title: slide3_ptK_tubules_MCD

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: RBE DMSO DMSO Replicate 1

status: Public on Apr 30 2025

type: SRA

city: Chapel Hill

first: John

middle: P.

last: Morris IV

state: NC

address: 450 West Drive, 32-048 Lineberger Comprehensive Cancer Center

department: Pharmacology, Lineberger Comprehensive Cancer Center, UNC School of Medicine

country: USA

institute: University of North Carolina at Chapel Hill

library_source: transcriptomic

data_processing:
Fastq Files were processed using Partek Flow Web Software Version 10.0.23.0720.
Bases were trimmed to min quality level (Phred) of 20 from the 3' end and minimum read length threshold was set to 25 bp.
Reads were mapped with STAR - 2.7.8a to hg19.
Reads were counted using HTSeq - 0.11.0.
Reads were normalized with DESeq2 filtering out features with lowest average coverage less than 1.0 and significance was determined using correction for multiple testing with the FDR step-up adjusted p-value.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Liver/Bile Duct

growth_protocol: RBE cell lines were passaged in sterile tissue culture plates containing RPMI media supplemented with 10% FBS (Gemini) and 1% Penicillin Streptomycin in a humidified incubator at 5% CO2 and 37 C.

extract_protocol:
Cells were scraped into lysis buffer and homogenized using QIAShredders (Qiagen). RNA was extracted using the RNeasy mini kit.
The mRNA library preparation (poly A enrichment) was performed with Novogene Co. polyA capture was used to isolate mRNAs followed by cDNA preparation with reverse transcription.
RNA-seq with Novogene
NovaSeq PE150

treatment_protocol: RBE cholangiocarcinoma cells were treated with 5 uM AG-120 for 22 days to block production of 2-HG followed by activation of p53 using 5 uM MDM2 inhibitor Nutlin for 72 hours.

tag: tissue

value: Liver/Bile Duct

tag: cell line

value: RBE

tag: treatment

value: 22 days of 5 uM DMSO


title: slide3_ptK_glomerulus_MCD_rep1

city: Seattle

first: Shreeram

last: Akilesh

state: WA

address: 1959 NE Pacific St, Box 356100

department: Laboratory Medicine and Pathology

institute: University of Washington

library_source: other

data_processing:
Illumina BaseSpace FASTQ Generation
Nanostring GeoMx NGS Pipeline Version 2.0.21
Assembly: Not applicable, sequences mapped to Nanostring directory of probe-gene associations
Supplementary files format and content: .dcc, digital count files for input into GeoMx DSP. Each .dcc file represents counts from one region of interest (ROI)
Supplementary files format and content: A .png overview of the entire slide with ROI outlines and numbers
Library strategy: Spatial Transcriptomics

molecule: other

source_name: Kidney

extract_protocol:
Nanostring pretreatment for GeoMx DSP = HIER + proteinase K 1µg/ml
Nanostring GeoMx DSP SeqCode H
Nanostring GeoMx DSP readout (2x27bp with standard 8bp indexes)

