title: PT id10 tumor tissue

description:
CRC15019T
Ion AmpliSeq Transcriptome

source_name: PMP tumor

value: PMP tumor


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_075

status: Public on Apr 30 2025

type: SRA

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 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'.

molecule: polyA RNA

organism: Homo sapiens

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 line

tag: cell type

value: spinal neuron differentiation

tag: genotype

value: Control

tag: treatment

value: heterogenous protocol

tag: sequencing batch


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_952

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.0/RTA v3.4.4) with a 51nt(Read1)-8nt(Index1)-8nt(Index2)-51nt(Read2) setup using 'NovaSeqXp' workflow in 'S1' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 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: homogenous protocol


title: PT id9 normal tissue

city: Tsukiji

first: Rei

last: Noguchi

state: Tokyo

address: 5-1-1, Chuo-ku, Tokyo, Japan

department: Division of Rare Cancer Research

country: Japan

institute: National Cancer Center Research Institute

description:
CRC15014N
Ion AmpliSeq Transcriptome

library_source: transcriptomic

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program (TMAP).
QC metrics and normalized read counts per gene were obtained using AmpliSeqRNA plug-in v5.2.0.3, a Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: hg19
Supplementary files format and content: A tab-delimited text file includes RPM values for each sample.

molecule: total RNA

source_name: normal colon

extract_protocol:
Tumor and non-tumorous cells were collected from the sections using laser microdissection (LMD 7000, Leica, Benshein, Germany). Total RNAs were extracted using RNeasy Micro Kit (Qiagen, Hilden, Germany).
RNA-seq libraries were prepared with 100 ng of total RNA using an Ion AmpliSeq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific, Waltham, MA) according to manufacturer's instructions. The generated cDNAs were subjected to multiplex amplification with Ion AmpliSeq Transcriptome Human Gene Expression Core Panel containing 18,574 protein-coding RNAs and 2,228 non-coding RNAs. The libraries were sequenced with 100 bp single-end reads on Ion Proton using an Ion PI Sequencing 200 kit v3 and Ion PI Chip v2 (Thermo Fisher Scientific).

tag: tissue

value: normal colon


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_951


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_074


title: PT id9 tumor tissue

description:
CRC15014T
Ion AmpliSeq Transcriptome


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_073


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_950


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_072


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_949


title: PT id8 tumor tissue

description:
CRC14016T
Ion AmpliSeq Transcriptome


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_071


title: PT id8 normal tissue

description:
CRC14016N
Ion AmpliSeq Transcriptome


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_070


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_069


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_947


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_948


title: PT id7 normal tissue

description:
CRC14010N
Ion AmpliSeq Transcriptome


title: PT id7 tumor tissue

description:
CRC14010T
Ion AmpliSeq Transcriptome


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_946


title: PT id6 normal tissue

description:
CRC13014N
Ion AmpliSeq Transcriptome


title: PT id6 tumor tissue

description:
CRC13014T
Ion AmpliSeq Transcriptome


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_068


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_066


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_945


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_067


title: PT id5 normal tissue

description:
CRC15025N
Ion AmpliSeq Transcriptome


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_943


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_944


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_942


title: PT id5 tumor tissue

description:
CRC15025T
Ion AmpliSeq Transcriptome


title: PT id4 normal tissue

description:
CRC15011N
Ion AmpliSeq Transcriptome


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_941


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_063


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_940


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_061


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_062


title: PT id3 normal tissue

description:
CRC15004N
Ion AmpliSeq Transcriptome


title: PT id4 tumor tissue

description:
CRC15011T
Ion AmpliSeq Transcriptome


title: PT id3 tumor tissue

description:
CRC15004T
Ion AmpliSeq Transcriptome


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_938


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_060


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_937


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_064


title: PT id2 normal tissue

description:
CRC14040N
Ion AmpliSeq Transcriptome


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_939


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_059


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_936


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_058


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_065


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_935


title: PT id1 tumor tissue

description:
CRC14002T
Ion AmpliSeq Transcriptome


title: PT id2 tumor tissue

description:
CRC14040T
Ion AmpliSeq Transcriptome


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_933


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_057


title: PT id1 normal tissue

description:
CRC14002N
Ion AmpliSeq Transcriptome


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_055


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_932


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_056


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_931


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_053


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_054


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_930


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_052


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_928


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_929


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_051


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_050


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_927


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_048


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_925


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_049


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_924


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_046


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_934


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_084


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_045


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_047


title: sALS_vehicle

city: Taipei

first: Ya-Ping

last: Yen

address: 128 Academia Road, Section 2, Nankang

department: Institute of molecular biology

country: Taiwan

institute: Academia Sinica

description:
Library name: sALS_vehicle
N517-1_S1

data_processing:
For the gene expression z score analysis (including published data revealed in Supplementary Fig. 1) by aligning raw RNA-seq data to the GRCh38 genome using the STAR aligner. Subsequently, gene expression was estimated using the GenCode v41 gene annotation file (gtf), focusing on gene types categorized as protein_coding and lncRNA. Genes originating from the mitochondrial genome (chrM) were also excluded from further analysis. The expression levels of each gene were then quantified using the salmon tool. Next, differential expression analysis was conducted using the edgeR package. Raw read count information was processed to identify genes showing significant changes in expression across different conditions. The filterByExpr function was applied to remove genes with low expression levels to ensure robust results. The remaining genes were subjected to TMM normalization and dispersion estimation methods to identify differentially expressed genes accurately. Subsequently, genes were categorized as upregulated or downregulated based on fold change values. The expression trends of the same genes across different samples were analyzed by calculating z-scores, allowing for the observation of consistent or divergent expression patterns among compared samples. This analysis pipeline enabled the identification of differentially expressed genes and provided insights into their expression trends across various conditions.
Assembly: GRCh38
Supplementary files format and content: tsv files containing defferential gene feature compare with the control

source_name: iPSC~MNs

growth_protocol: Human iPSCs were differentiated into MNs using an improved protocol (Maury, Y. et al., 2015 )

extract_protocol:
RNA was harvested using Trizol reagent.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: To accelerate MN degeneration, day 31 cultures were switched to N2/B27 medium without BDNF/GDNF, with CPA added for seven days. FB23-2 was co-treated for 15–30 days.

