title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_756


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_758

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:
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'.

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

tag: treatment

value: homogenous protocol

tag: sequencing batch


title: isolate g2g_032, replicate 2

city: Boston

first: Peter

last: Culviner

state: MA

address: 677 Huntington Ave

department: IID

country: USA

institute: Harvard School of Public Health

description: Library name: g2g_032_2

library_source: transcriptomic

data_processing:
See publication for complete details. Paired end reads were demultiplexed by their inline barcodes using cutadapt and a custom demultiplexer script.
Reads were mapped with bowtie2 to H37Rv reference.
Non-unique reads were removed with picard.
Reads were mapped to H37Rv regions with a custom script, removing low mapq reads. Reported values are log2 transformed and library depth normalized.
Assembly: NC_000962.3
Supplementary files format and content: 2D csvs with gene IDs and sample names

molecule: total RNA

organism: Mycobacterium tuberculosis

source_name: bacterial

growth_protocol: Mtb was grown in a 1 mL volume in 24-well plates, covered with breathe-easy film, at 37°C x 100 RPM, in 7H9 media supplemented with 0.2% glycerol, 0.05% Tween-80, and 10% OADC. Strains were grown and back diluted as necessary over a 8 day period to achieve a final OD of ~0.4.

extract_protocol:
Crosslinks were reversed by incubating at 70°C. Cells were lysed in Trizol using bead beating tubes. RNA was extracted by adding chloroform and removing the aqueous upper layer. RNA was precipitated onto carboxylate-modified magnetic beads with isopropanol-GuHCl and beads were washed with ethanol. RNA was resuspended into tris-buffered water. See publication for full details.
RNA library preps were prepared for Illumina sequencing using a custom protocol, see publication for complete details. Briefly, cDNA was barcoded using random primers with inline barcodes and an Illumina sequencing adapter. Barcoded, single-stranded cDNA was pooled and a second adapter was added using a splint ligation. Reads corresponding to rRNA were depleted using Taq polymerase's endonuclease activity, combined with a library of guides. Libraries were amplified and sequenced on either a MiSeq or NovaSeq instrument.

treatment_protocol: To halt transcriptome dynamics and sterilize cultures, PFA was added to each 1 mL culture to a final concentration of 2% and allowed to incubate for 1 hour at room temperature.

value: bacterial

value: Clinical Isolate


title: female GWI patient, baseline_replicate 9

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

description: Library name: 0725sGF0

data_processing:
Raw reads were mapped to the reference human genome (GRCh38, release 86) using GSNAP, HISAT2, and STAR software.
For the analysis of differentially expressed known genes, reads for each gene aligned by GSNAP and HISAT2 were counted using HTSeq software. Alignment by STAR was run with the option “quantMode TranscriptomeSAM” that allowed for the counting of reads aligned to each gene.
Raw counts from HTSeq and STAR were imported into Bioconductor/R package DESeq2, normalized, and tested for differential gene expression. This analysis was done separately for the files produced by each aligner.
Only genes with raw counts equal or more than 50 in all samples in at least one group were used for the differential gene expression analysis
For further analysis, we selected genes and exons that were differentially expressed based on one of the following two criteria: (a) either a fold change (FC) > |1.5| and false discovery rate (FDR) < 0.10 in one out of the three aligners and FC > |1.4| and FDR < 0.15 in the remaining two aligners, OR (b) a FC > |1.5| and FDR < 0.10 in two out of three aligners.
Assembly: GRCh38, release 103
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample, where only genes that had raw counts equal or more than 50 in all samples in at least one group

source_name: peripheral blood mononuclear cells

extract_protocol:
Total RNA was extracted using RNAzol (Molecular Research Center) according to the manufacturer’s instructions. RNA quality was assessed using Agilent TapeStation 4200 (Agilent Technologies). All RNA samples had an RNA Integrity number (RIN) above seven.
The libraries were generated using Illumina TruSeq Stranded Total RNA Library Prep Kit