value: Kidney

tag: donor

value: K

tag: geomx dsp_probe_set

tag: disease

value: MCD

tag: slide number

tag: roi histology

value: glomerulus


title: RBE AG-120 DMSO Replicate 3

value: 22 days of 5 uM AG-120


title: RBE AG-120 Nutlin Replicate 2

value: 22 days of 5 uM AG-120 + 72 hours of 5 uM Nutlin


title: RBE AG-120 DMSO Replicate 2


title: slide3_ptJ_glomerulus_Normal_rep7

value: J

value: Normal


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1005

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

description: The rows in 'counts.txt' and 'rpkms.txt' are genes and the columns are the cell ids ('Cell_001', 'Cell_002', 'Cell_003', 'Cell_004', 'Cell_005', 'Cell_006', 'Cell_007', 'Cell_008', 'Cell_009', 'Cell_010', 'Cell_011', 'Cell_012', 'Cell_013', 'Cell_014', 'Cell_015', 'Cell_016', 'Cell_017', 'Cell_018', 'Cell_019', 'Cell_020', 'Cell_021', 'Cell_022', 'Cell_023', 'Cell_024', 'Cell_025', 'Cell_026', 'Cell_027', 'Cell_028', 'Cell_029', 'Cell_030', 'Cell_031', 'Cell_032', 'Cell_033', 'Cell_034', 'Cell_035', 'Cell_036', 'Cell_037', 'Cell_038', 'Cell_039', 'Cell_040', 'Cell_041', 'Cell_042', 'Cell_043', 'Cell_044', 'Cell_045', 'Cell_046', 'Cell_047', 'Cell_048', 'Cell_049', 'Cell_050', 'Cell_051', 'Cell_052', 'Cell_053', 'Cell_054', 'Cell_055', 'Cell_056', 'Cell_057', 'Cell_058', 'Cell_059', 'Cell_060', 'Cell_061', 'Cell_062', 'Cell_063', 'Cell_064', 'Cell_065', 'Cell_066', 'Cell_067', 'Cell_068', 'Cell_069', 'Cell_070', 'Cell_071', 'Cell_072', 'Cell_073', 'Cell_074', 'Cell_075', 'Cell_076', 'Cell_077', 'Cell_078', 'Cell_079', 'Cell_080', 'Cell_081', 'Cell_082', 'Cell_083', 'Cell_084', 'Cell_085', 'Cell_086', 'Cell_087', 'Cell_088', 'Cell_089', 'Cell_090', 'Cell_091', 'Cell_092', 'Cell_093', 'Cell_094', 'Cell_095', 'Cell_096', 'Cell_097', 'Cell_098', 'Cell_099', 'Cell_100', 'Cell_101', 'Cell_102', 'Cell_103', 'Cell_104', 'Cell_105', 'Cell_106', 'Cell_107', 'Cell_108', 'Cell_109', 'Cell_110', 'Cell_111', 'Cell_112', 'Cell_113', 'Cell_114', 'Cell_115', 'Cell_116', 'Cell_117', 'Cell_118', 'Cell_119', 'Cell_120', 'Cell_121', 'Cell_122', 'Cell_123', 'Cell_124', 'Cell_125', 'Cell_126', 'Cell_127', 'Cell_128', 'Cell_129', 'Cell_130', 'Cell_131', 'Cell_132', 'Cell_133', 'Cell_134', 'Cell_135', 'Cell_136', 'Cell_137', 'Cell_138', 'Cell_139', 'Cell_140', 'Cell_141', 'Cell_142', 'Cell_143', 'Cell_144', 'Cell_145', 'Cell_146', 'Cell_147', 'Cell_148', 'Cell_149', 'Cell_150', 'Cell_151', 'Cell_152', 'Cell_153', 'Cell_154', 'Cell_155', 'Cell_156', 'Cell_157', 'Cell_158', 'Cell_159', 'Cell_160', 'Cell_161', 'Cell_162', 'Cell_163', 'Cell_164', 'Cell_165', 'Cell_166', 'Cell_167', 'Cell_168', 'Cell_169', 'Cell_170', 'Cell_171', 'Cell_172', 'Cell_173', 'Cell_174', 'Cell_175', 'Cell_176', 'Cell_177', 'Cell_178', 'Cell_179', 'Cell_180', 'Cell_181', 'Cell_182', 'Cell_183', 'Cell_184', 'Cell_185', 'Cell_186', 'Cell_187', 'Cell_188', 'Cell_189', 'Cell_190', 'Cell_191', 'Cell_192', 'Cell_193', 'Cell_194', 'Cell_195', 'Cell_196', 'Cell_197', 'Cell_198', 'Cell_199', 'Cell_200', 'Cell_201', 'Cell_202', 'Cell_203', 'Cell_204', 'Cell_205', 'Cell_206', 'Cell_207', 'Cell_208', 'Cell_209', 'Cell_210', 'Cell_211', 'Cell_212', 'Cell_213', 'Cell_214', 'Cell_215', 'Cell_216', 'Cell_217', 'Cell_218', 'Cell_219', 'Cell_220', 'Cell_221', 'Cell_222', 'Cell_223', 'Cell_224', 'Cell_225', 'Cell_226', 'Cell_227', 'Cell_228', 'Cell_229', 'Cell_230', 'Cell_231', 'Cell_232', 'Cell_233', 'Cell_234', 'Cell_235', 'Cell_236', 'Cell_237', 'Cell_238', 'Cell_239', 'Cell_240', 'Cell_241', 'Cell_242', 'Cell_243', 'Cell_244', 'Cell_245', 'Cell_246', 'Cell_247', 'Cell_248', 'Cell_249', 'Cell_250', 'Cell_251', 'Cell_252', 'Cell_253', 'Cell_254', 'Cell_255', 'Cell_256', 'Cell_257', 'Cell_258', 'Cell_259', 'Cell_260', 'Cell_261', 'Cell_262', 'Cell_263', 'Cell_264', 'Cell_265', 'Cell_266', 'Cell_267', 'Cell_268', 'Cell_269', 'Cell_270', 'Cell_271', 'Cell_272', 'Cell_273', 'Cell_274', 'Cell_275', 'Cell_276', 'Cell_277', 'Cell_278', 'Cell_279', 'Cell_280', 'Cell_281', 'Cell_282', 'Cell_283', 'Cell_284', 'Cell_285', 'Cell_286', 'Cell_287', 'Cell_288', 'Cell_289', 'Cell_290', 'Cell_291', 'Cell_292', 'Cell_293', 'Cell_294', 'Cell_295', 'Cell_296', 'Cell_297', 'Cell_298', 'Cell_299', 'Cell_300', 'Cell_301', 'Cell_302', 'Cell_303', 'Cell_304', 'Cell_305', 'Cell_306', 'Cell_307', 'Cell_308', 'Cell_309', 'Cell_310', 'Cell_311', 'Cell_312', 'Cell_313', 'Cell_314', 'Cell_315', 'Cell_316', 'Cell_317', 'Cell_318', 'Cell_319', 'Cell_320', 'Cell_321', 'Cell_322', 'Cell_323', 'Cell_324', 'Cell_325', 'Cell_326', 'Cell_327', 'Cell_328', 'Cell_329', 'Cell_330', 'Cell_331', 'Cell_332', 'Cell_333', 'Cell_334', 'Cell_335', 'Cell_336', 'Cell_337', 'Cell_338', 'Cell_339', 'Cell_340', 'Cell_341', 'Cell_342', 'Cell_343', 'Cell_344', 'Cell_345', 'Cell_346', 'Cell_347', 'Cell_348', 'Cell_349', 'Cell_350', 'Cell_351', 'Cell_352', 'Cell_353', 'Cell_354', 'Cell_355', 'Cell_356', 'Cell_357', 'Cell_358', 'Cell_359', 'Cell_360', 'Cell_361', 'Cell_362', 'Cell_363', 'Cell_364', 'Cell_365', 'Cell_366', 'Cell_367', 'Cell_368', 'Cell_369', 'Cell_370', 'Cell_371', 'Cell_372', 'Cell_373', 'Cell_374', 'Cell_375', 'Cell_376', 'Cell_377', 'Cell_378', 'Cell_379', 'Cell_380', 'Cell_381', 'Cell_382', 'Cell_383', 'Cell_384', 'Cell_385', 'Cell_386', 'Cell_387', 'Cell_388', 'Cell_389', 'Cell_390', 'Cell_391', 'Cell_392', 'Cell_393', 'Cell_394', 'Cell_395', 'Cell_396', 'Cell_397', 'Cell_398', 'Cell_399', 'Cell_400', 'Cell_401', 'Cell_402', 'Cell_403', 'Cell_404', 'Cell_405', 'Cell_406', 'Cell_407', 'Cell_408', 'Cell_409', 'Cell_410', 'Cell_411', 'Cell_412', 'Cell_413', 'Cell_414', 'Cell_415', 'Cell_416', 'Cell_417', 'Cell_418', 'Cell_419', 'Cell_420', 'Cell_421', 'Cell_422', 'Cell_423', 'Cell_424', 'Cell_425', 'Cell_426', 'Cell_427', 'Cell_428', 'Cell_429', 'Cell_430', 'Cell_431', 'Cell_432', 'Cell_433', 'Cell_434', 'Cell_435', 'Cell_436', 'Cell_437', 'Cell_438', 'Cell_439', 'Cell_440', 'Cell_441', 'Cell_442', 'Cell_443', 'Cell_444', 'Cell_445', 'Cell_446', 'Cell_447', 'Cell_448', 'Cell_449', 'Cell_450', 'Cell_451', 'Cell_452', 'Cell_453', 'Cell_454', 'Cell_455', 'Cell_456', 'Cell_457', 'Cell_458', 'Cell_459', 'Cell_460', 'Cell_461', 'Cell_462', 'Cell_463', 'Cell_464', 'Cell_465', 'Cell_466', 'Cell_467', 'Cell_468', 'Cell_469', 'Cell_470', 'Cell_471', 'Cell_472', 'Cell_473', 'Cell_474', 'Cell_475', 'Cell_476', 'Cell_477', 'Cell_478', 'Cell_479', 'Cell_480', 'Cell_481', 'Cell_482', 'Cell_483', 'Cell_484', 'Cell_485', 'Cell_486', 'Cell_487', 'Cell_488', 'Cell_489', 'Cell_490', 'Cell_491', 'Cell_492', 'Cell_493', 'Cell_494', 'Cell_495', 'Cell_496', 'Cell_497', 'Cell_498', 'Cell_499', 'Cell_500', 'Cell_501', 'Cell_502', 'Cell_503', 'Cell_504', 'Cell_505', 'Cell_506', 'Cell_507', 'Cell_508', 'Cell_509', 'Cell_510', 'Cell_511', 'Cell_512', 'Cell_513', 'Cell_514', 'Cell_515', 'Cell_516', 'Cell_517', 'Cell_518', 'Cell_519', 'Cell_520', 'Cell_521', 'Cell_522', 'Cell_523', 'Cell_524', 'Cell_525', 'Cell_526', 'Cell_527', 'Cell_528', 'Cell_529', 'Cell_530', 'Cell_531', 'Cell_532', 'Cell_533', 'Cell_534', 'Cell_535', 'Cell_536', 'Cell_537', 'Cell_538', 'Cell_539', 'Cell_540', 'Cell_541', 'Cell_542', 'Cell_543', 'Cell_544', 'Cell_545', 'Cell_546', 'Cell_547', 'Cell_548', 'Cell_549', 'Cell_550', 'Cell_551', 'Cell_552', 'Cell_553', 'Cell_554', 'Cell_555', 'Cell_556', 'Cell_557', 'Cell_558', 'Cell_559', 'Cell_560', 'Cell_561', 'Cell_562', 'Cell_563', 'Cell_564', 'Cell_565', 'Cell_566', 'Cell_567', 'Cell_568', 'Cell_569', 'Cell_570', 'Cell_571', 'Cell_572', 'Cell_573', 'Cell_574', 'Cell_575', 'Cell_576', 'Cell_577', 'Cell_578', 'Cell_579', 'Cell_580', 'Cell_581', 'Cell_582', 'Cell_583', 'Cell_584', 'Cell_585', 'Cell_586', 'Cell_587', 'Cell_588', 'Cell_589', 'Cell_590', 'Cell_591', 'Cell_592', 'Cell_593', 'Cell_594', 'Cell_595', 'Cell_596', 'Cell_597', 'Cell_598', 'Cell_599', 'Cell_600', 'Cell_601', 'Cell_602', 'Cell_603', 'Cell_604', 'Cell_605', 'Cell_606', 'Cell_607', 'Cell_608', 'Cell_609', 'Cell_610', 'Cell_611', 'Cell_612', 'Cell_613', 'Cell_614', 'Cell_615', 'Cell_616', 'Cell_617', 'Cell_618', 'Cell_619', 'Cell_620', 'Cell_621', 'Cell_622', 'Cell_623', 'Cell_624', 'Cell_625', 'Cell_626', 'Cell_627', 'Cell_628', 'Cell_629', 'Cell_630', 'Cell_631', 'Cell_632', 'Cell_633', 'Cell_634', 'Cell_635', 'Cell_636', 'Cell_637', 'Cell_638', 'Cell_639', 'Cell_640', 'Cell_641', 'Cell_642', 'Cell_643', 'Cell_644', 'Cell_645', 'Cell_646', 'Cell_647', 'Cell_648', 'Cell_649', 'Cell_650', 'Cell_651', 'Cell_652', 'Cell_653', 'Cell_654', 'Cell_655', 'Cell_656', 'Cell_657', 'Cell_658', 'Cell_659', 'Cell_660', 'Cell_661', 'Cell_662', 'Cell_663', 'Cell_664', 'Cell_665', 'Cell_666', 'Cell_667', 'Cell_668', 'Cell_669', 'Cell_670', 'Cell_671', 'Cell_672', 'Cell_673', 'Cell_674', 'Cell_675', 'Cell_676', 'Cell_677', 'Cell_678', 'Cell_679', 'Cell_680', 'Cell_681', 'Cell_682', 'Cell_683', 'Cell_684', 'Cell_685', 'Cell_686', 'Cell_687', 'Cell_688', 'Cell_689', 'Cell_690', 'Cell_691', 'Cell_692', 'Cell_693', 'Cell_694', 'Cell_695', 'Cell_696', 'Cell_697', 'Cell_698', 'Cell_699', 