value: iPSC~MNs

value: vehicle


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_922


title: sALS_CPA+FB23-2

description:
Library name: sALS_CPA+FB23-2
N517-3_S3


title: C9ORF72exp_CPA+FB23-2

description:
Library name: C9ORF72exp_CPA+FB23-2
N517-18_S18


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_044


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_921


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_923


title: C9ORF72exp_CPA

description:
Library name: C9ORF72exp_CPA
N517-17_S17

value: CPA


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_919


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_918


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_042


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_041


title: SOD1+/L144F_CPA+FB23-2

description:
Library name: SOD1+/L144F_CPA+FB23-2
N517-12_S12


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_040


title: sALS_CPA

description:
Library name: sALS_CPA
N517-2_S2


title: SOD1+/L144F_vehicle

description:
Library name: SOD1+/L144F_vehicle
N517-10_S10


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_917


title: GSKS32M4M1

city: San Francisco

first: Scot

middle: M

last: Federman

state: CA

address: 499 Illinois St

department: Biochemistry

country: USA

institute: UCSF

description:
Library name: GSKS32M4M1
GSK S32 population M4 M1

library_source: genomic

data_processing:
For each barcoded sample, fastq files were inspected to determine the BC14/BC30 sequence present at the defined location within the sequenced read, using perfect matching. Number of unique barcodes matching the expected barcodes from CloneTracker were counted, as well as numbers derived from earlier cellular stages. The Shannon Index/Maximum/Evenness were calculated for each sample.
Assembly: BC14.txt.gz,BC30.txt.gz
Supplementary files format and content: tab-delimited text file containing raw readcounts for each sample

molecule: genomic DNA

extract_protocol:
Genomic DNA was isolated using Macherey-Nagel kit.  2 ug sample was used for construction for the library.
Library is prepared with NGS Prep Kit for Barcode Libraries in pScribe (CloneTracker XPTM) according to manufacture protocol.

value: iPSC

value: WT


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_926


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_916


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_038


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_037


title: GSKS32M4M2

description:
Library name: GSKS32M4M2
GSK S32 population M4 M2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_915


title: GSKS2HPC15

description:
Library name: GSKS2HPC15
GSK S2 population HPC 15 Million


title: C9ORF72exp_vehicle

description:
Library name: C9ORF72exp_vehicle
N517-16_S16


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_043


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_035


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_036


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_920


title: SDMCW4iMAC1

description:
Library name: SDMCW4iMAC1
Stemcell Technologies Differentiated Week 4 Media C iMacrophage 1 Million


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_912


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_034


title: SDMCW3iMAC125

description:
Library name: SDMCW3iMAC125
Stemcell Technologies Differentiated Week 3 Media C iMacrophage 12.5 Million


title: SOD1+/L144F_CPA

description:
Library name: SOD1+/L144F_CPA
N517-11_S11


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_911


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_910


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_033


title: SDMCW1MCiMAC14

description:
Library name: SDMCW1MCiMAC14
Stemcell Technologies Differentiated Media C Week 1 iMacrophage 14 Milion


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_039


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_032


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_909


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_031


title: SDD16HPC15

description:
Library name: SDD16HPC15
Stemcell Technologies Differentiated Day 16 HPC 15 Millions


title: GSKD20HPC15

description:
Library name: GSKD20HPC15
GSK Day 20 HPC 15 Million


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_908


title: iPSC15

description:
Library name: iPSC15
initial iPSC population 15 Million cells


title: GSKS3D2112

description:
Library name: GSKS3D2112
GSK S3 population Day 21 12 Million


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_914

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', 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'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').


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_913


title: iMac, knockout, rep2

description: Library name: iMac_KO2

data_processing:
Reads were aligned via STAR 2.7.9a to hg38
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw readcounts for each sample

extract_protocol:
RNA samples were isolated with NEB Monarch kit according to manufacture protocol.
RNA library was prepared with Lexogen QuantSeq according to manufacture protocol.

value: iMac

value: SAMHD1 KO


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_029


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_907


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_906


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_028


title: iMac, knockout, rep1

description: Library name: iMac_KO1


title: iMac, wildtype, rep2

description: Library name: iMac_WT2

value: SAMHD1 WT


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_905


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_904


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_026


title: iMac, wildtype, rep1

description: Library name: iMac_WT1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_025


title: IPSC, knockout, rep2

description: Library name: IPSC_KO2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_903


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_024


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_902


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_901


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_899


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_900


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_030


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_022


title: IPSC, wildtype, rep1

description: Library name: IPSC_WT1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_021


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_896


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_897


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_898


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_018


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_016


title: IPSC, wildtype, rep2

description: Library name: IPSC_WT2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_894


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_895


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_017


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_023


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_892


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_020


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_891


title: liver, NaCl (6h) + PBS (2h), replicate 3

city: Gent

first: Steven

last: Timmermans

address: Technologiepark 71

country: Belgium

institute: VIB-UGent

description:
Library name: NaCl_PBS-3
NaCl_PBS-3

data_processing:
Reads were quality checked with fastqc
Reads were aligned to the mm39 reference genome with the STAR aligner (v2.7.10b) and read counts were directly obtained using the "--quantMode GeneCounts" parameter for STAR
Differential expression analysis was done using the DESeq2 package, with the FDR set at 5%
Assembly: mm39
Supplementary files format and content: matrix of raw counts for all samples provided as a tab separated text file

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was isolated with Aurum total RNA mini kit (Biorad) according to the manufacturer’s instructions. RNA concentration was measured, and RNA quality was checked with the Agilent RNA 6000 Pico Kit (Agilent Technologies)
library preparation was done with the illumina truseq stranded mRNA library kit according to the manufacturers instructions

treatment_protocol: Mice were given 300mg/kg FeSO4 or 0.9% sline solution of equal volume. 6 hours afterwards they were treated with 10 mg/kg DEX or an equal volume of PBS. Livers were isolated 2 hours later (8 hours total treatment time)

value: liver

tag: treatment 1

tag: treatment 2

value: PBS (2h)