tag: tissue

value: peripheral blood mononuclear cells

tag: disease state

value: GWI patient

tag: time point_in_exercise

value: T0 (baseline)

tag: Sex

value: female


title: Aged BMDM, β-glucan, 4h, biol rep 3

city: Nashville

first: Margaret

middle: Ann

last: Mcbride

state: Tennessee

address: 1211 Medical Center Drive

department: Anesthesiology

institute: Vanderbilt University Medical Center

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated. STAR-software was used to align reads to the reference genome. Expression levels were quantified using FPKM.
Reads that met the following citeria were removed. 1. reads containing adapters; 2., reads containing N > 10% (N represents base that could not be determined); 3. low quality reads: The Qscore (Quality value) of over 50% bases of the read is <= 5.
Assembly: mm10
Supplementary files format and content: excel file including raw counts for each sample
Supplementary files format and content: excel file including FPKM  for each sample

organism: Mus musculus

source_name: bone marrow-derived macrophage

growth_protocol: Murine bone marrow-servied macrophages were cultured from whole bone marrow and maintained in RPMI 1640 supplemented with 10% FBS, 1% antibiotic/anitbmycotic solution, and 10ug/mL murine macrophage colony stimulating factor

extract_protocol:
Total RNA was isolated under an RNase-free environment using the RNeasy Mini Kit (Qiagen, Hilden, Germany) which included a DNAse treatment step. Total RNA quality and concentration were verified with a Thermo Scientific NanoDrop 2000 spectrophotometer.
Sequencing libraries were prepared using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s protocol.

treatment_protocol: WT C57BL/6 mice were treated with β-glucan (5µg/mL), lipopolysaccaride (LPS 100ng/mL), vehicle  (normal saline (NS)), or multiple treatments in sequence.

value: bone marrow-derived macrophage

tag: strain

value: Male

value: WT

tag: mouse age

value: 18-20 months

value: 4hrs post 5μg/mL β-Glucan


title: microglia, WT, monocyte_transplanted, P35, sample2

city: Philadelphia

first: F. Chris

last: Bennett

address: 3150 Civic center blvd

institute: UPenn

description:
Library name: A4-2
analysis_id: wt___2
Tx_integrated_seurat_object.rds

data_processing:
Sequencing data of scRNA-seq libraries were analyzed using Cell Ranger 6.1.2 (10x Genomics), mm10 reference genome assembly and corresponding gene annotation, which generated filtered gene-by-cell unique molecular identifiers (UMI) count matrix for each scRNA-seq sample.
Assembly: mm10
Supplementary files format and content: RDS (R Data Serialization)

source_name: brain

extract_protocol:
Dissected brains 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 (unmanipulated conditions) and GFP positivity (transplanted conditions) into PBS using a BD FACS ARIA cell sorter equipped with a 100 um nozzle. Cell viability after sorting exceeded 80%.
Sorted cells were pelleted by centrifugation then resuspended in PBS to a final concentration of 1,000 cells per µl. Cells were loaded into a Chromium NextGem Chip G (10x Genomics) and inserted into a chromium controller to generate single-cell gel beads-in-emulsion (GEM). GEMs and scRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (10x Genomics, PN-1000121) according to the manufacturer’s instructions. Briefly, GEM reverse-transcription incubation was performed. Next, GEMs were broken and complementary DNA (cDNA) was cleaned up with DynaBeads MyOne Silane Beads and SPRIselect beads. Barcoded cDNA was PCR amplified for twelve cycles. Following clean up with SPRIselect beads and enzymatic fragmentation, adaptor ligation, a single index primer was used to barcode samples (10x Genomics, PN-2000240 Single Index Plate T Set A). Sample index PCR was performed per the manufacturers cycling instructions for thirteen cycles. The cDNA content of pre-fragmentation and post-sample index PCR samples was analyzed using a 4150 TapeStation (Agilent). Sequencing libraries were loaded on an Illumina NovaSeq S2 flow cell with the following sequencing settings: read 1: 28 cycles; read 2: 90 cycles; index i7: ten cycles; index i5: ten cycles; 1.75 nM loading concentration.