'Cell_700', 'Cell_701', 'Cell_702', 'Cell_703', 'Cell_704', 'Cell_705', 'Cell_706', 'Cell_707', 'Cell_708', 'Cell_709', 'Cell_710', 'Cell_711', 'Cell_712', 'Cell_713', 'Cell_714', 'Cell_715', 'Cell_716', 'Cell_717', 'Cell_718', 'Cell_719', 'Cell_720', 'Cell_721', 'Cell_722', 'Cell_723', 'Cell_724', 'Cell_725', 'Cell_726', 'Cell_727', 'Cell_728', 'Cell_729', 'Cell_730', 'Cell_731', 'Cell_732', 'Cell_733', 'Cell_734', 'Cell_735', 'Cell_736', 'Cell_737', 'Cell_738', 'Cell_739', 'Cell_740', 'Cell_741', 'Cell_742', 'Cell_743', 'Cell_744', 'Cell_745', 'Cell_746', 'Cell_747', 'Cell_748', 'Cell_749', 'Cell_750', 'Cell_751', 'Cell_752', 'Cell_753', 'Cell_754', 'Cell_755', 'Cell_756', 'Cell_757', 'Cell_758', 'Cell_759', 'Cell_760', 'Cell_761', 'Cell_762', 'Cell_763', 'Cell_764', 'Cell_765', 'Cell_766', 'Cell_767', 'Cell_768', 'Cell_769', 'Cell_770', 'Cell_771', 'Cell_772', 'Cell_773', 'Cell_774', 'Cell_775', 'Cell_776', 'Cell_777', 'Cell_778', 'Cell_779', 'Cell_780', 'Cell_781', 'Cell_782', 'Cell_783', 'Cell_784', 'Cell_785', 'Cell_786', 'Cell_787', 'Cell_788', 'Cell_789', 'Cell_790', 'Cell_791', 'Cell_792', 'Cell_793', 'Cell_794', 'Cell_795', 'Cell_796', 'Cell_797', 'Cell_798', 'Cell_799', 'Cell_800', 'Cell_801', 'Cell_802', 'Cell_803', 'Cell_804', 'Cell_805', 'Cell_806', 'Cell_807', 'Cell_808', 'Cell_809', 'Cell_810', 'Cell_811', 'Cell_812', 'Cell_813', 'Cell_814', 'Cell_815', 'Cell_816', 'Cell_817', 'Cell_818', 'Cell_819', 'Cell_820', 'Cell_821', 'Cell_822', 'Cell_823', 'Cell_824', 'Cell_825', 'Cell_826', 'Cell_827', 'Cell_828', 'Cell_829', 'Cell_830', 'Cell_831', 'Cell_832', 'Cell_833', 'Cell_834', 'Cell_835', 'Cell_836', 'Cell_837', 'Cell_838', 'Cell_839', 'Cell_840', 'Cell_841', 'Cell_842', 'Cell_843', 'Cell_844', 'Cell_845', 'Cell_846', 'Cell_847', 'Cell_848', 'Cell_849', 'Cell_850', 'Cell_851', 'Cell_852', 'Cell_853', 'Cell_854', 'Cell_855', 'Cell_856', 'Cell_857', 'Cell_858', 'Cell_859', 'Cell_860', 'Cell_861', 'Cell_862', 'Cell_863', 'Cell_864', 'Cell_865', 'Cell_866', 'Cell_867', 'Cell_868', 'Cell_869', 'Cell_870', 'Cell_871', 'Cell_872', 'Cell_873', 'Cell_874', 'Cell_875', 'Cell_876', 'Cell_877', 'Cell_878', 'Cell_879', 'Cell_880', 'Cell_881', 'Cell_882', 'Cell_883', 'Cell_884', 'Cell_885', 'Cell_886', 'Cell_887', 'Cell_888', 'Cell_889', 'Cell_890', 'Cell_891', 'Cell_892', 'Cell_893', 'Cell_894', 'Cell_895', 'Cell_896', 'Cell_897', 'Cell_898', 'Cell_899', 'Cell_900', 'Cell_901', 'Cell_902', 'Cell_903', 'Cell_904', 'Cell_905', 'Cell_906', 'Cell_907', 'Cell_908', 'Cell_909', 'Cell_910', 'Cell_911', 'Cell_912', 'Cell_913', 'Cell_914', 'Cell_915', 'Cell_916', 'Cell_917', 'Cell_918', 'Cell_919', 'Cell_920', 'Cell_921', 'Cell_922', 'Cell_923', 'Cell_924', 'Cell_925', 'Cell_926', 'Cell_927', 'Cell_928', 'Cell_929', 'Cell_930', 'Cell_931', 'Cell_932', 'Cell_933', 'Cell_934', 'Cell_935', 'Cell_936', 'Cell_937', 'Cell_938', 'Cell_939', 'Cell_940', 'Cell_941', 'Cell_942', 'Cell_943', 'Cell_944', 'Cell_945', 'Cell_946', 'Cell_947', 'Cell_948', 'Cell_949', 'Cell_950', 'Cell_951', 'Cell_952', 'Cell_953', 'Cell_954', 'Cell_955', 'Cell_956', 'Cell_957', 'Cell_958', 'Cell_959', 'Cell_960', 'Cell_961', 'Cell_962', 'Cell_963', 'Cell_964', 'Cell_965', 'Cell_966', 'Cell_967', 'Cell_968', 'Cell_969', 'Cell_970', 'Cell_971', 'Cell_972', 'Cell_973', 'Cell_974', 'Cell_975', 'Cell_976', 'Cell_977', 'Cell_978', 'Cell_979', 'Cell_980', 'Cell_981', 'Cell_982', 'Cell_983', 'Cell_984', 'Cell_985', 'Cell_986', 'Cell_987', 'Cell_988', 'Cell_989', 'Cell_990', 'Cell_991', 'Cell_992', 'Cell_993', 'Cell_994', 'Cell_995', 'Cell_996', 'Cell_997', 'Cell_998', 'Cell_999', 'Cell_1000', 'Cell_1001', 'Cell_1002', 'Cell_1003', 'Cell_1004', 'Cell_1005', 'Cell_1006', 'Cell_1007', 'Cell_1008', 'Cell_1009', 'Cell_1010', 'Cell_1011', 'Cell_1012', 'Cell_1013', 'Cell_1014', 'Cell_1015', 'Cell_1016', 'Cell_1017', 'Cell_1018', 'Cell_1019', 'Cell_1020', 'Cell_1021', 'Cell_1022', 'Cell_1023', 'Cell_1024', 'Cell_1025', 'Cell_1026', 'Cell_1027', 'Cell_1028', 'Cell_1029', 'Cell_1030', 'Cell_1031', 'Cell_1032', 'Cell_1033', 'Cell_1034', 'Cell_1035', 'Cell_1036', 'Cell_1037', 'Cell_1038', 'Cell_1039', 'Cell_1040', 'Cell_1041', 'Cell_1042', 'Cell_1043', 'Cell_1044', 'Cell_1045', 'Cell_1046', 'Cell_1047', 'Cell_1048', 'Cell_1049', 'Cell_1050', 'Cell_1051', 'Cell_1052', 'Cell_1053', 'Cell_1054', 'Cell_1055', 'Cell_1056', 'Cell_1057', 'Cell_1058', 'Cell_1059', 'Cell_1060', 'Cell_1061', 'Cell_1062', 'Cell_1063', 'Cell_1064', 'Cell_1065', 'Cell_1066', 'Cell_1067', 'Cell_1068', 'Cell_1069', 'Cell_1070', 'Cell_1071', 'Cell_1072', 'Cell_1073', 'Cell_1074', 'Cell_1075', 'Cell_1076', 'Cell_1077', 'Cell_1078', 'Cell_1079', 'Cell_1080', 'Cell_1081', 'Cell_1082', 'Cell_1083', 'Cell_1084', 'Cell_1085', 'Cell_1086', 'Cell_1087', 'Cell_1088', 'Cell_1089', 'Cell_1090', 'Cell_1091', 'Cell_1092', 'Cell_1093', 'Cell_1094', 'Cell_1095', 'Cell_1096', 'Cell_1097', 'Cell_1098', 'Cell_1099', 'Cell_1100', 'Cell_1101', 'Cell_1102', 'Cell_1103', 'Cell_1104', 'Cell_1105', 'Cell_1106', 'Cell_1107', 'Cell_1108', 'Cell_1109', 'Cell_1110', 'Cell_1111', 'Cell_1112', 'Cell_1113', 'Cell_1114', 'Cell_1115', 'Cell_1116', 'Cell_1117', 'Cell_1118', 'Cell_1119', 'Cell_1120', 'Cell_1121', 'Cell_1122', 'Cell_1123', 'Cell_1124', 'Cell_1125', 'Cell_1126', 'Cell_1127', 'Cell_1128', 'Cell_1129', 'Cell_1130', 'Cell_1131', 'Cell_1132', 'Cell_1133', 'Cell_1134', 'Cell_1135', 'Cell_1136', 'Cell_1137', 'Cell_1138', 'Cell_1139', 'Cell_1140', 'Cell_1141', 'Cell_1142', 'Cell_1143', 'Cell_1144', 'Cell_1145', 'Cell_1146', 'Cell_1147', 'Cell_1148', 'Cell_1149', 'Cell_1150', 'Cell_1151', 'Cell_1152', 'Cell_1153', 'Cell_1154', 'Cell_1155', 'Cell_1156', 'Cell_1157', 'Cell_1158', 'Cell_1159', 'Cell_1160', 'Cell_1161', 'Cell_1162', 'Cell_1163', 'Cell_1164', 'Cell_1165', 'Cell_1166', 'Cell_1167', 'Cell_1168', 'Cell_1169', 'Cell_1170', 'Cell_1171', 'Cell_1172', 'Cell_1173', 'Cell_1174', 'Cell_1175', 'Cell_1176', 'Cell_1177', 'Cell_1178', 'Cell_1179', 'Cell_1180', 'Cell_1181', 'Cell_1182', 'Cell_1183', 'Cell_1184', 'Cell_1185', 'Cell_1186', 'Cell_1187', 'Cell_1188', 'Cell_1189', 'Cell_1190', 'Cell_1191', 'Cell_1192', 'Cell_1193', 'Cell_1194', 'Cell_1195', 'Cell_1196', 'Cell_1197', 'Cell_1198', 'Cell_1199', 'Cell_1200', 'Cell_1201', 'Cell_1202', 'Cell_1203', 'Cell_1204', 'Cell_1205', 'Cell_1206', 'Cell_1207', 'Cell_1208', 'Cell_1209', 'Cell_1210', 'Cell_1211', 'Cell_1212', 'Cell_1213', 'Cell_1214', 'Cell_1215', 'Cell_1216', 'Cell_1217', 'Cell_1218', 'Cell_1219', 'Cell_1220', 'Cell_1221', 'Cell_1222', 'Cell_1223', 'Cell_1224', 'Cell_1225', 'Cell_1226', 'Cell_1227', 'Cell_1228', 'Cell_1229', 'Cell_1230', 'Cell_1231', 'Cell_1232', 'Cell_1233', 'Cell_1234', 'Cell_1235', 'Cell_1236', 'Cell_1237', 'Cell_1238', 'Cell_1239', 'Cell_1240', 'Cell_1241', 'Cell_1242', 'Cell_1243', 'Cell_1244', 'Cell_1245', 'Cell_1246', 'Cell_1247', 'Cell_1248', 'Cell_1249', 'Cell_1250', 'Cell_1251', 'Cell_1252', 'Cell_1253', 'Cell_1254', 'Cell_1255', 'Cell_1256', 'Cell_1257', 'Cell_1258', 'Cell_1259', 'Cell_1260', 'Cell_1261', 'Cell_1262', 'Cell_1263', 'Cell_1264', 'Cell_1265', 'Cell_1266', 'Cell_1267', 'Cell_1268', 'Cell_1269', 'Cell_1270', 'Cell_1271', 'Cell_1272', 'Cell_1273', 'Cell_1274', 'Cell_1275', 'Cell_1276', 'Cell_1277', 'Cell_1278', 'Cell_1279', 'Cell_1280', 'Cell_1281', 'Cell_1282', 'Cell_1283', 'Cell_1284', 'Cell_1285', 'Cell_1286', 'Cell_1287', 'Cell_1288', 'Cell_1289', 'Cell_1290', 'Cell_1291', 'Cell_1292', 'Cell_1293', 'Cell_1294', 'Cell_1295', 'Cell_1296', 'Cell_1297', 'Cell_1298', 'Cell_1299', 'Cell_1300', 'Cell_1301', 'Cell_1302', 'Cell_1303', 'Cell_1304', 'Cell_1305', 'Cell_1306', 'Cell_1307', 'Cell_1308', 'Cell_1309', 'Cell_1310', 'Cell_1311', 'Cell_1312', 'Cell_1313', 'Cell_1314', 'Cell_1315', 'Cell_1316', 'Cell_1317', 'Cell_1318', 'Cell_1319', 'Cell_1320', 'Cell_1321', 'Cell_1322', 'Cell_1323', 'Cell_1324', 'Cell_1325', 'Cell_1326', 'Cell_1327', 'Cell_1328', 'Cell_1329', 'Cell_1330', 'Cell_1331', 'Cell_1332', 'Cell_1333', 'Cell_1334', 'Cell_1335', 'Cell_1336', 'Cell_1337', 'Cell_1338', 'Cell_1339', 'Cell_1340', 'Cell_1341', 'Cell_1342', 'Cell_1343', 'Cell_1344', 'Cell_1345', 'Cell_1346', 'Cell_1347', 'Cell_1348', 'Cell_1349', 'Cell_1350', 'Cell_1351', 'Cell_1352', 'Cell_1353', 'Cell_1354', 'Cell_1355', 'Cell_1356', 'Cell_1357', 'Cell_1358', 'Cell_1359', 'Cell_1360', 'Cell_1361', 'Cell_1362', 'Cell_1363', 'Cell_1364', 'Cell_1365', 'Cell_1366', 'Cell_1367', 'Cell_1368', 'Cell_1369', 'Cell_1370', 'Cell_1371', 'Cell_1372', 'Cell_1373', 'Cell_1374', 'Cell_1375', 'Cell_1376', 'Cell_1377', 'Cell_1378', 'Cell_1379', 'Cell_1380', 'Cell_1381', 'Cell_1382', 'Cell_1383', 'Cell_1384', 'Cell_1385', 'Cell_1386', 'Cell_1387', 'Cell_1388', 'Cell_1389', 'Cell_1390', 'Cell_1391', 'Cell_1392', 'Cell_1393', 'Cell_1394', 'Cell_1395', 'Cell_1396', 'Cell_1397', 'Cell_1398', 'Cell_1399', 'Cell_1400', 'Cell_1401', 'Cell_1402', 'Cell_1403', 'Cell_1404', 'Cell_1405', 'Cell_1406', 'Cell_1407', 'Cell_1408', 'Cell_1409', 'Cell_1410', 'Cell_1411', 'Cell_1412', 'Cell_1413', 'Cell_1414', 'Cell_1415').

