) (same common genes), remove the top k sample PCs computed on expressed genes (bulk mean >3 and sc mean >1 log2 CPM), keep the 2000 genes with the highest residual variance in both modalities (rank sum), Pearson; paired bulk vs all sc and paired sc vs all 207 bulks; k=10 primary, 20/30 sensitivity. Uses no pairing information.",
+  "verdict_rule": "pass = sex concordant (bulk, sc, GEO) and residualised k=10 own pair ranked 1st in one direction and <=5th in the other; fail = sex discordant or own pair >5th in both directions; else borderline",
+  "policy": "reported only; no row dropped on identity results; features.npz carries identity_pass / identity_check"
+ },
+ "checks": {
+  "gene_positions_sha256_ok": true,
+  "panel_gene_ids_match_selected_genes_csv": true,
+  "bulk_integer_nonnegative_inside_mask": true,
+  "pseudo_raw_sum_equals_sum_of_retained_cells_full_axis": true,
+  "cells_panel_sums_equal_pseudo_raw_sum_positions_exactly": true,
+  "cells_per_row_equal_qc_cell_counts": true,
+  "no_sc_mass_outside_sc_valid": true,
+  "one_sample_id_per_library": true,
+  "sex_concordant_pairs": "84/85",
+  "expression_best_match_is_own_pair": "6/85",
+  "expression_best_match_is_own_pair_centred": "32/85",
+  "expression_reverse_best_match_is_own_pair": "13/85",
+  "expression_residualised_k10_top1_bulk_to_sc": "81/85",
+  "expression_residualised_k10_top1_sc_to_bulk": "82/85",
+  "expression_residualised_k20_top1_bulk_to_sc": "82/85",
+  "expression_residualised_k30_top1_bulk_to_sc": "82/85",
+  "identity_check_pass": "82/85",
+  "identity_check_fail": [
+   "Abd-PS13",
+   "Abd-S8",
+   "Uri-S112"
+  ],
+  "identity_check_borderline": []
+ },
+ "excluded": {
+  "quarantined_sc_libraries_among_pairs": [],
+  "sc_libraries_without_bulk": [
+   {
+    "sc_gsm": "GSM8571086",
+    "sc_sample_id": "Abd-PS18",
+    "group": "ped_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571091",
+    "sc_sample_id": "Abd-S101",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571094",
+    "sc_sample_id": "Abd-S11",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571095",
+    "sc_sample_id": "Abd-S111",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571096",
+    "sc_sample_id": "Abd-S12",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571099",
+    "sc_sample_id": "Abd-S13",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571101",
+    "sc_sample_id": "Abd-S23",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571104",
+    "sc_sample_id": "Abd-S45",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571106",
+    "sc_sample_id": "Abd-S49",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571108",
+    "sc_sample_id": "Abd-S53",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571110",
+    "sc_sample_id": "Abd-S55",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571112",
+    "sc_sample_id": "Abd-S58",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571113",
+    "sc_sample_id": "Abd-S59",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571115",
+    "sc_sample_id": "Abd-S67",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571116",
+    "sc_sample_id": "Abd-S72",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571117",
+    "sc_sample_id": "Abd-S73",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571118",
+    "sc_sample_id": "Abd-S75",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571121",
+    "sc_sample_id": "Abd-S80",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571122",
+    "sc_sample_id": "Abd-S81",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571125",
+    "sc_sample_id": "Abd-S9",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571126",
+    "sc_sample_id": "Abd-S91",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571128",
+    "sc_sample_id": "CNS-S189",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571129",
+    "sc_sample_id": "CNS-S50",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571130",
+    "sc_sample_id": "CNS-S61",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571138",
+    "sc_sample_id": "IC08",
+    "group": "adult_ICU_ctrl",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571139",
+    "sc_sample_id": "IC09",
+    "group": "adult_ICU_ctrl",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571156",
+    "sc_sample_id": "Res-S70",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571166",
+    "sc_sample_id": "Res-S100",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571167",
+    "sc_sample_id": "Res-S110",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571168",
+    "sc_sample_id": "RES-S118",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571173",
+    "sc_sample_id": "Res-S144",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571174",
+    "sc_sample_id": "Res-S145",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571177",
+    "sc_sample_id": "Res-S15",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571181",
+    "sc_sample_id": "Res-S167",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571182",
+    "sc_sample_id": "Res-S168",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571183",
+    "sc_sample_id": "Res-S170",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571185",
+    "sc_sample_id": "RES-S176",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571187",
+    "sc_sample_id": "Res-S18",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571188",
+    "sc_sample_id": "Res-S183",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571190",
+    "sc_sample_id": "Res-S21",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571191",
+    "sc_sample_id": "Res-S22",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571192",
+    "sc_sample_id": "Res-S3",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571193",
+    "sc_sample_id": "Res-S32",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571195",
+    "sc_sample_id": "Res-S41",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571196",
+    "sc_sample_id": "Res-S56",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571207",
+    "sc_sample_id": "Uri-S116",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571212",
+    "sc_sample_id": "Uri-S85",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   },
+   {
+    "sc_gsm": "GSM8571213",
+    "sc_sample_id": "Uri-S88",
+    "group": "adult_sepsis",
+    "id_match": "no_bulk"
+   }
+  ],
+  "bulk_samples_without_sc": [
+   {
+    "gsm": "GSM8570835",
+    "sample_id": "Abd-S114",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570836",
+    "sample_id": "Abd-S115",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570839",
+    "sample_id": "Abd-S126",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570840",
+    "sample_id": "Abd-S128",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570841",