value: brain

value: myeloid

tag: batch


title: isolate g2g_030, replicate 2

description: Library name: g2g_030_2


title: isolate g2g_031, replicate 1

description: Library name: g2g_031_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_754


title: Aged BMDM, β-glucan, 4h, biol rep 1


title: isolate g2g_030, replicate 1

description: Library name: g2g_030_1


title: female GWI patient, baseline_replicate 7

description: Library name: 0719sGF0


title: female GWI patient, baseline_replicate 8

description: Library name: 0722sGF0


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_753


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_752


title: female GWI patient, baseline_replicate 6

description: Library name: 0716sGF0


title: isolate g2g_027, replicate 2

description: Library name: g2g_027_2


title: Aged BMDM, NS control, 3dp, biol rep 3

value: 3 days post 0.1% NS for 24 hrs


title: female GWI patient, baseline_replicate 5

description: Library name: 0713sGF0


title: Aged BMDM, NS control, 3dp, biol rep 2


title: isolate g2g_027, replicate 1

description: Library name: g2g_027_1


title: female GWI patient, baseline_replicate 4

description: Library name: 0710sGF0


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_749


title: isolate g2g_026, replicate 2

description: Library name: g2g_026_2


title: Young BMDM, LPS, 4hr, biol rep 6

value: 10-12 weeks

value: 4hrs post 100ng/mL LPS


title: isolate g2g_028, replicate 1

description: Library name: g2g_028_1


title: Young BMDM, LPS, 4hr, biol rep 5


title: female GWI patient, baseline_replicate 3

description: Library name: 0707sGF0


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_748

value: spinal neuron differentiation

value: homogenous protocol


title: isolate g2g_026, replicate 1

description: Library name: g2g_026_1

value: bacterial

value: Clinical Isolate


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_747


title: female GWI patient, baseline_replicate 2

description: Library name: 0704sGF0

value: peripheral blood mononuclear cells

value: GWI patient


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_751


title: Aged BMDM, NS control, 3dp, biol rep 1


title: Young BMDM, LPS, 4hr, biol rep 4


title: female GWI patient, baseline_replicate 1

description: Library name: 0701sGF0

value: T0 (baseline)

value: female


title: isolate g2g_024, replicate 1

description: Library name: g2g_024_1


title: Young BMDM, NS control, 3dp, biol rep 6

value: bone marrow-derived macrophage

value: Male


title: isolate g2g_023, replicate 2

description: Library name: g2g_023_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_746


title: A549_shNRF2_6hr_paired_rep3

city: South San Francisco

first: Scott

last: Foster

address: Genentech

institute: Genentech

library_source: other

data_processing:
Initial data processing preformed by Arpeggio Biosciences. Reads were aligned to GrCH38 by bowtie2 using end-to-end alignment and --very-sensitive processing
Full protocol described in detail in Mahat et al. 2016. PMID:  27442863, DOI: 10.1038/nprot.2016.086
Assembly: GrCH38/hg38
Supplementary files format and content: Two bigwig files per file representing the plus and minus strand
Library strategy: Pro-seq

molecule: other

extract_protocol:
Cell nuclei were isolated and provided to Arpeggio Biosciences
Library construction was performed by Arpeggio Biosciences as describe in Mahat et al. 2016. PMID:  27442863, DOI: 10.1038/nprot.2016.086

value: Non-Small Cell Lung Cancer

value: 6h, 250ng/mL dox


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_745


title: isolate g2g_023, replicate 1

description: Library name: g2g_023_1


title: Young BMDM, NS control, 3dp, biol rep 5

value: WT


title: isolate g2g_021, replicate 2

description: Library name: g2g_021_2


title: Young BMDM, NS control, 3dp, biol rep 4


title: A549_shNRF2_6hr_paired_rep2


title: isolate g2g_021, replicate 1

description: Library name: g2g_021_1


title: A549_shNRF2_6hr_paired_rep1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_750