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_014


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_890


title: IPSC, knockout, rep1

description: Library name: IPSC_KO1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_893


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_015


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_027


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_019


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_889


title: liver, NaCl (6h) + PBS (2h), replicate 1

description:
Library name: NaCl_PBS-1
NaCl_PBS-1


title: liver, NaCl (6h) + PBS (2h), replicate 2

description:
Library name: NaCl_PBS-2
NaCl_PBS-2


title: liver, NaCl (6h) + dexamethasone (2h), replicate 3

description:
Library name: NaCl_DEX-3
NaCl_DEX-3

value: 10 mg/kg dexamethasone (2h)


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_010


title: liver, NaCl (6h) + dexamethasone (2h), replicate 1

description:
Library name: NaCl_DEX-1
NaCl_DEX-1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_009


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_887


title: liver, NaCl (6h) + dexamethasone (2h), replicate 2

description:
Library name: NaCl_DEX-2
NaCl_DEX-2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_886


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_008


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_006


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_007


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_885


title: liver, ironsulfate (6h) + PBS (2h), replicate 3

description:
Library name: FeSO4_PBS-3
FeSO4_PBS-3

value: 300 mg/kg FeSO4 (6h)


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_013

value: spinal neuron differentiation


title: liver, ironsulfate (6h) + PBS (2h), replicate 2

description:
Library name: FeSO4_PBS-2
FeSO4_PBS-2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_012

value: Control


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_883


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_005

value: heterogenous protocol


title: liver, ironsulfate (6h) + PBS (2h), replicate 1

description:
Library name: FeSO4_PBS-1
FeSO4_PBS-1


title: liver, ironsulfate (6h) + dexamethasone (2h), replicate 2

description:
Library name: FeSO4_DEX-2
FeSO4_DEX-2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_004


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_882

value: homogenous protocol


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_003


title: liver, ironsulfate (6h) + dexamethasone (2h), replicate 3

description:
Library name: FeSO4_DEX-3
FeSO4_DEX-3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_888


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_011


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_880


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_002


title: liver, ironsulfate (6h) + dexamethasone (2h), replicate 1

description:
Library name: FeSO4_DEX-1
FeSO4_DEX-1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_884


title: Sorted Kupffer cells from Hepa1-6_EpoOE HCC-bearing mice 3

city: Palo Alto

first: David Kung-Chun

last: Chiu

address: 3373 Hillview Ave, Rm 260

institute: Stanford University

description: Library name: OE_3

data_processing:
Raw sequencing reads were filtered, adapters trimmed using fastq-mcf program (v1.05), and data quality check was performed using FastQC (v0.11.8). Contamination removal was performed using Bowtie2 (v2.5.1). The paired-end reads were aligned to the reference Human or Mouse genome downloaded from the Ensembl database, and the alignment was performed using STAR (2.7.3a). The raw read counts were estimated using HTSeq (v0.11.2).
Assembly: GRCm39
Supplementary files format and content: Raw count

extract_protocol:
RNA was extracted using RNEasy Plus mini kits (Qiagen).
Libraries were prepared using the Illumina TruSeq stranded mRNA kit. Libraries were checked for size using the Agilent DNA 100 kit on a BioAnalyzer (Agilent) and quantified by qPCR using the KAPA Library Quantification Kit for Illumina.

value: Hepa1-6 (tumor model)

value: Kupffer cells

value: wild type


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_879


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_001


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_878


title: Sorted Kupffer cells from Hepa1-6_EpoOE HCC-bearing mice 2

description: Library name: OE_2


title: Sorted Kupffer cells from Hepa1-6_EpoOE HCC-bearing mice 1

description: Library name: OE_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_881


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_875


title: Sorted Kupffer cells from Hepa1-6_EV HCC-bearing mice 3

description: Library name: EV_3


title: Sorted Kupffer cells from Hepa1-6_EV HCC-bearing mice 1

description: Library name: EV_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_872


title: Sorted Kupffer cells from Hepa1-6_EV HCC-bearing mice 2

description: Library name: EV_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_874


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_873


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_871


title: CpoxeRNA_EVEN_bio rep1

city: Bethesda

first: Bingning

last: Xie

address: 50 South Drive

institute: NIDDK

description: Library name: CpoxeRNA_EVEN_bio rep1

data_processing:
Raw reads were trimmed with Trim Galore (v0.6.7) and aligned to the mm10 genome using Bowtie2 (v 2.5.3)57. Peaks were called for each probe set and replicate by using the callpeak function from MACS258 relative to the input.  The result peaks within 1kb regions were merged by Bedtools merge function, then the merged peaks were extend 2kb with slop function from Bedtools28 and common peaks among all the replicates from EVEN and ODD probe sets were found by using the pybedtools59.
Assembly: mm10
Supplementary files format and content: narrowPeak

source_name: MEL

growth_protocol: MEL cells were cultured in Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% fetal bovine serum in a humidified incubator with 5% CO2. Differentiation of MEL cells was induced by 2% Dimethylsulfoxide for 5 days.

extract_protocol:
50 million cells per sample were crosslinked with 3% formaldehyde at room temperature for 30min. Cells were sonicated in the ChIRP lysis buffer with probe sonicator (Branson SFX150 Sonifier) with 30s ON, 45s OFF, 30min total ON time, at 38% J. The following steps were performed according to the protocol from "Chu, C., Quinn, J., and Chang, H.Y. (2012). Chromatin isolation by RNA purification (ChIRP). J Vis Exp. 10.3791/3912.".
1ng DNA was used in library preparation. The sequencing library were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina.