+    "sample_id": "Abd-S132",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570842",
+    "sample_id": "Abd-S133",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570843",
+    "sample_id": "Abd-S137",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570844",
+    "sample_id": "Abd-S141",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570845",
+    "sample_id": "Abd-S148",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570847",
+    "sample_id": "Abd-S159",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570848",
+    "sample_id": "Abd-S165",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570849",
+    "sample_id": "Abd-S185",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570850",
+    "sample_id": "Abd-S190",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570851",
+    "sample_id": "Abd-S197",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570852",
+    "sample_id": "Abd-S198",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570853",
+    "sample_id": "Abd-S24",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570854",
+    "sample_id": "Abd-S25",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570855",
+    "sample_id": "Abd-S35",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570856",
+    "sample_id": "Abd-S37",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570867",
+    "sample_id": "Abd-S92",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570868",
+    "sample_id": "Abd-S96",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570869",
+    "sample_id": "Abd-S97",
+    "ch_group": "Adult Sepsis"
+   },
+   {
+    "gsm": "GSM8570872",
+    "sample_id": "HC03",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570873",
+    "sample_id": "HC04",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570875",
+    "sample_id": "HC06",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570877",
+    "sample_id": "HC08",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570879",
+    "sample_id": "HC10",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570880",
+    "sample_id": "HC11",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570883",
+    "sample_id": "HC14",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570884",
+    "sample_id": "HC15",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570886",
+    "sample_id": "HC17",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570887",
+    "sample_id": "HC18",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570888",
+    "sample_id": "HC19",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570889",
+    "sample_id": "HC20",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570890",
+    "sample_id": "HC21",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570891",
+    "sample_id": "HC22",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570892",
+    "sample_id": "HC23",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570893",
+    "sample_id": "HC24",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570894",
+    "sample_id": "HC25",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570895",
+    "sample_id": "HC26",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570896",
+    "sample_id": "HC27",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570897",
+    "sample_id": "HC28",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570898",
+    "sample_id": "HC29",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570899",
+    "sample_id": "HC30",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570900",
+    "sample_id": "HC31",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570901",
+    "sample_id": "HC32",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570902",
+    "sample_id": "HC33",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570903",
+    "sample_id": "HC34",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
+    "gsm": "GSM8570904",
+    "sample_id": "HC35",
+    "ch_group": "Adult Healthy Control"
+   },
+   {
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+    "median": 0.994665085951393,
+    "min": 0.5223458038422649,
+    "pooled": 0.9816102123356926
+   },
+   "conclusion": "GEX barcodes come from the 737K-august-2016 whitelist (every library's sorted first barcode starts AAACCTG; 3' v3/v3.1 uses the 3M-february-2018 list) and nearly all TCR contig cells are GEX cells. The GEX was therefore captured in the same 5' GEM reaction as the V(D)J libraries: 10x 5' gene expression, not 3' v3.1 as the GEO GEX records state.",
+   "mtx_header": "cellranger-6.1.1 (MatrixMarket metadata_json)",
+   "features_file_identical_across_libraries": true
+  },
+  "author_filtering": {
+   "cells_total_133_libraries": 980095,
+   "cells_below_500_umi": 0,
+   "cells_at_or_below_200_genes": 23106,
+   "cells_at_or_above_20pct_mito": 20487,
+   "cells_at_or_above_2x_median_genes": 39338,
+   "conclusion": "GEO matrices are Cell Ranger cell-called barcodes (no cell under 500 UMIs) but NOT the authors' Seurat-filtered set: cells violating the stated MT%<20, genes>200 and genes<2x median rules remain."
+  },
+  "sex_vs_geo": {
+   "sc_all_libraries_discordant": [
+    {
+     "sc_gsm": "GSM8571206",
+     "sc_sample_id": "Uri-S112",
+     "sc_gender": "Male",
+     "sc_sex_call": "female"
+    }
+   ],
+   "bulk_all_samples_discordant_or_ambiguous": [
+    {
+     "bulk_gsm": "GSM8570892",
+     "sample_id": "HC23",
+     "geo": "male",
+     "bulk_sex_call": "ambiguous",
+     "bulk_XIST_cpm": 224.54182681870617,
+     "bulk_Ysum_cpm": 500.4572854088851
+    },
+    {
+     "bulk_gsm": "GSM8570899",
+     "sample_id": "HC30",
+     "geo": "male",
+     "bulk_sex_call": "ambiguous",
+     "bulk_XIST_cpm": 177.66428578864168,
+     "bulk_Ysum_cpm": 458.7298365209736
+    },
+    {
+     "bulk_gsm": "GSM8570992",
+     "sample_id": "Res-S34",
+     "geo": "male",
+     "bulk_sex_call": "female",
+     "bulk_XIST_cpm": 1247.143948508534,
+     "bulk_Ysum_cpm": 1.5057275617858994
+    }
+   ]
+  }
+ }
+}

paper-releases/20260928/diffusion/data/cohorts/ye2026_sepsis/PREPARE.json

@@ -0,0 +1,109 @@
+{
+ "schema": "pbisc_sdd.ft_intradataset.conditions.v1",
+ "dataset": "ye2026_sepsis",
+ "written_utc": "2026-09-27T06:17:50.556291+00:00",
+ "features_sha256": "0cfda4b0cf1caf5e5319d071697c228d894e992fd090e2b3ed450bd6c9887d46",
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+ "cells_per_bulk": 1500,
+ "recipe_k": 1000,
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+ "builder_sha256": "e818d69e6801b5699579db7fc450590a266708d1fc2d544743e8624c9ee6a30a",
+ "files": {
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+  "4": {
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+   },
+   "alpha_genes_estimated": 11599
+  }
+ },
+ "checks": {}
+}