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_744


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_742


title: A549_shNRF2_3hr_paired_rep2

value: 3h, 250ng/mL dox


title: A549_shNRF2_3hr_paired_rep3


title: Young BMDM, β-glucan then LPS, biol rep 2

value: 3 days post 5μg/mL β-Glucan for 24 hours, then restimulated 4 hours prior to harvest with 100ng/mL LPS


title: isolate g2g_020, replicate 1

description: Library name: g2g_020_1


title: isolate g2g_020, replicate 2

description: Library name: g2g_020_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_741


title: Young BMDM, β-glucan then LPS, biol rep 3

value: 10-12 weeks


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_743


title: Young BMDM, β-glucan then LPS, biol rep 1


title: A549_shNRF2_3hr_paired_rep1


title: isolate g2g_019, replicate 2

description: Library name: g2g_019_2


title: Young BMDM, LPS, 4hr, biol rep 3

value: 4hrs post 100ng/mL LPS


title: A549_shNRF2_0hr_paired_rep3

value: no dox


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_738

value: spinal neuron differentiation

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_739


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_740


title: isolate g2g_019, replicate 1

description: Library name: g2g_019_1

value: bacterial

value: Clinical Isolate


title: Young BMDM, LPS, 4hr, biol rep 2


title: Aged BMDM, β-glucan, 4h, biol rep 2

value: 18-20 months

value: 4hrs post 5μg/mL β-Glucan


title: Young BMDM, LPS, 4hr, biol rep 1


title: Young BMDM, β-glucan, 3dp, biol rep 3

value: 3 days post 5μg/mL β-Glucan for 24 hours


title: PBMC AMI rep12

city: 武汉

first: yi

last: he

address: 武汉市蔡甸区同济医院科研大楼

country: China

institute: 华中科技大学附属同济医院

data_processing:
Cutadapt was used to trim adapters and filter for sequences.
SPORTS1.1 (Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs) was used to perfom PANDORA-seq analysis.Junchao Shi, Eun-A Ko, Kenton M. Sanders, Qi Chen, Tong Zhou. SPORTS1.0: a tool for annotating and profiling non-coding RNAs optimized for rRNA-and tRNA-derived small RNAs. Genomics, Proteomics & Bioinformatics (2018) doi.org/10.1016/j.gpb.2018.04.004
Assembly: hg19
Supplementary files format and content: tab-delimited text files include read counts for each sample

source_name: PBMC

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen). RNAs were treated with T4PNK, then AlkB before cDNA library construction.The RNA segment was separated by PAGE, then a 15- to 45-nucleotide stripe was selected and recycled.
The adapters were obtained from the QIAseq® miRNA Library Kit (QIAGEN: 331505) and ligated sequentially. The amplified flow cell was sequenced on the Illumina system by epibiotek (Guangzhou Epibiotek Co., Ltd., Guangzhou, China).

value: PBMC

value: acute myocardial infarction


title: A549_shNRF2_0hr_paired_rep1

value: Non-Small Cell Lung Cancer


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_737


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_736


title: isolate g2g_018, replicate 1

description: Library name: g2g_018_1


title: isolate g2g_013, replicate 4

description: Library name: g2g_013_4


title: Young BMDM, β-glucan, 3dp, biol rep 2

value: bone marrow-derived macrophage

value: Male


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_735


title: isolate g2g_013, replicate 3

description: Library name: g2g_013_3


title: Young BMDM, β-glucan, 24h, biol rep 3

value: WT

value: 24hrs post 5μg/mL β-Glucan


title: PBMC AMI rep10

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_734


title: Young BMDM, β-glucan, 3dp, biol rep 1

value: 10-12 weeks


title: isolate g2g_013, replicate 2

description: Library name: g2g_013_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_733


title: PBMC AMI rep8

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: PBMC AMI rep9

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: isolate g2g_010, replicate 4