library_source: transcriptomic single cell

data_processing:
Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using bcl2fastq_2.17 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Demultiplexing and quality control was performed at NGI Sweden (Stockholm node) as described for each fastq file. Each fastq file corresponds to a single cell.
Reads were mapped to the human reference genome hg38 using STAR version 2.7.0e (with parameter “-outSAMstrandField=intronMotif”) (Dobin A, et al. 2013. Bioinformatics, PMID: 23104886).
Aligned reads were assigned to genomic locations with the ‘rpkmforgenes.py’ script (Ramsköld  D, et al. 2009. PLoS Comput Biol, PMID: 20011106), using an annotation GTF file from Ensembl version 95 (GRCh38.95) (with parameters “-fulltranscript” and “-rmnameoverlap”).
Cells with less than 100,000 uniquely mapped reads and/or less than 5,000 detected genes were excluded.
Assembly: hg38
Supplementary files format and content: A counts table for all single cells named 'counts.txt'.
Supplementary files format and content: A data table with normalized abundance in reads per kilobase million (rpkm) for all single cells called 'rpkms.txt'.

molecule: polyA RNA

extract_protocol:
Neuronal cultures were treated for 1 hour with 5 µM Y-27632 before dissociation with trypsin or accutase. The cells were resuspended in FACS buffer (HBSS with magnesium and calcium, 2% w/v bovine serum albumine, 2% v/v knockout serum replacement, 2% v/v B-27 supplement, 25 mM D-glucose, 5 µM Y-27632). Single live cells were isolated by fluorescence activated cell sorting (FACS) using Topro-3 iodide and were directly lysed in ice-cold single-cell lysis buffer (0.2% w/v Triton X-100, 0.5% v/v recombinant RNase inhibitor, 10 µM Smarter_oligo-dTVN, 25 mM dNTP, 100 mM DL-dithiothreitol, 4e-5 diluted ERCC spike-in RNAs, in ultrapure water). Protocol according to Schweingruber C, et al. 2023. Methods Mol Biol (PMID: 36264494).
Individual single cell libraries were prepared using the Smart-Seq2 protocol followed by tagmentation using components form the Nextera XT DNA library preparation kit (Illumina). Protocols with adaptations according to Schweingruber C, et al. 2023. Methods Mol Biol (PMID: 36264494).

treatment_protocol:
Heterogenous protocol: Differentiation of adherent cells for two days in medium 1 (200 nM LDN193189, 10 µM SB431542, 25 ng/mL SHH-C25II, 250 nM Purmorphamine, 1 µM retinoic acid), followed by seven days medium 2 (medium 1 with 3 µM CHIR99021), one day of medium d3 (Medium 2 with 200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT-3, and CNTF), and three days of medium 4 (3 µM CHIR99021, 25 ng/mL SHH-C25II, 250 nM Purmorphamine, 1 µM retinoic acid, with 200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT-3, and CNTF). From day 14 onwards, culture was kept in medium 5 (200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT3, and CNTF).
Homogenous protocol according to Nijssen J, et al. 2019. Bioprotocol (PMID: 33654821). The neurons were cultured until day 28.

tag: cell type

value: spinal neuron differentiation

tag: genotype

value: Control

value: heterogenous protocol

tag: sequencing batch


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1004


title: slide3_ptJ_glomerulus_Normal_rep6


title: RBE AG-120 DMSO Replicate 1


title: RBE DMSO Nutlin Replicate 3

value: 22 days of 5 uM DMSO + 72 hours of 5 uM Nutlin


title: slide3_ptK_glomerulus_MCD_rep3


title: SAS, KDM4C, CUT&Tag

city: Hsinchu

first: Wen-Ching

last: Wang

address: NO.101, Sec. 2, Kuang-Fu Road, Hsinchu 300044, Taiwan (R.O.C)

department: Insitute of Molecular & Cellular Biology

country: Taiwan

institute: National Tsing Hua University

library_source: genomic

data_processing:
Basecalls were performed using bcl2fastq v2.20 for Novaseq (Novaseq 6000, PE150) output.
The adapter sequences of Cut and Tag-Seq reads were removed, and reads with quality score > 25 and length > 140 were retained using fastq v0.22.
Cut and Tag-Seq reads were aligned to the UCSC hg38 genome using Bowtie2 v2.4.5 with parameters : --end-to-end --very-sensitive --no-mixed --no-discordant.
The mapping of insert length between 10-700 bp is retained as mapped fragments. The fragments were then normalized by chromosome size of hg38 genome and converted to bedgraph with bedtools v2.30.0.
Output bedgraph files were called peaks by SEACR v1.3 with stringent model of top 0.01 fraction of peaks based on the total signal within peaks. The called peaks were then annotated by ChIPSeeker v1.28.3.
Assembly: bigwig files were generated using bamcoverage and the scores were normalized coverage to 1X or CPM by the effective genome size of hg38.
Supplementary files format and content: bigwig, narrowPeak
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: Oral cavity, tongue

growth_protocol: SAS cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
SAS cells (1x10^6 cells) were seede in a 10-cm dish and incubated at 37℃ overnight. Follow the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD904) protocol for experiment.
The Hyperactive Universal CUT&Tag Assay Kit complemented with TruePrep Index Kit V2 (#TD904, Vazyme Biotech, Nanjing, CN) was used to prepare the libraries. Cut and Tag Libraries construction was initiated using 10^5 cells as starting material. The libraries were amplified with 12 cycles on the thermocycler. Post amplification, the libraries were size selected at 250-600bp in length with DNA Clean Beads (#N411, Vazyme Biotech, Nanjing, CN). The amount and length distribution of the library were quantified using microfluidic electrophoresis with DNA-2500 Kit on MultiNA MCE-202 (Shimadzu, Kyoto, JP).

value: Oral cavity, tongue

value: SAS

value: squamous cell

value: WT

tag: chip antibody


title: slide3_ptJ_glomerulus_Normal_rep5

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1003


title: SAS, IgG, CUT&Tag

value: Bioss (bs-0295P)


title: alveolar macrophages, Printex90, overload, biol rep2

city: Woluwé

first: Jérôme

last: Ambroise

address: Avenue Hippocrate 54

department: Institut de Recherche Expérimentale et Clinique

country: Belgium

institute: Université catholique de Louvain

description:
Human volunteer
P90_O_BR2

data_processing:
All sequencing data were analyzed using the Automated Reproducible MOdular workflow for preprocessing and differential analysis of RNA-seq data (ARMOR v1.5.4) pipeline48.
In this pipeline, reads underwent a quality check using FastQC (Babraham Bioinformatics). Quantification and quality control results were summarized in a MultiQC report before being mapped using Salmon to the transcriptome index which was built using all Ensembl cDNA sequences obtained in the Homo_sapiens.GRCh38.cdna.all.fa file.
Assembly: Homo_sapiens.GRCh38.cdna.all.fa
Supplementary files format and content: excell file with the counts matrix

source_name: Primary alveolar macrophages

growth_protocol: Primary alveolar macrophages were maintained during 5 days in DMEM supplemented with 10% fetal bovine serum (FBS) and 1 % antibiotic-antimycotic (AA) in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. Residual DNA was removed by on-column DNase digestion using the RNAse-Free DNase Set (Qiagen)
The Libraries were prepared starting from 150 ng of total RNA using the KAPA RNA HyperPrep Kit with RiboErase (HMR) (KAPA Biosystems, KK8560) following the manufacturer’s recommendations (KR1351 – v1.16).

treatment_protocol: Cells were exposed during 4 days to control, non-overload or overload conditions of G1-1 or Printex90 particles

value: Primary alveolar macrophages

tag: Sex

value: Male

tag: time

value: 4 days


title: slide3_ptJ_glomerulus_Normal_rep4

value: Kidney

value: glomerulus


title: alveolar macrophages, Printex90, overload, biol rep1

description:
Human volunteer
P90_O_BR1


title: alveolar macrophages, Printex90, non-overload, biol rep3

description:
Human volunteer
P90_NO_BR3


title: slide3_ptJ_tubules_Normal

value: J

value: tubules


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1001

value: spinal neuron differentiation


title: RBE AG-120 Nutlin Replicate 1

value: Liver/Bile Duct

value: RBE

value: 22 days of 5 uM AG-120 + 72 hours of 5 uM Nutlin


title: alveolar macrophages, Printex90, non-overload, biol rep2

description:
Human volunteer
P90_NO_BR2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1000

value: Control

value: heterogenous protocol


title: slide3_ptJ_glomerulus_Normal_rep3

value: Normal


title: alveolar macrophages, Printex90, control, biol rep3

description:
Human volunteer
P90_CTL_BR3


title: alveolar macrophages, Printex90, control, biol rep2

description:
Human volunteer
P90_CTL_BR2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_999


title: alveolar macrophages, Printex90, control, biol rep1

description:
Human volunteer
P90_CTL_BR1


title: slide3_ptJ_glomerulus_Normal_rep2


title: slide3_ptJ_glomerulus_Normal_rep1


title: alveolar macrophages, G1-1, overload, biol rep2

description:
Human volunteer
G1_O_BR2


title: alveolar macrophages, G1-1, overload, biol rep1

description:
Human volunteer
G1_O_BR1


title: slide3_ptI_tubules_Normal

value: I


title: alveolar macrophages, Printex90, overload, biol rep3

description:
Human volunteer
P90_O_BR3


title: alveolar macrophages, G1-1, non-overload, biol rep3

description:
Human volunteer
G1_NO_BR3


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1002


title: alveolar macrophages, G1-1, non-overload, biol rep2

description:
Human volunteer
G1_NO_BR2


title: alveolar macrophages, G1-1, non-overload, biol rep1

description:
Human volunteer
G1_NO_BR1


title: slide3_ptI_glomerulus_Normal_rep7

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_995


title: alveolar macrophages, G1-1, control, biol rep3

description:
Human volunteer
G1_CTL_BR3


title: alveolar macrophages, Printex90, non-overload, biol rep1

description:
Human volunteer
P90_NO_BR1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_994


title: alveolar macrophages, G1-1, control, biol rep2

description:
Human volunteer
G1_CTL_BR2


title: slide3_ptI_glomerulus_Normal_rep5


title: HARP patient 5062, baseline

city: New York City

first: Florencia

last: Schlamp

state: New York

address: 435 East 30th Street

institute: NYU Langone Health

data_processing:
FASTQ files from RNA-sequencing were processed using the Seq-N-Slide pipeline [Dolgalev, https://github.com/igordot/sns]
Read quality was assessed using FASTQC (v0.11.7)
Reads were aligned to the human reference genome hg38 using STAR (v2.6.1) and quantified using Subread featureCounts (v1.6.3).
Normalization and differential expression analyses were performed with R package DESeq2 (v.1.34.0), only genes with at least 0.4 average log2 normalized counts in at least half samples were kept
Assembly: hg38
Supplementary files format and content: space delimited text file with raw counts for each sample

source_name: isolated platelets

extract_protocol:
[Collection ]  Whole blood was collected from MI patients or controls and platelets subsequently isolated.
[Isolation] Platelets were isolated and purified by incubation with microbeads to deplete leukocytes and red blood cells (EasySep™ Human CD45 Depletion Kit II and EasySep™ RBC Depletion Reagent). Isolated platelets were lysed in 500 uL of QIAzol Lysis Reagent (Qiagen) and stored at −80°C.
Platelet RNA was isolated with Direct-zol RNA microspin columns (Zymo Research), and quality and quantity were determined with a Bioanalyzer 2100 (Agilent Technologies).
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA), and libraries were sequenced paired-end on an Illumina NovaSeq 6000