tag: probe

value: EVEN

value: MEL

value: mouse erytrhoidblast


title: Incisor proximal tissue from 15 day old KO2 mice

city: College Station

first: James

last: Cai

state: TX

address: 4458 TAMU

department: Veterinary Intergrative Biosciences

institute: Texas A&M University

description:
Library name: CD2-KO
10x Genomics

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software. The CellRanger (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) was used to perform barcode processing and 3’ gene counting. The cDNA insert was aligned to the mm10/GRCm38 reference genome. Only confidently mapped, non-PCR duplicates with valid barcodes and UMIs were used to generate the gene-barcode matrix. Further analysis included quality filtering, the identification of highly variable genes, dimensionality reduction, and standard unsupervised clustering. Low-quality cells with fewer than 1,000 detected genes were removed. Cells with more than 10% of the transcripts coming from mitochondrial genes or more than 3% Hbb/Hba content were also removed. Dimensionality reduction was performed with UMAP as described previously. A joint analysis of Din-KO and WT data was performed following the Seurat integration procedure. Cell-cycle scoring and regression were performed with the default list of cell-cycle genes. Clustering was performed with ‘FindClusters’ and ‘resolution=1’. Cluster marker genes were identified with ‘FindAllMarkers’. Trajectory analyses were carried out on the odontogenic subset using Monocle 3  and TradeSeq. Cell-cell communication analysis were performed using CellChat and CellphoneDB v2.1.4
Assembly: Mouse mm10
Supplementary files format and content: mtx file for each sample along with associated tsv files with feature and barcode information.

source_name: Incisor proximal

extract_protocol:
The proximal tissues of the lower incisors of P15 Din-KO mice and WT mice were obtained with fine forceps in ice-cold PBS. The tissue was minced into 0.5 mm pieces and dissociated into single-cell suspension by digesting in a-MEM containing 2.5 mg/ml liberase and 1U/µl DNase at 37C° for 30 min, then terminated with 10% FBS and passed through Pluri-strainer Mini 70μm (PluriSelect, 43-10070-40, El Cajon, CA, USA). Dead cells were removed using the Dead Cell Removal Kit (Miltenyi Biotec, 130-090-101, MD, USA).
Cell barcoding, cDNA synthesis, and library preparation were done following the protocols of 10X Next GEM single-cell 3’ reagent kits V3.1 (10× Genomics, 1000128, Peasanton, CA, USA). Quality control for cDNA and library was performed on a 2100 Bioanalyzer (Agilent Technology). Sequencing was performed with NovaSeq PE-150 at LC Sciences (Houston, TX, USA).

treatment_protocol: Din gene knockout versus WT

value: Incisor proximal

value: Mixed

value: Din-KO


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_877


title: CpoxeRNA_ODD_bio rep2

description: Library name: CpoxeRNA_ODD_bio rep2

value: ODD

value: WT


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_876


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_870


title: Incisor proximal tissue from 15 day old KO1 mice

description:
Library name: KO-2
10x Genomics


title: Incisor proximal tissue from 15 day old WT2 mice

description:
Library name: CD1-WT
10x Genomics


title: CpoxeRNA_ODD_bio rep1

description: Library name: CpoxeRNA_ODD_bio rep1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_869


title: GCS control

type: RNA

city: Monroe

first: Yong-Yu

last: Liu

state: LA

address: 1800 Bienville Dr Rm368, 1800 Bienville Dr

institute: University of Louisiana at Monroe

description: RMA expression value derived from Expression Console software; core-exon analysis

hyb_protocol: The labeled cRNA was hybridized onto an Affymetrix GeneChip® Human Genome U133 Plus 2.0 chip for 16 hours at 45°C in 300 ml premixed hybridization solution containing labeled hybridization control prokaryotic genes (bioB, bioC, bioD and cre).

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Raw data were processed with the Exon Array Computational Tool (ExACT) (Affymetrix) for background correction and normalization. The data from the Affymetrix microarray were further analyzed by Transcriptome Analysis Console (TAC) v4.0 Software (http://www.affymetrix.com/support/technical/byproduct.affx?product=tac). We defined a probeset as present when it had a P value <0.001 and an Intensity value >200.

label: biotin

source_name: NCI-ADR-RES cells

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: Cells were cultured in 5% FBS RPMI-1640 medium containing 25 nM dactinomycin (DAC) or vehicle for 48h. NCI/ADR-RES/GCS and ADR-RES/asGCS are sublines of NCI/ADR-RES ovary adenocarcinoma cells generated from clone selections with geneticin (G418, 400 μg/ml) after transfection of parental cells with pcDNA 3.1‐asGCS (GCS antisense) or pcDNA 3.1‐GCS (10 μg/ml, 100‐mm dish) by co‐precipitation with calcium phosphate (Mammalian Transfection Kit; Stratagene, La Jolla, CA) [25].

extract_protocol: RNA samples of cell lines were extracted using an SV total RNA isolation kit (Promega, Madison, WI, USA) and the quality of RNA was assessed by using Bioana-lyzer with Agilent RNA 6000 Nano kit (Agilent, Santa Clara, CA) for RNA integrity

value: ovarian cancer cultured cells


title: NCI-ADR-RES control


title: INPUT_bio rep2

description: Library name: INPUT_bio rep2


title: CpoxeRNA_EVEN_bio rep2

description: Library name: CpoxeRNA_EVEN_bio rep2


title: asGCS treated


title: Incisor proximal tissue from 15 day old WT1 mice

description:
Library name: WT-2
10x Genomics


title: asGCS control


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_868


title: INPUT_bio rep1

description: Library name: INPUT_bio rep1


title: GCS treated


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_867


title: Rapa,D30,Rep2

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

description:
Library name: Rapa_2_d30
column name in raw_count_d30.txt:Rapa_d30_2

data_processing:
reads passed QC  are aligned to mouse  reference mm10 using aligner STAR v.2.5.2a
read counts were estimated using htseq (1.0.0)
Differential expression analysis is done using DESeq2 (V 1.30.1)
Assembly: mm10
Supplementary files format and content: tab-delimited files included the raw counts for each sample.