description: Library name: g2g_010_4


title: isolate g2g_018, replicate 2

description: Library name: g2g_018_2


title: A549_shNRF2_0hr_paired_rep2


title: isolate g2g_010, replicate 3

description: Library name: g2g_010_3


title: Young BMDM, β-glucan, 24h, biol rep 2


title: Young BMDM, β-glucan, 24h, biol rep 1


title: isolate g2g_010, replicate 2

description: Library name: g2g_010_2


title: Young BMDM, β-glucan, 4h, biol rep 2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_730


title: Young BMDM, β-glucan, 4h, biol rep 3


title: PBMC AMI rep11

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: PBMC AMI rep5

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_729


title: Young BMDM, NS control, 3dp, biol rep 3

value: 3 days post 0.1% NS for 24 hrs


title: isolate g2g_009, replicate 2

description: Library name: g2g_009_2


title: isolate g2g_013, replicate 1

description: Library name: g2g_013_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_727


title: Young BMDM, β-glucan, 4h, biol rep 1


title: PBMC AMI rep4

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: PBMC AMI rep3

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_728


title: PBMC AMI rep2

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: PBMC AMI rep7

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: isolate g2g_009, replicate 1

description: Library name: g2g_009_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_732


title: isolate g2g_008, replicate 2

description: Library name: g2g_008_2


title: PBMC AMI rep1

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: isolate g2g_008, replicate 1

description: Library name: g2g_008_1


title: PBMC AMI rep6

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Jag mutant 2

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

institute: Cincinnati Children's Hospital

description:
scRNA-Seq on P15 mouse liver
ICGS-annotations.txt

data_processing:
CellRanger version 3.0.2 was applied to the  scRNA-Seq FASTQ files, alinged to both the mm10 genome.
SoupX ambient RNA removal was perfomred using an estimated contamination fraction of 15% on all samples.
Cell populations were defined through joint integration in ICGS2 (AltAnalyze v.2.1.4), with doublets excluded using stringent cluster re-classification in cellHarmony (rho>0.5 – excludes 5,068 out of total 49,440 cells from the 4 captures). ICGS2 robustly detects transcriptionally distinct populations without the need to set a predefined resolution (iteratively determines number of clusters from the data). Direct comparative analyses between Jag1+/− and wild-type control was further evaluated using the software cellHarmony.
Assembly: mm10
Supplementary files format and content: CellRanger filtered HDF5 sparse count matrix (h5)
Supplementary files format and content: Cell barcode cluster annotations

source_name: Liver

extract_protocol:
Postnatal day (P)15 mouse livers were dissociated from two animals of each genotype, wild-type and Jag1+/−, using a cold protease protocol to avoid thermal and long collagenase incubation times that may induce technical changes to the transcriptional signatures (dx.doi.org/10.17504/protocols.io.bhpcj5iw). Given the small sample size, only left lobes from females were used to reduce variability.
Single cell RNA Sequencing was performed using 10x Genomics 3’ version 3.1 chemistry, targeting a minimum of 30,000 UMI per cell barcode (on average) and 7k cell barcodes per sample
Dual-indexed transcriptome libraries were pooled and sequenced across multiple Illumina Novaseq 6000 S4 or X plus flow cells (Illumina) with PE150+10+10 or PE100+10+10 settings.

value: Liver

tag: age


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_731

value: spinal neuron differentiation


title: PBMC UA rep12

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院

value: unstable angina


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_726

value: homogenous protocol


title: PBMC UA rep11

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Young BMDM, NS control, 3dp, biol rep 1


title: isolate g2g_010, replicate 1

description: Library name: g2g_010_1

value: bacterial

value: Clinical Isolate


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_725


title: isolate g2g_007, replicate 2

description: Library name: g2g_007_2


title: PBMC UA rep9

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Young BMDM, NS control, 3dp, biol rep 2