value: isolated platelets

tag: timepoint

value: baseline

tag: angiography report

value: Obstructive

tag: group

value: control

tag: individual

value: HARP patient 5062


title: HARP patient 5061, baseline

value: HARP patient 5061


title: slide3_ptI_glomerulus_Normal_rep4

tag: tissue

value: Kidney

value: glomerulus


title: HARP patient 5057, baseline

value: HARP patient 5057


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_993

tag: cell line

value: spinal neuron differentiation

tag: treatment


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_992


title: slide3_ptI_glomerulus_Normal_rep3

tag: donor

tag: geomx dsp_probe_set


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_998


title: HARP patient 5059, baseline

value: Non-obstructive

value: HARP patient 5059


title: HARP patient 5056, baseline

value: HARP patient 5056


title: HARP patient 5055, baseline

value: HARP patient 5055


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_997

value: Control

value: heterogenous protocol


title: alveolar macrophages, G1-1, overload, biol rep3

description:
Human volunteer
G1_O_BR3

value: Primary alveolar macrophages

value: Male

value: 4 days


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_991


title: slide3_ptI_glomerulus_Normal_rep2

value: I

value: Human NGS Whole Transcriptome Atlas RNA_1.0

tag: disease

value: Normal

tag: slide number


title: HARP patient 5050, baseline

tag: cell type

value: isolated platelets

value: baseline

value: control

value: HARP patient 5050


title: slide3_ptI_glomerulus_Normal_rep1

value: Kidney

tag: roi histology

value: glomerulus


title: slide3_ptI_glomerulus_Normal_rep6


title: HARP patient 5049, baseline

value: Non-obstructive

value: HARP patient 5049


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_989

value: spinal neuron differentiation

tag: genotype

tag: sequencing batch


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_996

value: Control


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_990

value: heterogenous protocol


title: alveolar macrophages, G1-1, control, biol rep1

description:
Human volunteer
G1_CTL_BR1

value: Primary alveolar macrophages

tag: Sex


title: HARP patient 5048, baseline

value: HARP patient 5048


title: slide2_ptH_glomerulus_MCD_rep3

value: H

value: MCD


title: HARP patient 5047, baseline

value: HARP patient 5047


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_988


title: HARP patient 5046, baseline

value: Obstructive

value: HARP patient 5046


title: slide2_ptH_glomerulus_MCD_rep2

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: slide2_ptH_glomerulus_MCD_rep1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_986


title: HARP patient 5038, baseline

value: isolated platelets

value: baseline

value: control

value: HARP patient 5038


title: slide2_ptG_glomerulus_Normal_rep3

value: Kidney

value: G

value: Normal

value: glomerulus


title: HARP patient 5044, baseline

value: Non-obstructive

value: HARP patient 5044


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_985

value: spinal neuron differentiation

value: Control

value: heterogenous protocol


title: HARP patient 5040, baseline

value: HARP patient 5040


title: HARP patient 5037, baseline

value: HARP patient 5037


title: slide2_ptG_glomerulus_Normal_rep2


title: HARP patient 5035, baseline

value: HARP patient 5035


title: HARP patient 5051, baseline

value: HARP patient 5051


title: HARP patient 5039, baseline

value: isolated platelets

value: HARP patient 5039


title: HARP patient 5034, baseline

value: baseline

value: control

value: HARP patient 5034


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_984


title: slide2_ptG_glomerulus_Normal_rep1

value: Kidney

value: G

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: slide2_ptF_glomerulus_MCD_rep7

value: F

value: MCD

value: glomerulus


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_982

value: spinal neuron differentiation

value: Control


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_983

value: heterogenous protocol


title: HARP patient 5033, baseline

value: Obstructive

value: HARP patient 5033


title: HARP patient 5028, baseline

value: Non-obstructive

value: HARP patient 5028


title: slide2_ptF_glomerulus_MCD_rep6


title: HARP patient 5045, baseline

value: isolated platelets

value: HARP patient 5045


title: HARP patient 5027, baseline

value: baseline

value: control

value: HARP patient 5027


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_981


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_987


title: HARP patient 5025, baseline

value: HARP patient 5025


title: slide2_ptH_tubules_MCD

value: Kidney

value: H

value: Human NGS Whole Transcriptome Atlas RNA_1.0

value: tubules


title: HARP patient 5024, baseline

value: HARP patient 5024


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_980

value: spinal neuron differentiation

value: Control


title: HARP patient 5019, baseline

value: HARP patient 5019


title: HARP patient 5017, baseline

value: HARP patient 5017


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_979

value: heterogenous protocol


title: slide2_ptF_glomerulus_MCD_rep5

value: F

value: MCD

value: glomerulus


title: slide2_ptF_glomerulus_MCD_rep4


title: HARP patient 5016, baseline

value: isolated platelets

value: baseline

value: Non-obstructive

value: HARP patient 5016


title: HARP patient 5015, baseline

value: control

value: HARP patient 5015


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_978


title: HARP patient 5029, baseline

value: HARP patient 5029


title: HARP patient 5012, baseline

value: Obstructive

value: HARP patient 5012


title: slide2_ptF_glomerulus_MCD_rep3

value: Kidney

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_977

value: spinal neuron differentiation

value: Control


title: HARP patient 5026, baseline

value: HARP patient 5026


title: slide2_ptF_glomerulus_MCD_rep2

value: F


title: HARP patient 5003, baseline

value: HARP patient 5003


title: HARP patient 5004, baseline

value: HARP patient 5004


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_976

value: heterogenous protocol


title: slide2_ptF_glomerulus_MCD_rep1

value: MCD

value: glomerulus


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_975


title: HARP patient 5002, baseline

value: isolated platelets

value: baseline

value: Non-obstructive

value: HARP patient 5002


title: HARP patient 5009, baseline

value: control

value: HARP patient 5009


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_974


title: slide2_ptG_tubules_Normal

value: Kidney

value: G

value: Normal

value: tubules


title: HARP patient 0245, baseline

value: MI-CAD

value: MI

value: HARP patient 0245


title: HARP patient 5020, baseline

value: HARP patient 5020


title: slide2_ptE_tubules_MCD

value: E

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: HARP patient 0244, baseline

value: MINOCA

value: HARP patient 0244


title: HARP patient 0246, baseline

value: isolated platelets

value: baseline

value: HARP patient 0246


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_973

value: spinal neuron differentiation

value: Control

value: heterogenous protocol


title: HARP patient 5013, baseline

value: Obstructive

value: control

value: HARP patient 5013


title: HARP patient 0242, baseline

value: HARP patient 0242


title: HARP patient 0243, baseline

value: MI-CAD

value: MI

value: HARP patient 0243


title: slide2_ptE_glomerulus_MCD_rep8

value: Kidney

value: E

value: MCD

value: glomerulus


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_972


title: HARP patient 0241, baseline

value: isolated platelets

value: HARP patient 0241


title: HARP patient 0238, baseline

value: baseline

value: MINOCA

value: HARP patient 0238


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_971

value: spinal neuron differentiation

value: Control

value: heterogenous protocol


title: HARP patient 0236, baseline

value: HARP patient 0236


title: HARP patient 0231, followup

value: followup

value: HARP patient 0231


title: slide2_ptE_glomerulus_MCD_rep6

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_970


title: HARP patient 0231, baseline

value: MI


title: HARP patient 0228, followup

value: HARP patient 0228


title: HARP patient 0228, baseline


title: slide2_ptF_tubules_MCD

value: Kidney

value: F

value: tubules


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_969


title: slide2_ptE_glomerulus_MCD_rep5

value: E

value: MCD

value: glomerulus


title: HARP patient 0204, followup

value: isolated platelets

value: MI-CAD

value: HARP patient 0204


title: HARP patient 0201, baseline

value: baseline

value: MINOCA

value: HARP patient 0201


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_968

value: spinal neuron differentiation

value: Control

value: heterogenous protocol


title: HARP patient 0204, baseline

value: MI


title: slide2_ptE_glomerulus_MCD_rep4

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: slide2_ptE_glomerulus_MCD_rep3

value: Kidney


title: HARP patient 0184, baseline

value: HARP patient 0184


title: HARP patient 0184, followup

value: followup


title: HARP patient 0177, baseline

value: HARP patient 0177


title: HARP patient 0174, followup

value: HARP patient 0174


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_350

data_processing:
Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using bcl2fastq_v2.19.1.403 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Demultiplexing and quality control was performed at NGI Sweden (Stockholm node) as described for each fastq file. Each fastq file corresponds to a single cell.
Reads were mapped to the human reference genome hg38 using STAR version 2.7.0e (with parameter “-outSAMstrandField=intronMotif”) (Dobin A, et al. 2013. Bioinformatics, PMID: 23104886).
Aligned reads were assigned to genomic locations with the ‘rpkmforgenes.py’ script (Ramsköld  D, et al. 2009. PLoS Comput Biol, PMID: 20011106), using an annotation GTF file from Ensembl version 95 (GRCh38.95) (with parameters “-fulltranscript” and “-rmnameoverlap”).
Cells with less than 100,000 uniquely mapped reads and/or less than 5,000 detected genes were excluded.
Assembly: hg38
Supplementary files format and content: A counts table for all single cells named 'counts.txt'.
Supplementary files format and content: A data table with normalized abundance in reads per kilobase million (rpkm) for all single cells called 'rpkms.txt'.


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_349


title: slide2_ptE_glomerulus_MCD_rep7

value: E

value: MCD

value: glomerulus


title: slide2_ptE_glomerulus_MCD_rep1


title: HARP patient 0173, followup

value: isolated platelets

value: HARP patient 0173


title: HARP patient 0174, baseline

value: baseline

value: MI-CAD


title: slide2_ptE_glomerulus_MCD_rep2


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_348

value: spinal neuron differentiation


title: HARP patient 0173, baseline

value: MINOCA


title: HARP patient 0136, followup

value: HARP patient 0136


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_347

value: Control

value: heterogenous protocol


title: slide1_ptD_tubules_MCD

value: Kidney

value: D

value: Human NGS Whole Transcriptome Atlas RNA_1.0

value: tubules


title: slide1_ptB_tubules_MCD

value: B


title: HARP patient 0136, baseline

value: MI


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_346


title: HARP patient 0135, baseline

value: HARP patient 0135


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_351


title: HARP patient 0128, followup

value: followup

value: HARP patient 0128


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_345


title: HARP patient 0128, baseline

value: isolated platelets


title: slide1_ptD_glomerulus_MCD_rep4

value: MCD

value: glomerulus


title: HARP patient 0114, followup

value: HARP patient 0114


title: slide1_ptD_glomerulus_MCD_rep3


title: slide1_ptD_glomerulus_MCD_rep2


title: HARP patient 0111, baseline

value: baseline

value: MINOCA

value: HARP patient 0111


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_344

value: spinal neuron differentiation

value: Control

value: heterogenous protocol


title: HARP patient 0109, baseline

value: MI-CAD

value: HARP patient 0109


title: HARP patient 0114, baseline


title: slide1_ptD_glomerulus_MCD_rep1

value: Kidney

value: D

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: HARP patient 0094, baseline