source_name: Jejum

growth_protocol: C57BL/6 Mice received daily  immunosuppressant classes rapamycin

extract_protocol:
The Jejum tissues of the mice were dissected according to their anatomic features and stored immediately in RNAlater solution (QIAGEN) in RNAse-free 1.7-ml tubes (Denville Scientific, Holliston, MA) at -80°C to stabilize and protect the integrity of RNA. For each sample, total RNA was extracted from ~1 cm of ileum. Prior to the extraction, 500 µl of ice-cold RNase free PBS was added to the sample. To remove the RNAlater, the mixture was centrifuged at 8,000xg for 10 min and the resulting pellet resuspended in 500 µl ice-cold RNase-free PBS with 10 µl of β-mercaptoethanol.
Ribosomal RNA depletion and library construction were performed using the RiboZero Plus kit and TruSeq stranded mRNA library preparation kit Ribosomal RNA depletion and library construction were performed using the RiboZero Plus kit and TruSeq stranded mRNA library preparation kit (Illumina) according to the manufacturer’s recommendations and sequenced using Illumina NovaSeq 6000 S2 flow cell

treatment_protocol: mice received 3, 7, and 30 days of rapamycin treatment

value: Jejum

value: Rapamycin

tag: batch


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_865

value: spinal neuron differentiation

value: Control


title: Rapa,D30,Rep3

description:
Library name: Rapa_3_d30
column name in raw_count_d30.txt:Rapa_d30_3


title: Rapa,D30,Rep1

description:
Library name: Rapa_1_d30
column name in raw_count_d30.txt:Rapa_d30_1


title: Control,D30,Rep3

description:
Library name: control_3_d30
column name in raw_count_d30.txt:control_d30_3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_862

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_863


title: Injured CsA treated, treated, HA, 12

city: Villanova

first: Susan

last: Margulies

address: 805 Stoke Road

institute: Emory University

description:
G1HA130111U-2
Count

data_processing:
Data was sequenced using the NovaSeq 6000 by the Emory Integrated Computational Core (https://www.cores.emory.edu/eicc/). Sequences were quality-checked by the Emory Integrated Computational Core using FastQC v.0.11.8, Fastq-Screen, and MultiQC v.12. Raw reads were trimmed using Trimmomatic v0.3682 and cleaned using cutadapt v3.4.
Cleaned reads were aligned to the Sus scrofa (ss11.1) reference genome using STAR aligner v2.5.2. Raw count generation from were performed using HTSeq-count v0.13.5. Swine gene names were retrieved via R annotation package org.Ss.eg.db .
Samples with <10M reads were removed and genes with <50 counts in >20 samples were filtered out. Normalization was performed via R using the DESeq2 package and outliers were removed using via R using the mahalanobis distance and multivariate outlier detection package.
Assembly: ss11.1
Supplementary files format and content: Excel file includes the raw counts for all samples (.xlsx format).

organism: Sus scrofa

source_name: brain

extract_protocol:
Total RNA was extracted from frontal cortex (FC) and hippocampus + amygdala (HA) FFPE brain tissue by the Emory Integrated Genomics Core (https://www.cores.emory.edu/eigc/) using the TruXTRAC FFPE Total NA Plus Kit (Covaris LLC, 520255, Woburn, MA, USA) and automated on a KingFisher Flex instrument using the manufacturer’s protocol.
cDNA libraries were generated by the Emory Integrated Genomics Core (https://www.cores.emory.edu/eigc/) from 50ng of RNA using the SMART-Seq Stranded kit (Takara Bio Inc, 634444, Kusatsu, Shiga, Japan).

treatment_protocol: Piglets were treated with 20mg/kg/day dose of CsA intravenously via an ambulatory wireless programmable infusion pump, delivering a loading dose at 6 hour post-injury, followed by continuous infusion for 24 hours, thereby making up 30 hours of survival post-injury.

value: brain

tag: brain region

value: hippocampus + amygdala

tag: group name

value: Injured CsA treated

tag: survival time_post_injury

value: 30 hours

value: Cyclosporine A treated

tag: Sex

value: female


title: NCI-ADR-RES treated


title: Control,D30,Rep2

description:
Library name: control_2_d30
column name in raw_count_d30.txt:control_d30_2


title: Injured CsA treated, treated, FC, 25

description:
G1FA121214U-2
Count

value: frontal cortex


title: Injured CsA treated, treated, HA, 6

description:
G1HA121214U-2
Count


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_861


title: Control,D30,Rep1

description:
Library name: control_1_d30
column name in raw_count_d30.txt:control_d30_1


title: Rapa,D7,Rep3

description:
Library name: Rapa_3_d7
column name in raw_count_d7.txt:Rapa_d7_3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_866


title: Injured CsA treated, treated, HA, 58

description:
G1HA121128U-2
Count


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_859


title: Injured CsA treated, treated, FC, 7

description:
G1FA121214U-1
Count


title: Injured CsA treated, treated, FC, 51

description:
G1FA130111U-2
Count


title: Rapa,D7,Rep2

description:
Library name: Rapa_2_d7
column name in raw_count_d7.txt:Rapa_d7_2


title: Rapa,D7,Rep1

description:
Library name: Rapa_1_d7
column name in raw_count_d7.txt:Rapa_d7_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_860


title: Injured CsA treated, treated, FC, 48

description:
G1FA121128U-2
Count


title: 2and24moBrain_WTandSTING-KO

city: Boston

first: Katherine

last: Sulka

state: MA

address: 136 Harrison Avenue

department: Immunology

institute: Tufts Medical School- Graduate School of Biomedical Sciences

description:
Library name: SS002
10x Genomics v3

data_processing:
Sequenced samples were processed using Cell Ranger (v3.0.2) mkfastq pipeline. FASTQ files were assigned to the mm10 transcriptome, filters, and quantified.
Assembly: mouse mm10
Supplementary files format and content: tab separated values files and matrix files