title: Jag mutant 1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_720


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_723


title: PNMT-Cre mice, sleep deprivation ,rep2

city: Shijiazhuang

first: Shuxian

last: Yin

state: Hebei province

address: zhongshan road

institute: Hebei Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using fastp version 0.19.5；RNA-seq reads were aligned to the hg38 genome assembly using Hisat2 version 2.1.0 .
Gene abundance measurements were generationed and normalized  using Stringtie ; The normalized standard were Fragments Per Kilobase of exon per Megabase of library size (FPKM)
Differential expression were analysed  using edgeR package in R program version 3.4.3
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw fragment counts for each Sample

source_name: metastatic tumor of lung

growth_protocol: The experimental animals were purchased and subsequently housed in a specific pathogen-free (SPF) animal facility, where the temperature was maintained at approximately 23 ± 1°C, humidity at about 60 ± 5%, and a 12-hour light-dark cycle was provided.

extract_protocol:
Total RNA was extracted from tissue using the RNeasy mini kit (Qiagen, Germany).  1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: a treatment group with clozapine N-oxide daily via intraperitoneal injection

value: metastatic tumor of lung

value: SD+clozapine N-oxide


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_722


title: PBMC UA rep7

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院

value: PBMC


title: isolate g2g_006, replicate 2

description: Library name: g2g_006_2


title: WT1


title: PNMT-Cre mice, sleep deprivation ,rep1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_718


title: C57 BL/6J, sleep deprivation ,rep2

value: SD


title: PBMC UA rep6

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_721


title: isolate g2g_006, replicate 1

description: Library name: g2g_006_1


title: PBMC UA rep8

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: isolate g2g_005, replicate 2

description: Library name: g2g_005_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_719


title: C57 BL/6J, normal sleep,rep3

value: no


title: PBMC UA rep2

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_714


title: isolate g2g_005, replicate 1

description: Library name: g2g_005_1


title: isolate g2g_007, replicate 1

description: Library name: g2g_007_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_724


title: WT2


title: PBMC UA rep10

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: C57 BL/6J, sleep deprivation ,rep3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_717


title: PBMC UA rep5

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: isolate g2g_003, replicate 2

description: Library name: g2g_003_2


title: PNMT-Cre mice, sleep deprivation ,rep3


title: PBMC UA rep4

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_716


title: isolate g2g_001, replicate 2

description: Library name: g2g_001_2


title: isolate g2g_003, replicate 1

description: Library name: g2g_003_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_712


title: C57 BL/6J, normal sleep,rep1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_715


title: C57 BL/6J, sleep deprivation ,rep1


title: isolate g2g_002, replicate 1

description: Library name: g2g_002_1


title: isolate g2g_004, replicate 2

description: Library name: g2g_004_2


title: PBMC CON rep11

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院

value: healthy control


title: PBMC UA rep3

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: isolate g2g_002, replicate 2

description: Library name: g2g_002_2


title: C57 BL/6J, normal sleep,rep2


title: PBMC UA rep1

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: PBMC CON rep12

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_713


title: isolate g2g_001, replicate 1

description: Library name: g2g_001_1


title: isolate vci_h37, replicate 2

description: Library name: vci_h37_2


title: 2_Eo_DEG_G9_day5_VC_ATAC

city: Cambridge

first: Bertie

last: Gottgens

address: Jeffrey Cheah Biomedical Centre

country: United Kingdom

institute: University of Cambridge

library_source: genomic single cell

data_processing:
Demultiplexing, barcode processing, gene counting, and aggregation were carried out using the Cell Ranger-Arc software (version 2.0.1)  by mapping to the mm10 reference genome (arc-mm10-2020-A-2.0.0).
Assembly: 10x Genomics multiome mm10 reference (arc-mm10-2020-A-2.0.0)
Supplementary files format and content: transcriptomic and ATAC peak count matrices and additional metadata