value: MI

value: HARP patient 0094


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_342


title: HARP patient 0088, baseline

value: isolated platelets

value: HARP patient 0088


title: HARP patient 0088, followup

value: followup


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_341


title: slide1_ptC_glomerulus_Normal_rep7

value: C

value: Normal

value: glomerulus


title: HARP patient 0070, baseline

value: baseline

value: HARP patient 0070


title: slide1_ptA_tubules_MCD

value: A

value: MCD

value: tubules


title: HARP patient 0057, baseline

value: MI-CAD

value: HARP patient 0057


title: HARP patient 0058, baseline

value: MINOCA

value: HARP patient 0058


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_340

value: spinal neuron differentiation

value: Control

value: heterogenous protocol


title: HARP patient 0055, baseline

value: isolated platelets

value: MI

value: HARP patient 0055


title: slide1_ptC_glomerulus_Normal_rep6

value: Kidney

value: C

value: Human NGS Whole Transcriptome Atlas RNA_1.0

value: Normal


title: HARP patient 0052, followup

value: followup

value: HARP patient 0052


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_339


title: HARP patient 0052, baseline

value: baseline


title: slide1_ptC_glomerulus_Normal_rep5

value: glomerulus


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_338


title: HARP patient 0049, baseline

value: HARP patient 0049


title: slide1_ptC_glomerulus_Normal_rep4


title: HARP patient 0043, baseline

value: MI-CAD

value: HARP patient 0043


title: HARP patient 0036, baseline

value: MINOCA

value: HARP patient 0036


title: slide1_ptC_glomerulus_Normal_rep3


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_337

value: spinal neuron differentiation

value: Control

value: heterogenous protocol


title: HARP patient 0039, baseline

value: isolated platelets

value: MI

value: HARP patient 0039


title: HARP patient 0035, baseline

value: HARP patient 0035


title: HARP patient 0098, baseline

value: HARP patient 0098


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_336


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_343


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_335


title: HARP patient 0034, baseline

value: HARP patient 0034


title: slide1_ptC_glomerulus_Normal_rep2

value: Kidney

value: C

value: Human NGS Whole Transcriptome Atlas RNA_1.0

value: Normal


title: HARP patient 0033, followup

value: followup

value: MI-CAD

value: HARP patient 0033


title: HARP patient 0033, baseline

value: baseline


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_334

value: spinal neuron differentiation


title: slide1_ptB_glomerulus_MCD_rep6

value: B

value: MCD

value: glomerulus


title: HARP patient 0031, followup

value: isolated platelets

value: MINOCA

value: MI

value: HARP patient 0031


title: slide1_ptC_glomerulus_Normal_rep1


title: HARP patient 0031, baseline


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_333

value: Control

value: heterogenous protocol


title: HARP patient 0002, baseline

value: HARP patient 0002


title: HARP patient 0028, baseline

value: HARP patient 0028


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_332


title: slide1_ptB_glomerulus_MCD_rep5

value: Kidney

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: Keratinocytes, bio rep 2_day2_shSFRP1

city: Irvine

first: Bryan

last: Sun

state: California

address: 829 Medical Sciences Ct

institute: University of California Irvine

data_processing:
Partek flow
Sequence reads were trimmed from both ends with end minimal quality score of 30.
Trimmed reads were aligned to the human reference genome (hg38) using STAR
The aligned reads were applied quantification with annotation of hg38-Ensembl Transcripts release 105.
The gene counts were applied differential analysis by Gene Specific Analysis, with applying lowest average coverage filter of 1.00 and the default normalization methods of CPM (counts per million) and add 0.0001.
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts of each sample

source_name: skin

growth_protocol: Keratinocytes were maintained in 50:50 mixture of Keratinocyte-SFM and 154 media with manufacturer-recommended supplements and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvest using Rneasy mini plus kit (Qiagen). 2 µg of total RNA was used for the construction of sequencing libraries.
RNA library prepartion was conducted at Azenta Life Sciences with PolyA selection, using the NEBNext Ultra II RNA Library Prep Kit for Illumina, with manufacturer's instruction (NEB, Ipswich, MA, USA).

treatment_protocol: Prolferation cells were mainted in subconfluent(d0), differentitition cells were seeded confluent supplementing with 1.2 mM Ca2+ for 2 days(d2)

value: skin

value: primay keratinocytes

value: SFRP1 knockdown

value: differentiation


title: Keratinocytes, bio rep 2_day2_shSCR

value: WT


title: Keratinocytes, bio rep 2_day0_shSCR

value: prolifertion


title: slide1_ptB_glomerulus_MCD_rep3

value: B

value: MCD

value: glomerulus


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_330

value: spinal neuron differentiation


title: Keratinocytes, bio rep 2_day0_shSFRP1


title: Kerationcytes, bio rep 1_day2_shSFRP1


title: Keratinocytes, bio rep 1_day2_shSCR


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_329


title: slide1_ptB_glomerulus_MCD_rep2


title: Keratinocytes, bio rep 1_day0_shSCR


title: slide1_ptB_glomerulus_MCD_rep1


title: slide1_ptA_glomerulus_MCD_rep7

value: A


title: Keratinocytes, bio rep 1_day0_shSFRP1


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_328

value: Control


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_327

value: heterogenous protocol


title: biol rep2_shSFRP1

description: NovaSeq S4

data_processing:
ATAC-seq were analyzed by Partek flow.
ATAC-seq reads were aligned to Homo sapiens(human)-hg38, index Ensemble Transcripts release 105 with alignment algorithm BWA-MEM.
Aligned reads were filtered the duplicates, considering each read end separately, treat the alignment as duplicate if “same start and same sequence”, and keep the alignment with highest mapping score.
The filtered reads were called peaks by MACS with the BAMPE format, effective genome size of Human 2.7e9, and ATAC data type. The peaks were quantified to region with strict paired-end compatibility, with minimum region size of 50 and minimum 50% of bases overlapped with feature.
The Region counts were normalized with the normalization method “Add 1.0 and TPM”. The normalized counts were annotated with homo sapiens (human)-hg38, annotation model Ensembl Transcripts release 105, and report all gene regions per feature.
Assembly: hg38
Supplementary files format and content: narrowPeak

extract_protocol:
5x10e4 cells for each sample were harvest for ATAC assay using Illumina Nextera DNA Sample Preparation Kit (Cat#FC-121-1030).
Transposed DNA fragments were amplified with NEBNext master mix using primer Ad1.noMX, and  primer Ad2.Index with barcode. Library quantification was performed using the NEBNext Library Quant for Illumina

treatment_protocol: Prolferation cells were mainted in subconfluent and harvest after 72 hours of puromycin treatment for selection.

value: primary keratinocytes

value: proliferation


title: biol rep2_SCR1

description: NovaSeq S4


title: biol rep1_shSFRP1

description: NovaSeq S4


title: biol rep1_SCR1

description: NovaSeq S4


title: slide1_ptC_tubules_Normal

value: Kidney

value: C

value: Normal

value: tubules


title: slide1_ptA_glomerulus_MCD_rep6

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: White_blood_cells_patient_14

city: Biberach a.d. Riss

first: Eric

last: Simon

address: Birkendorfer Str. 65

country: Germany

institute: Boehringer Ingelheim Pharma GmbH & Co KG

data_processing:
Demultiplexing and count matrix generation were performed with cellranger v6.0.0. Reads were mapped to reference genome GRCh38.86.
Quality control and clustering were performed in Python using scanpy v1.9.3 with following parameters: Cells with <30 genes or with >30% mitochondrial genes expressed were excluded. Moreover, cells were removed if they deviated from the expected ratio of number of expressed genes by total counts.
Raw read counts were normalized to 10,000 counts and log-transformed.
Doublets were removed using scrublet.
One sample with a very high cell number captured, was randomly downsampled to the next largest sample size (n= 3252) before integration with all samples to avoid its overrepresentation.
Samples were integrated with scVI based on the latent representation derived from top 6,000 highly variable genes using percentage of mitochondrial and ribosomal genes as covariates. Subsequently, a nearest neighbour graph was constructed and graph-based clustering of 29,890 cells that passed quality control was performed at resolution 0.4.
Assembly: GRCh38.86
Supplementary files format and content: counts_RNAseq_sc_WBC.txt: raw counts of all cells passing quality control as txt file
Supplementary files format and content: metadata_RNAseq_sc_WBC.txt: Metadata information for each cell in the final dataset

source_name: White blood cells

extract_protocol:
For scRNA-seq, isolated WBCs were resuspended in ice-cold buffer (1xPBS + 0.04% BSA) and filtered through a 40µm Flowmi® cell filter (Partec). Cell concentration, viability, and aggregate were determined with the NucleoCounter NC-3000 (Chemometec). 15 single-cell suspensions (healthy n=6; NASH n= 9) with an average cell viability of 93% and cell aggregate <1% were employed for scRNA-seq library preparation. Libraries were prepared with the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) according to the manufacturer’s instructions (CG000315 Rev D). Briefly, ~8,250 cells were loaded into a GEM Chip G with a targeted cell recovery of ~5,000 cells and capture and GEM generation was conducted with the Chromium controller followed by reverse transcription and cDNA amplification (13 cycles) as per manufacturer’s instructions (10x Genomics). Qualitative and quantitative measurement of cDNA was conducted with the High Sensitivity NGS Fragment 1-6000bp kit on a 48-channel Fragment Analyzer (Agilent) and 1x dsDNA kit on the Qubit 4 Fluorometer (ThermoFisher), respectively. A total of 50 ng of cDNA per sample was employed for library preparation with an additional 1x SPRISelect bead clean-up (Beckman Coulter) to ensure full removal of primer and adaptor dimers prior to the final elution. Libraries were amplified with 13 PCR cycles and quantified with the 1x dsDNA kit on the Qubit 4 Fluorometer (ThermoFisher) and qualitatively assessed with the High Sensitivity NGS Fragment 1-6000bp Kit on a 96-channel Fragment Analyzer (Agilent). Final libraries were normalized, pooled, spiked in with 5% PhiX Control v3 (Illumina) and sequenced on an Illumina Novaseq 6000 at a depth of ~50,000 reads/cell with dual index, paired end reads (Read parameters: Rd1: 28 bp, Rd2: 10 bp, Rd3: 10 bp Rd4: 91bp)
Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) according to the manufacturer’s instructions (CG000315 Rev D)

value: White blood cells

value: f

value: MAFLD/MASH

tag: id sample

tag: type patient

value: patient

tag: assaytype

value: sc

tag: celltype

value: wbc

tag: condition

tag: batch


title: slide1_ptB_glomerulus_MCD_rep4

tag: tissue

value: B

value: MCD

value: glomerulus


title: White_blood_cells_control_9

value: Control

value: control


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_331

tag: cell line

value: spinal neuron differentiation

tag: treatment

value: heterogenous protocol


title: slide1_ptA_glomerulus_MCD_rep5

value: Kidney

tag: donor

value: A

tag: geomx dsp_probe_set


title: White_blood_cells_patient_36

value: m

tag: disease


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_326

tag: cell type


title: White_blood_cells_control_5


title: White_blood_cells_control_3


title: White_blood_cells_patient_13


title: slide1_ptA_glomerulus_MCD_rep4

value: Human NGS Whole Transcriptome Atlas RNA_1.0

tag: slide number

tag: roi histology


title: slide1_ptA_glomerulus_MCD_rep3


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_324

tag: genotype

tag: sequencing batch


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_322


title: White_blood_cells_control_4

value: White blood cells

tag: Sex

tag: id sample


title: White_blood_cells_patient_10

tag: type patient

tag: assaytype


title: slide1_ptA_glomerulus_MCD_rep2


title: White_blood_cells_control_1

value: f

tag: celltype

tag: condition


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_323


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_321


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_325


title: White_blood_cells_patient_6

tag: tissue

value: MAFLD/MASH

tag: batch


title: slide1_ptA_glomerulus_MCD_rep1


title: White_blood_cells_patient_5

value: patient


title: White_blood_cells_patient_8

value: sc


title: RAM002_day4_Glomeruli_replicate11

data_processing:
Illumina BaseSpace FASTQ Generation
Nanostring GeoMx NGS Pipeline Version 2.0.21
Assembly: Not applicable, sequences mapped to Nanostring directory of probe-gene associations
Supplementary files format and content: .dcc, digital count files for input into GeoMx DSP. Each .dcc file represents counts from one region of interest (ROI)
Supplementary files format and content: A .png overview of the each slide with overlaid ROI outlines and numbers
Library strategy: Spatial Transcriptomics