source_name: Brain

extract_protocol:
Tissues were extracted and placed is appropriate enzymatic digestion buffer for the specific tissue and incubated at 37C. Samples were passed through a 70μm strainer, brought up to 10mL in 2% DMEM, and centrifuged for 5 minutes at 500g at 4°C. Debris was removed from samples using Debris Removal (Miltenyi, 130-109-398) and after cells were pelleted, samples were lysed by resuspension in 1mL ACK lysis buffer (Fisher Scientific, NC0829166) for 1 minute at room temperature, followed by the addition of 9mL of 2% DMEM. Samples were pelleted, resuspended in PBS, and kept cold. Cells were counted (Countessa, Thermo, with Trypan Blue viability stain) and aliquoted for experimental use.
Single cell preparations were resuspended into enriched PBS (0.5% BSA). Approximately 9,000 cells were loaded into each well of the Chromium Chip A/B (10x Genomics v2 and v3, respectively), depending on the run, and then run on the Chromium controller. GEM formation quality was visualized manually before GEMs were transferred to a thermal cycler. GEM-RT cleanup and cDNA amplification steps were completed, and quantification was run inhouse. 3’ gene expression library as constructed and post-library construction quality control was completed in-house as described in 10x Manual.

value: Brain

tag: age

value: 2-mo and 240mo

value: WT and STING-KO

value: total brain

value: pooled male and female


title: Control,D7,Rep3

description:
Library name: control_3_d7
column name in raw_count_d7_rapa.txt:control_d7_3

value: Jejum


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_857


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_864


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_858


title: Injured CsA treated, treated, HA, 57

description:
G1HA121114U-1
Count


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_856


title: Control,D7,Rep2

description:
Library name: control_2_d7
column name in raw_count_d7_rapa.txt:control_d7_2


title: Injured CsA treated, treated, FC, 40

description:
G1FA121114U-1
Count


title: Injured CsA treated, treated, HA, 49

description:
G1HA111209U-1
Count


title: Control,D7,Rep1

description:
Library name: control_1_d7
column name in raw_count_d7_rapa.txt:control_d7_1


title: Injured CsA treated, treated, FC, 79

description:
G1FA111209U-1
Count


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_855


title: WT, myeloid, P20, sample3

city: Philadelphia

first: F. Chris

last: Bennett

address: 3150 Civic center blvd

institute: UPenn

description: Library name: W3_p20

data_processing:
RNA-seq reads were pseudo-aligned to the mouse GRCm39 cDNA transcriptome (Ensembl release 99) using Kallisto version 0.46.0. In R, transcripts were mapped to genes using Bioconductor tximport.
Assembly: GRCm39
Supplementary files format and content: TPM_Only.csv
Supplementary files format and content: TMM_Normalized.csv

extract_protocol:
Dissected hind-brains (brainstem and cerebellum) were placed in ice cold Medium A and homogenized with 4 strokes of a 7ml glass dounce homogenizer. The homogenate was filtered through a 70 μm filter. Homogenates were pelleted at 200 x g for 7 min. To remove myelin, the pellet was resuspended in Iso-percoll and spun 700 x g 20 min with no brake. The myelin layer was removed, and the remaining cell pellet was washed with Medium A. Cells were transferred to a u-bottom 96 well plate and blocked with CD16/CD32 (BD biosciences 553142) then stained for CD45 (103113, Biolegend) and CD11b (101228, Biolegend) and incubated with a dead cell detection dye (L34974, Invitrogen) on ice for 20 min. Following washes cells were sorted based on CD45, CD11b positivity into Trizol-LS using a BD FACS ARIA cell sorter equipped with a 100 um nozzle.
Bulk RNA seq Libraries were generated using the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (#E6420S), with 16-19 cycles of PCR cDNA amplification, which were experimentally determined using a dilution curve. Libraries were quality checked and quantified using an Agilent TapeStation using High Sensitivity D5000 ScreenTape (5067-5592), and High Sensitivity D5000 Reagents (5067-5593). Libraries were sequenced by NovaSeq6000 on an SP flowcell (Illumina), using sequencing chemistry v 1.5. We obtained at least 29x10^6 paired reads per sample, with a range of 29-42x106. A mean of 70.24% of reads were mapped across all samples.

value: myeloid

value: WT


title: Injured CsA treated, treated, HA, 21

description:
G1HA111123U-1
Count


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_854

value: spinal neuron differentiation

value: Control


title: WT, myeloid, P20, sample2

description: Library name: W2_p20

value: brain


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_853

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_852


title: twitcher, myeloid, P20, sample3

description: Library name: T3_p20

value: twitcher


title: WT, myeloid, P20, sample1

description: Library name: W1_p20


title: Injured CsA treated, treated, HA, 18

description:
G1HA111116U-1
Count

value: hippocampus + amygdala

value: Injured CsA treated

value: 30 hours


title: twitcher, myeloid, P20, sample2

description: Library name: T2_p20


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_849


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_851


title: Injured CsA treated, treated, HA, 104

description:
G1HA111028U-2
Count

value: Cyclosporine A treated

value: female


title: Injured CsA treated, treated, FC, 19

description:
G1FA111028U-2
Count

value: frontal cortex


title: twitcher, myeloid, P20, sample1

description: Library name: T1_p20


title: WT, myeloid, P15, sample2

description: Library name: W2_p15


title: Injured CsA treated, treated, HA, 34

description:
G1HA111026U-1
Count


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_847


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_850


title: Injured CsA treated, treated, FC, 26

description:
G1FA111026U-1
Count


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_848


title: WT, myeloid, P15, sample1

description: Library name: W1_p15


title: twitcher, myeloid, P15, sample2

description: Library name: T2_p15


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_846


title: Injured 1 week, untreated, HA, 31

description:
G3HA170721U-1
Count

value: Injured 1 week

value: 8 days

value: untreated


title: Injured CsA treated, treated, FC, 87

description:
G1FA111123U-1
Count


title: twitcher, myeloid, P15, sample1

description: Library name: T1_p15


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_845


title: Injured CsA treated, treated, FC, 14

description:
G1FA111116U-1
Count


title: Injured 1 week, untreated, FC, 17

description:
G3FA170721U-1
Count


title: WT, myeloid, P10, sample2

description: Library name: W2_p10


title: Injured 1 week, untreated, HA, 46

description:
G3HA150717U-2
Count


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_844


title: WT, myeloid, P10, sample1

description: Library name: W1_p10


title: Donor_D_day1_BCG_p300_H3K18lac

city: Parkville

first: Boris

last: Novakovic

state: Victoria

address: Murdoch Children's Research Institute, Royal Children's Hospital, Flemington Road