molecule: genomic DNA

growth_protocol: Runx1Venus EomesmCherry-degron ESC lines were maintained in feeder free culture conditions in serum + LIF as previously described(Costello et al., 2011). 48-72 hrs prior to induction of hematopoietic differentiation cells were washed with PBS and cultured in serum free ES media containing 50% Neurobasal Media (Gibco, Cat # 21103049), 50% DMEM/F12 (Gibco, Cat # 11320033), supplemented with 0.5X of both N2 (Gibco, Cat#17502048) and B27 (Gibco, Cat# 17504044), 1%Pen/Strep, 1% glutamine, 0.05% BSA (Gibco, Cat# 15260037), 1 uM PD0325091, 3 uM CHIR99021 and 1000 U/ml LIF. At D0 cells were dissociated using Trypsin-LE (Gibco) and seeded at a density of 1×10^5 cells ml in serum-free differentiation (SF-D) media(Nostro et al., 2008) and cultured on an orbital shaker at 70 rpm for ~18 hrs in the absence of growth factors to form EBs. At D2, EBs were split 1:3 in SF-D media containing recombinant human (rh) VEGF (5 ng ml-1; R&D Systems), rhBMP4 (10 ng ml-1; R&D Systems) and Activin A (5 ng ml-1; R&D Systems) for 48 hr. At D3,  EBs were treated with either DMSO for WT controls or dTAG-13 for Eomes KD (100 nM, Biotechne Tocris Cat #6605). At D4, EBs were split 1:2 in SF-D media containing rhVEGF (5 ng ml-1; R&D Systems), rhBMP4 (10 ng ml-1; R&D Systems) and Activin A (5 ng ml-1; R&D Systems) for 24 hr.

extract_protocol:
Nuclear isolation was performed according to 10X protocol for cell lines and PBMCs, using the low-cell input version (https://assets.ctfassets.net/an68im79xiti/6t5iwATCRaHB4VWOJm2Vgc/bdfd23cdc1d0a321 487c8b231a448103/CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Seque ncing_RevB.pdf). Briefly, the 50μl cell suspension was transferred to a 0.2ml PCR tube and centrifuged for 5 minutes at 300g. After removing the supernatant, cells were resuspended in 50μl ice cold nuclear extraction (NE) buffer (10mM Tris pH 7.5, 10mM NaCl, 3mM MgCl2, 1% BSA, 0.1% Tween, 1mM DTT, 1U/ul RNaseIn (Promega), 0.1% NP40, 0.01% Digitonin) followed by 4 minutes incubation on ice. 50μl of wash buffer (NE buffer without NP40 and digitonin) was added and nuclei were centrifuged for 5 minutes at 500g and 4°C. After removing the supernatant, nuclei were washed once in 50μl of diluted nuclei buffer (10x Genomics), span down, and resuspended in 7ul of diluted nuclei buffer (10x Genomics). 1μl was used to assess quality using a microscope and to count nuclei using a Countess II instrument. >99% of nuclei stained positive for trypan blue, and the nuclei had the expected morphology. Nuclei were then diluted such that a maximum of 16,000 were used for 10x Multiome library preparation.
Libraries were prepared using the 10x Genomics Chromium and sequenced on a Novaseq 6000 instrument (Illumina) using the recommended read-lengths.

treatment_protocol: At D3, cells EBs were treated with either DMSO for WT controls or dTAG-13 for Eomes KD (100 nM, Biotechne Tocris Cat #6605).

value: in vitro cell line

tag: time

value: ESC to hematovascular mesoderm differentiation

tag: replicate

tag: sequencing protocol

value: Single Cell Multiome ATAC + Gene Expression v1


title: 2_Eo_DEG_G9_day4_VC_ATAC

value: WT


title: 2_Eo_DEG_G9_day5_dTAG_ATAC

value: Eomes KD


title: PBMC CON rep10

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_709


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_710


title: isolate vci_h37, replicate 1

description: Library name: vci_h37_1


title: 2_Eo_DEG_G9_day3_5_VC_ATAC


title: PBMC CON rep7

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: isolate vci_erd, replicate 2