tag: donor id

value: Glomeruli

value: Human NGS Cancer Transcriptome Atlas RNA_1.0

tag: acquisition day


title: White_blood_cells_control_2

value: wbc


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_319

tag: cell line

tag: treatment


title: RAM002_day4_Glomeruli_replicate9

tag: geomx dsp_probe_set


title: RAM002_day4_Glomeruli_replicate10


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_314

tag: cell type


title: RAM030_day4_Glomeruli_replicate5

tag: roi histology


title: RAM003_day4_Glomeruli_replicate2


title: White_blood_cells_patient_2

tag: disease


title: White_blood_cells_patient_15


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_317

tag: genotype

tag: sequencing batch


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_320


title: RAM007_day4_Glomeruli_replicate7


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_313


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_312


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_318


title: RAM007_day4_Glomeruli_replicate8


title: RAM002_day4_Cortex_replicate7

value: Cortex


title: RAM007_day4_Glomeruli_replicate6


title: RAM030_day4_Glomeruli_replicate4


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_311

value: Control


title: RAM003_day4_Glomeruli_replicate1


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_308


title: RAM030_day4_Glomeruli_replicate3


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_310


title: RAM002_day4_Cortex_replicate6


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_307


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_309


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_316


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_315


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_306


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_305


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_303


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_301


title: RAM003_day4_Medulla_replicate3

value: Medulla


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_302

value: spinal neuron differentiation


title: RAM030_day4_Cortex_replicate3


title: PBS_WT_a_S1

city: Jackson

first: Lavanya

last: Challagundla

state: MS

address: 2500 North State Street

department: Cell and Molecular Biology

description:
1388_PBS_WT_a_S1
1388_PBS_WT_a_S1

data_processing:
The raw reads were aligned using the SALMON aligner (salmon/1.1.0).The transcriptome index was constructed using the Zebrafish reference genome (GRCz11) with corresponding annotation GTF files. The quantification was conducted in mapping-based mode with default settings,generting transcript level abundance estimates.
The differential expression analysis was conducted using the DESeq2 package in R (4.4.1)
Assembly: Danio rerio (GRCz11)
Supplementary files format and content: The gene-level count data, obtained from SALMON

organism: Danio rerio

source_name: whole zebrafish embryos at 3 days post-fertilization

extract_protocol:
RNA was extracted using TRIzol Reagent along with Pure Link RNA Mini Kit (Invitrogen) according to manufacturer instructions and assessed for quality control parameters of minimum concentration and fidelity (i.e. 18S and 28S bands, RIS >9).
Libraries were developed at the University of Mississippi Medical Center’s Molecular and Genomics Core Facility (UMMC MGCF) using the Illumina TruSeq mRNA Stranded Library Prep Kit (IDT for Illumina – TruSeq RNA UD Indexes), quantified with a Qubit fluorimeter (Invitrogen), and assessed for quality and size using the QIAxcel Advanced System as done previously
Samples were pooled  (n=18 pooled samples per library) and sequenced using the NextSeq 2000 P3 200 cycles (paired-end 100bp) on the Illumina NextSeq2000 platform. The run generated ~1.3 billion reads (%QC30=91.77)

value: WT

value: PBS yolk sac injection. 5 hour incubation.


title: PBS_C4_c_S6

institute: University of Mississippi Medical Center

description:
1388_PBS_C4_c_S6
1388_PBS_C4_c_S6

value: whole zebrafish embryos at 3 days post-fertilization


title: PBS_WT_b_S2

description:
1388_PBS_WT_b_S2
1388_PBS_WT_b_S2


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_298

value: heterogenous protocol


title: RAM007_day4_Cortex_replicate4

value: Kidney


title: RAM003_day4_Medulla_replicate2


title: RAM003_day4_Cortex_replicate1


title: RAM030_day4_Cortex_replicate2


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_304


title: RAM002_day4_RCC_replicate3

value: RCC


title: PBS_CA_c_S9

description:
1388_PBS_CA_c_S9
1388_PBS_CA_c_S9


title: PBS_WT_c_S3

description:
1388_PBS_WT_c_S3
1388_PBS_WT_c_S3


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_299


title: RAM007_day4_Cortex_replicate5


title: Liver_patient_36

data_processing:
The bulk RNA-Seq analysis pipeline has been described before (Simon et al., 2023). In brief, reads passing quality control filter were mapped against GRCh38 using STAR (v2.5.2b) aligner.
Gene expression levels were quantified using RSEM (v1.3.0) and featureCounts (v1.5.1).
For quality control FastQC (v0.11.5), picardmetrics (v0.2.4) and dupRadar (v1.2.2) were employed.
Assembly: GRCh38
Supplementary files format and content: counts_RNASeq_Liver.txt: raw counts of all samples as txt file
Supplementary files format and content: tpm_RNASeq_Liver.txt: transcripts per million of all samples as txt file

source_name: Liver

extract_protocol:
Approximately 2 mg of liver biopsies were used for isolation of RNA. Samples were kept in 100 μL of RNAlater buffer and saved at -80°C for further isolation of RNA. In brief, for RNA isolation the RNeasy Lipid Tissue Mini Kit (Qiagen) was used according to manufacturer’s instructions.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina #E7760, together with the NEBNext Poly(A) mRNA Magnetic Isolation Module #E7490 and NEBNext Multiplex Oligos for Illumina #E7600 (New England Biolabs) as per manufacturer’s instructions

value: Liver

tag: Sex

value: m

tag: nas

tag: id sample

value: liver


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_300


title: RAM003_day4_Medulla_replicate1


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_297


title: PBS_C4_b_S5

description:
1388_PBS_C4_b_S5
1388_PBS_C4_b_S5


title: RAM002_day4_RCC_replicate2


title: PBS_CA_b_S8

description:
1388_PBS_CA_b_S8
1388_PBS_CA_b_S8


title: PBS_CA_a_S7

description:
1388_PBS_CA_a_S7
1388_PBS_CA_a_S7


title: PBS_C4_a_S4

description:
1388_PBS_C4_a_S4
1388_PBS_C4_a_S4


title: Liver_patient_15

value: MAFLD/MASH

tag: type patient

value: patient

tag: celltype


title: RAM002_day3_Glomeruli_replicate11

tag: tissue

value: Glomeruli

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: LPS_WT_c_S12

description:
1388_LPS_WT_c_S12
1388_LPS_WT_c_S12

value: LPS (1mg/mL) yolk sac injection. 5 hour incubation.


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_296

value: Control


title: Liver_patient_21

value: f

tag: condition

tag: batch


title: RAM002_day3_Glomeruli_replicate9

tag: donor id

tag: acquisition day


title: LPS_WT_a_S10

description:
1388_LPS_WT_a_S10
1388_LPS_WT_a_S10

tag: treatment


title: Liver_patient_19


title: RAM007_day3_Glomeruli_replicate8

tag: geomx dsp_probe_set


title: RAM002_day4_RCC_replicate1


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_292

tag: cell line

tag: cell type

value: spinal neuron differentiation


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_295


title: LPS_CA_c_S18

description:
1388_LPS_CA_c_S18
1388_LPS_CA_c_S18


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_293


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_291


title: RAM002_day3_Glomeruli_replicate10

tag: roi histology


title: Liver_patient_20

tag: disease


title: LPS_WT_b_S11

description:
1388_LPS_WT_b_S11
1388_LPS_WT_b_S11

tag: genotype

value: WT


title: Liver_patient_16

tag: Sex


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_294

tag: sequencing batch


title: RAM007_day3_Glomeruli_replicate7


title: Liver_patient_13

tag: nas

tag: id sample


title: Liver_patient_11

tag: type patient

tag: celltype


title: RAM007_day3_Glomeruli_replicate6

tag: tissue


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_290


title: LPS_CA_a_S16

description:
1388_LPS_CA_a_S16
1388_LPS_CA_a_S16


title: LPS_CA_b_S17

description:
1388_LPS_CA_b_S17
1388_LPS_CA_b_S17


title: RAM030_day3_Glomeruli_replicate5


title: RAM030_day3_Glomeruli_replicate4


title: LPS_C4_b_S14

description:
1388_LPS_C4_b_S14
1388_LPS_C4_b_S14


title: Liver_patient_17

tag: condition

tag: batch


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_287


title: RAM003_day3_Glomeruli_replicate1

tag: donor id

tag: acquisition day


title: Liver_patient_8


title: Liver_patient_6


title: LPS_C4_c_S15

description:
1388_LPS_C4_c_S15
1388_LPS_C4_c_S15

tag: treatment


title: MEF_WT_Infected_48_h_B2

city: Hyderabad

first: Krishnan

middle: Harnivas

last: Harshan

state: Telangana

address: Uppal Rd, IICT Colony

department: Infectious Diseases Group

country: India

institute: CSIR-CCMB

description:
Library name: Sample 53
Column name in raw_count_data_MEF.csv: MEF_WT_Infected_48_h_B2

data_processing:
Raw sequencing reads were processed with Cutadapt to remove MGI adapters and low-quality sequences. Reads with a quality score below 20 and a length of less than 36 bp were excluded.
The remaining high-quality reads were aligned to the human reference genome (GRCh38) using HISAT2 with default parameters.
Uniquely aligned reads were quantified using the featureCounts function from the Subread package, utilizing a GTF annotation file obtained from Ensembl, which provided read count data for 60,683 genes.
Genes with fewer than 10 total read counts across all samples were filtered out, yielding a final dataset of 36,743 genes for further analysis.
Assembly: GRCh38
Supplementary files format and content: raw_count_data_Huh7.csv file contains raw count data for Sample 1-18
Supplementary files format and content: raw_count_data_MEF.csv file contains raw count data for Sample 19-54

organism: Mus musculus

source_name: MEFs

growth_protocol: Huh7 cells and MEFs were maintained in DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Cellular RNA samples were prepared using an MN NucleoSpin RNA kit
Library preparation was performed using the MGIEasy RNA Library Prep Set (MGI) following the manufacturer’s guidelines. Briefly, 500 ng of total RNA was used as the starting material, and rRNA was depleted using the Ribo-Zero Plus rRNA Depletion Kit (Illumina).