country: Australia

institute: Murdoch Children's Research Institute

description: Library name: Sample 22

data_processing:
ChIP-seq reads were aligned to the hg19 genome assembly using bwa. For peak calling the BAM files were first filtered to remove the reads with mapping quality less than 15. The peak calling algorithm MACS2 http://github.com/taoliu/MACS/) was used to detect the genomic regions enriched for H3K18lac at p-value of 10-5, using the default (narrow) setting.
Assembly: hg19
Supplementary files format and content: BigWig files for visualization

source_name: Adult Human Peripheral Blood

growth_protocol: Monocytes were isolated with negative selection with beads and differentiated into resting or trained  macrophages by ex vivo culture in Dutch modified RPMI 1640 culture medium supplemented with gentamicin (50 µg/mL; Centrafarm), glutamax (2 mM; GIBCO), pyruvate (1mM; GIBCO) and 10% (v/v) human pooled serum. Medium was excahenged in days 1, 3 and 6.

extract_protocol:
Purified cells were fixed with 1% methanol-free formaldehyde and quenched with glycine. Fixed cell preparations were lysed, and equal amounts of chromatin were incubated with 1µg of H3K18la antibody (PTM-1406; PTM Biolabs), and incubated overnight at 4ºC with rotation. Dynabeads protein A/G magnetic beads , were washed, centrifuged, mixed with the samples (20 µL/sample) and rotated for 1 hour at 4°C. The bead-bound chromatin complexes  were washed with 400µl buffer for 10 minutes at 4°C with five rounds of washes. After washing chromatin was eluted in 200µl of 0.1 M NaHCO3, 1% SDS elution buffer for 20 minutes in RT. Supernatant was collected, and incubated with proteinase K  for 4 hours at 65°C to disrupt cross‐links between proteins and DNA. Finally samples were purified using Qiaquick MinElute PCR purification Kit (Qiagen)  and eluted in 20µl EB.
ChIP-seq libraries were prepared using the Kapa Hyper Prep Kit according to manufacturer’s protocol, with the following modifications. 2.5 mL of the NEXTflex adaptor stock (600 nM, Bio Scientific) was used for adaptor ligation of each sample. Libraries were amplified with 12-15 PCR cycles followed by a double post-amplification clean-up was used to ensure proper removal of adapters. Libraries were paired-end sequenced to a read length of 50 bp on an Illumina NextSeq500.

treatment_protocol: Cells were cultured  to medium  for 6 days or treated with BCG vaccine for 24 hours, followed by 5 days culture.

value: Adult Human Peripheral Blood

tag: donor

value: Monocyte

tag: chip antibody

value: Rabbit anti-H3K18lac Antibody (PTM-1406; PTM Biolabs)

value: BCG and p300 inhibibitor exposed, collected at 24 hours post exposure


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_843

tag: cell line

value: spinal neuron differentiation


title: twitcher, myeloid, P10, sample3

description: Library name: T3_p10

value: brain

tag: cell type

value: myeloid


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_842

tag: genotype

value: homogenous protocol


title: twitcher, myeloid, P10, sample2

description: Library name: T2_p10

value: twitcher


title: Donor_A_day1_BCG_p300_H3K18lac

description: Library name: Sample 19

tag: treatment


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_841

tag: sequencing batch


title: Donor_C_day1_BCG_p300_H3K18lac

description: Library name: Sample 21

tag: tissue


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_840


title: twitcher, myeloid, P10, sample1

description: Library name: T1_p10


title: Injured 1 week, untreated, HA, 84

description:
G3HA150717U-1
Count

value: hippocampus + amygdala


title: Injured 1 week, untreated, HA, 97

description:
G3HA140808U-2
Count


title: Injured 1 week, untreated, FC, 89

description:
G3FA140808U-2
Count


title: Donor_B_day1_BCG_p300_H3K18lac

description: Library name: Sample 20


title: Injured 1 week, untreated, FC, 45

description:
G3FA150717U-1
Count


title: Lung, replicate 3, scRNAseq

city: Suita

first: Kei

last: Higaki

state: Osaka

address: Nanobiotechnology building 3F, 1-3 Yamadaoka

department: Graduate School of Frontier Biosciences, Graduate School of Medicine, Immunology Frontier Research Center, World Premier International Research Center (WPI)

institute: Osaka University

description:
Library name: Lung_3
10x Genomics

data_processing:
The sequencing data was first pre-processed using the 10X Genomics Cell Ranger software.
For alignment purposes, we generated and used a custom genome fasta and index file by including the sequences of eGFP and to the mouse genome (mm10).
Filtering was applied to remove low‐quality cells by excluding cells expressing <500 or >6,000 unique genes, as well as cells with >15% mitochondrial gene expression.
We removed cells expressing one of the markers Ptprc (Cd45), Pecam (Cd31), Myh11, or Msln. Next, individual Seurat objects obtained from the lung and the ectopic bones were merged and used for batch effect correction and integration using Harmony (v0.1.1).
Single-cell trajectories was computed using the algorithm slingshot (v1.8.0), which enables computation of lineage structures in a low-dimensional space.
Assembly: mm10_EGFP
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung

extract_protocol:
To isolate cells from ectopic bones, tissues were minced and digested with collagenase type I and DNase I at 37°C for 30 min. To isolate lung non-hematopoietic cells, the minced lung was placed in digestion solution containing collagenase Type I and DNase. The suspension was incubated at 37°C for 60 min under constant agitation. Cells were then incubated with red blood cell lysis buffer for 5 min. Preparations from all tissues were passed through a 100-μm cell strainer (Falcon) to remove debris.
Libraries were constructed following the recommended protocol for the Chromium Next GEM Single Cell 3’Reagent Kits (v3)

value: lung

value: Naïve


title: Injured 1 week, untreated, HA, 106

description:
G3HA140501U-2
Count

value: female


title: Fetal limbs, replicate 1, scRNAseq

description:
Library name: Fetal_limb_1
10x Genomics

source_name: fetal limbs

value: fetal limbs

value: Osx-cre::GFP R26R-Tomato/+


title: Donor_C_day1_BCG_LDHi_H3K18lac

description: Library name: Sample 17

value: BCG and LDH inhibibitor (LDHi) exposed, collected at 24 hours post exposure


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_838


title: Injured 1 week, untreated, FC, 3

description:
G3FA140730U-1
Count

value: frontal cortex

value: Injured 1 week

value: 8 days

value: untreated


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_839


title: Donor_D_day1_BCG_LDHi_H3K18lac

description: Library name: Sample 18

value: Adult Human Peripheral Blood

value: Monocyte

value: Rabbit anti-H3K18lac Antibody (PTM-1406; PTM Biolabs)


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_837

value: spinal neuron differentiation


title: Lung, replicate 2, scRNAseq

description:
Library name: Lung_2
10x Genomics


title: Injured 1 week, untreated, FC, 15

description:
G3FA140501U-1
Count

value: brain


title: HO, replicate 3, scRNAseq

description:
Library name: HO_3
10x Genomics

source_name: ectopic bone

value: ectopic bone

value: FACS-sorted populations from the lung of Ubc-GFP;CXCL12-tdTomato mice were intramuscularly injected into the mid-belly of the tibialis anterior muscle with growth factor-reduced Matrigel (BD Biosciences, Bedford, MA, USA)  and human recombinant BMP2 (PeproTech, 120-02) at a concentration of 2.5 μg/50 μl.


title: Donor_B_day1_BCG_LDHi_H3K18lac

description: Library name: Sample 16


title: Injured 1 week, untreated, HA, 67

description:
G3HA110126-3
Count

value: hippocampus + amygdala

value: 6 days


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_836

value: homogenous protocol


title: Injured 1 week, untreated, FC, 83

description:
G3FA110126-3
Count

value: female


title: control, replicate 2, scRNAseq, InDrop

city: Nashville

first: Guoqiang

last: Gu

state: TN

address: 2213 Garland Avenue, MRB4, Rm 9415

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
Library name: G1S2D1Con
cells were flowed into a microfluidic chip for droplet-formation. The droplets were then used for reverse transcription, library preparation and sequencing (targeting 120 million reads. Novaseq 6000, Illumina)

data_processing:
DropEst was used to preprocess scRNAseq reads and to generate count matrices of each gene in each cell. Cells with low proportion of uniquely mapping reads (<500), low proportion of expressed genes (<100) or high proportion of reads mapped to the mitochondrial RNA (>10%) will be considered as low quality and excluded from downstream analysis.
After quality control, scRNAseq data were normalized using UMI-filtered counts. Cell subpopulations were identified by the shared nearest neighbor modularity optimization and visualized by UMAP using Seurat based on the first 30 principal components generated from the top 2000 highly variable genes .
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: islet

growth_protocol: Mice were kept in standard ventilated mini-isolator cages with free access to water and food.

extract_protocol:
Dissociated cells from islets were washed and checked for viability with Trypan Blue. Samples with >90% viability were counted and mixed with 10% K562 cells to evaluate doublet formation rate. Cells were washed using 0.02%BSA in DPBS before resuspension in a solution of DPBS with 15% Optiprep at 100,000 cells/mL before proceeding to inDrops (1CellBio) encapsulation.
Cells were flowed into a microfluidic chip where cells were mixed with an RT/Lysis buffer and barcoded capture beads immediately before being portioned into droplets. Cell concentrations and flow rates were carefully controlled to minimize doublets and ensure droplet uniformity. The droplet emulsion was collected into a 1.5 ml tube in fractions of ~3,500 estimated captured cells. Droplets then proceeded to UV exposure using a UV Cleaver to release captured oligos from the beads, a 1-hour incubation at 50 oC to facilitate reverse transcription, and finally a 5-minute incubation at 85 oC to stop the reaction. Emulsions were then cooled on ice and demulsified to isolate the aqueous component containing barcoded cellular cDNA, which is stored at -80 oC for library preparation. Libraries were prepared for sequencing utilizing the TruDrop protocol. Samples were then sequenced using the Novaseq 6000 (Illumina) in a customized format. For each sample both tdT+ and tdT-  cells were processed and sequenced together and contained islets from 3-4 mice. During sequencing we targeted 120 million reads.

treatment_protocol: None.

value: islet

tag: strain

value: mixed pancreatic islets


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_834

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.0/RTA v3.4.4) with a 51nt(Read1)-8nt(Index1)-8nt(Index2)-51nt(Read2) setup using 'NovaSeqXp' workflow in 'S1' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 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'.

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).


title: Donor_C_day1_BCG_H3K18lac

description: Library name: Sample 13

value: BCG exposed, collected at 24 hours post exposure


title: Injured 1 week, untreated, FC, 80

description:
G3FA110112-2
Count

value: frontal cortex

value: Injured 1 week


title: Donor_D_day1_BCG_H3K18lac

description: Library name: Sample 14


title: Atf4 mut, replicate 2, scRNAseq, InDrop

description:
Library name: G2S1F2Mut
cells were flowed into a microfluidic chip for droplet-formation. The droplets were then used for reverse transcription, library preparation and sequencing (targeting 120 million reads. Novaseq 6000, Illumina)

value: Atf4F/F; Ins1Cre


title: Injured 1 week, untreated, HA, 16

description:
G3HA110112-2
Count

value: untreated