treatment_protocol: Experiment 1: Huh7 cells were either transfected with an Empty Vector control or a plasmid containing Full lengh MAVS. Huh7 cells were also treated with IFN-α or vehicle control at a concentration of 1000 Units/mL before subjecting the cells to Mock-infection or SARS-CoV-2 infection for 24 hours.                                                                                Experiment 2: WT and MAVS KO Mouse Embrynoic Fibroblasts (MEFs) were subjected to either mock-infection or SARS-COV-2 infection for different time points (12, 24 and 48 hours)

tag: cell line

value: MEFs

value: Primary Embryonic Fibroblasts

value: CoV-2 infected 48h

value: Batch 2


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_288

tag: cell type

value: heterogenous protocol


title: RAM002_day3_Cortex_replicate7

value: Kidney

tag: roi histology

value: Cortex

tag: geomx dsp_probe_set


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_286

tag: genotype


title: Liver_patient_12

value: Liver

tag: Sex

tag: disease

value: liver


title: Liver_patient_9

value: m

value: MAFLD/MASH

tag: nas

value: patient


title: MEF_WT_Infected_48_h_B3

description:
Library name: Sample 54
Column name in raw_count_data_MEF.csv: MEF_WT_Infected_48_h_B3

value: Batch 3


title: RAM003_day3_Glomeruli_replicate2

value: Glomeruli

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: MEF_WT_Infected_48_h_B1

description:
Library name: Sample 52
Column name in raw_count_data_MEF.csv: MEF_WT_Infected_48_h_B1

value: Batch 1


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_289

value: spinal neuron differentiation

value: Control

tag: sequencing batch


title: LPS_C4_a_S13

description:
1388_LPS_C4_a_S13
1388_LPS_C4_a_S13

value: whole zebrafish embryos at 3 days post-fertilization

value: LPS (1mg/mL) yolk sac injection. 5 hour incubation.


title: Liver_patient_14

value: f

tag: id sample

tag: type patient


title: RAM030_day3_Glomeruli_replicate3

tag: tissue


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_285

value: heterogenous protocol


title: Liver_patient_4

tag: celltype

tag: condition


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_284


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_283


title: MEF_WT_Mock_48_h_B3

description:
Library name: Sample 51
Column name in raw_count_data_MEF.csv: MEF_WT_Mock_48_h_B3

value: MEFs

value: Primary Embryonic Fibroblasts

value: Mock-infected 48h

value: WT

tag: batch


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_282


title: RAM007_day3_Cortex_replicate5

value: Kidney

tag: donor id

value: Cortex

tag: acquisition day


title: RAM007_day3_Cortex_replicate4


title: Liver_patient_7

value: Liver

value: MAFLD/MASH

value: patient

value: liver


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_280

tag: cell line

tag: treatment


title: OVCAR8_ATG9A_rep2

city: San Francisco

first: Meng

last: Zhang

address: 1450 3rd Street

institute: University of California, San Francisco

data_processing:
The RNA-seq paired-end fastq data generated by Illumina NovaSeq sequencing system were first trimmed to remove adapter sequence using Cutadapt. After adapter trimming, FASTQC was used to evaluate the sequence trimming as well as overall sequence quality. Using splice-aware aligner STAR, RNA-seq reads were aligned onto the Human reference genome build hg38 and exon-exon junctions, according to the known Human gene model annotation from the GENCODE v28.  Based on the reads that can only be mapped to a single genomic location, the gene expression quantification was performed using featurecount function within Rsubread R-package.
Assembly: hg38, gencode 28
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
RNA was extracted from the cells using the Zymo Quick-RNA extraction kit. QuantSeq 3’mRNA-Seq library prep kit FWD for Illumina was used to prepare the library as per the manufacturer’s protocol. Quality control was performed by using the Agilent Bioanalyzer 2100 system and the samples were sequenced in Illumina NovaSeq. The entire set of the experiment was done in two biological replicates.
QuantSeq 3’mRNA-Seq library prep kit FWD for Illumina was used to prepare the library as per the manufacturer’s protocol.

value: ATG9A KO


title: RAM003_day3_Cortex_replicate1

tag: roi histology

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: MEF_KO_Infected_48_h_B1

description:
Library name: Sample 46
Column name in raw_count_data_MEF.csv: MEF_KO_Infected_48_h_B1

tag: cell type

value: CoV-2 infected 48h

value: MAVS KO

value: Batch 1


title: Diff_D3_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_281

value: spinal neuron differentiation

tag: genotype

value: Control


title: RAM030_day3_Cortex_replicate2

tag: geomx dsp_probe_set


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_277

data_processing:
Clustering was done by 'cBot' and samples were sequenced on HiSeq2500 (HiSeq Control Software 2.2.58/RTA 1.18.64) with a 1x51 setup using 'HiSeq SBS Kit v4' chemistry. The Bcl to FastQ conversion was performed using None from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Demultiplexing and quality control was performed at NGI Sweden (Stockholm node) as described for each fastq file. Each fastq file corresponds to a single cell.
Reads were mapped to the human reference genome hg38 using STAR version 2.7.0e (with parameter “-outSAMstrandField=intronMotif”) (Dobin A, et al. 2013. Bioinformatics, PMID: 23104886).
Aligned reads were assigned to genomic locations with the ‘rpkmforgenes.py’ script (Ramsköld  D, et al. 2009. PLoS Comput Biol, PMID: 20011106), using an annotation GTF file from Ensembl version 95 (GRCh38.95) (with parameters “-fulltranscript” and “-rmnameoverlap”).
Cells with less than 100,000 uniquely mapped reads and/or less than 5,000 detected genes were excluded.
Assembly: hg38
Supplementary files format and content: A counts table for all single cells named 'counts.txt'.
Supplementary files format and content: A data table with normalized abundance in reads per kilobase million (rpkm) for all single cells called 'rpkms.txt'.

value: heterogenous protocol


title: Liver_patient_18

tag: Sex

value: f

tag: disease


title: RAM003_day3_Medulla_replicate3

value: Medulla


title: Liver_patient_10

value: m

tag: nas


title: OVCAR8_ATG9A_rep1


title: RAM030_day3_Cortex_replicate3

value: Kidney


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_279

tag: sequencing batch


title: OVCAR8_GAL4_rep2

value: GAL4 KO


title: MEF_KO_Infected_48_h_B3

description:
Library name: Sample 48
Column name in raw_count_data_MEF.csv: MEF_KO_Infected_48_h_B3

value: MEFs

value: Primary Embryonic Fibroblasts

value: Batch 3


title: RAM003_day3_Medulla_replicate2


title: MEF_WT_Mock_48_h_B1

description:
Library name: Sample 49
Column name in raw_count_data_MEF.csv: MEF_WT_Mock_48_h_B1

value: Mock-infected 48h

value: WT


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_278


title: MEF_KO_Mock_48_h_B3

description:
Library name: Sample 45
Column name in raw_count_data_MEF.csv: MEF_KO_Mock_48_h_B3


title: MEF_KO_Infected_48_h_B2

description:
Library name: Sample 47
Column name in raw_count_data_MEF.csv: MEF_KO_Infected_48_h_B2

value: Batch 2


title: RAM002_day3_Cortex_replicate6

value: Cortex

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: OVCAR8_GAL4_rep1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_276


title: MEF_WT_Mock_48_h_B2

description:
Library name: Sample 50
Column name in raw_count_data_MEF.csv: MEF_WT_Mock_48_h_B2


title: RAM003_day3_Medulla_replicate1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_275


title: corneal epithelial stem cells, AdMSC-EVs, 30 μg/ml, biol rep 3

city: Suita

first: Xiaoqin

last: Li

state: Osaka

department: Ophthalmology

country: Japan

institute: Osaka University

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 platform (Illumina).
Validation of sequencing quality was performed using FastQC v.0.11.7, followed by reads trimming via Trimmomatic v.0.38.
Sequenced reads were mapped onto the human hg38 reference genome by HISAT2 v.2.1.0.
The quantification of raw reads mapped to the exon regions was performed by FeatureCounts v.1.6.3.
Assembly: hg38
Supplementary files format and content: Text file includes raw counts for each gene and each sample

source_name: corneal epithelium

growth_protocol: CECs were cultured for three days in corneal epithelium maintenance medium (DMEM/F12 (Thermo Fisher Scientific, Tokyo, Japan), containing 2% B27 supplement (Thermo Fisher Scientific), 10 ng/mL KGF (Wako, Osaka, Japan), and 10 μM Y-27632 (Wako)) in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
RNA was harvested using Sepasol-RNA I Super G (Nacalai Tesque, Inc).
Briefly, the cDNA library was established by NEBNext Ultra Ⅱ Directional RNA Library Prep Kit for Illumina. Sequencing was performed on an Illumina NovaSeq 6000 platform (Illumina).

treatment_protocol: CECs were treated with eithor PBS control or AdMSC-EVs (at concentration of 120 μg/ml or 30 μg/ml) for three days.

value: corneal epithelium

value: corneal epithelial stem cells

value: 30 μg/ml AdMSC-EVs


title: RAM002_day3_RCC_replicate3

value: RCC


title: corneal epithelial stem cells, AdMSC-EVs, 30 μg/ml, biol rep 2


title: corneal epithelial stem cells, AdMSC-EVs, 30 μg/ml, biol rep 1


title: MEF_WT_Infected_24_h_B3

description:
Library name: Sample 42
Column name in raw_count_data_MEF.csv: MEF_WT_Infected_24_h_B3

value: CoV-2 infected 24h


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_273

value: spinal neuron differentiation

value: heterogenous protocol


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_272


title: RAM002_day3_RCC_replicate1

value: Kidney


title: corneal epithelial stem cells, AdMSC-EVs, 120 μg/ml, biol rep 3

value: 120 μg/ml AdMSC-EVs


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_274


title: corneal epithelial stem cells, AdMSC-EVs, 120 μg/ml, biol rep 2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_271


title: MEF_WT_Mock_24_h_B3

description:
Library name: Sample 39
Column name in raw_count_data_MEF.csv: MEF_WT_Mock_24_h_B3

value: MEFs

value: Mock-infected 24h


title: corneal epithelial stem cells, AdMSC-EVs, 120 μg/ml, biol rep 1


title: RAM002_day2_Glomeruli_replicate10

value: Glomeruli


title: MEF_WT_Infected_24_h_B1

description:
Library name: Sample 40
Column name in raw_count_data_MEF.csv: MEF_WT_Infected_24_h_B1

value: Primary Embryonic Fibroblasts

value: Batch 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_270


title: MEF_WT_Mock_24_h_B2

description:
Library name: Sample 38
Column name in raw_count_data_MEF.csv: MEF_WT_Mock_24_h_B2

value: WT

value: Batch 2


title: RAM002_day2_Glomeruli_replicate9

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: corneal epithelial stem cells, PBS, biol rep 3

value: corneal epithelium

value: PBS


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_269


title: MEF_KO_Mock_48_h_B2

description:
Library name: Sample 44
Column name in raw_count_data_MEF.csv: MEF_KO_Mock_48_h_B2

value: Mock-infected 48h

value: MAVS KO


title: MEF_KO_Mock_48_h_B1

description:
Library name: Sample 43
Column name in raw_count_data_MEF.csv: MEF_KO_Mock_48_h_B1


title: MEF_WT_Mock_24_h_B1

description:
Library name: Sample 37
Column name in raw_count_data_MEF.csv: MEF_WT_Mock_24_h_B1


title: corneal epithelial stem cells, PBS, biol rep 2

value: corneal epithelial stem cells


title: RAM002_day3_RCC_replicate2

value: RCC


title: RAM007_day2_Glomeruli_replicate8


title: MEF_WT_Infected_24_h_B2

description:
Library name: Sample 41
Column name in raw_count_data_MEF.csv: MEF_WT_Infected_24_h_B2

value: CoV-2 infected 24h