description: Library name: vci_erd_2


title: isolate vci_erd, replicate 1

description: Library name: vci_erd_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_708


title: 2_Eo_DEG_G9_day4_dTAG_ATAC


title: PBMC CON rep9

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_711


title: isolate vci_632, replicate 2

description: Library name: vci_632_2


title: isolate vci_632, replicate 1

description: Library name: vci_632_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_706


title: PBMC CON rep6

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: 1B_Eo_DEG_G9_day3_ATAC


title: PBMC CON rep5

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_705


title: isolate vci_625, replicate 2

description: Library name: vci_625_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_704

value: Control


title: PBMC CON rep4

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: 1A_Eo_DEG_G9_day3_ATAC


title: rv_eo_deg_day4_dtag_ATAC


title: PBMC CON rep3

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: isolate vci_617, replicate 2

description: Library name: vci_617_2


title: isolate vci_625, replicate 1

description: Library name: vci_625_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_702

value: spinal neuron differentiation


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_703


title: rv_eo_deg_day4_control_ATAC


title: PBMC CON rep8

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: PBMC CON rep2

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: huES3-D31-2

city: Taipei

first: Jun-An

last: Chen

address: 128 Academia Road, Section 2, Nankang

department: Institute of Molecular Biology

country: Taiwan

institute: Academia Sinica

data_processing:
Adapter contamination in the paired-end reads was removed using PEAT (Li et al, 2015), and the trimmed reads were aligned to GRCh38 using STAR aligner (Dobin et al, 2013). The standard GTF-formatted transcript annotation was defined by GRCh38 (Harrow et al, 2012), which includes many evidence-based lncRNAs. We used this annotation to aid the junction read alignment in STAR, the output of which was submitted to Cufflinks (Trapnell et al, 2010) for de novo transcript assembly with the option ‘library type; first-strand’ to allow strand-specific alignments.
Assembly: hg38
Supplementary files format and content: excel file include the count and FPKM value for each sample

source_name: HuES

growth_protocol: HuESs were cultured and differentiated into spinal MNs as previously described (Maury et al., 2014; Tung et al., 2019).

extract_protocol:
Cells were harvested using Trizol reagent at indicated timepoints for strand-specific RNA-seq.
100ng of total RNA was used to construct sequencing libraries with truseq-stranded-total-rna-ribo-zero-plus kit and TruSeq mRNA stranded library prep following the manual protocols.

value: HuES

value: human embryonic stem cell


title: rv_eo_deg_day4_5_dtag_ATAC


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_TARDBP_M337V_Cell_707

value: homogenous protocol


title: 2_Eo_DEG_G9_day3_5_dTAG_ATAC


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_701


title: rv_eo_deg_day3_5_dtag_ATAC


title: isolate vci_602, replicate 2

description: Library name: vci_602_2

value: bacterial

value: Clinical Isolate


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_700


title: rv_eo_deg_day4_5_control_ATAC


title: isolate vci_588, replicate 2

description: Library name: vci_588_2


title: isolate vci_588, replicate 1

description: Library name: vci_588_1


title: 2_Eo_DEG_G9_day5_VC_GEX

molecule: nuclear RNA


title: rv_eo_deg_day3_5_control_ATAC


title: huES3-D31-1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_698


title: huES3-D16-2


title: huES3-D16-3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_697


title: 2_Eo_DEG_G9_day5_dTAG_GEX


title: huES3-D16-1


title: isolate vci_617, replicate 1

description: Library name: vci_617_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_696


title: PBMC CON rep1

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: isolate vci_569, replicate 2

description: Library name: vci_569_2


title: isolate vci_569, replicate 1

description: Library name: vci_569_1


title: huES3-D8-2


title: 2_Eo_DEG_G9_day4_VC_GEX


title: isolate vci_602, replicate 1

description: Library name: vci_602_1


title: isolate vci_567, replicate 2

description: Library name: vci_567_2


title: 2_Eo_DEG_G9_day4_dTAG_GEX


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_699


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_695


title: huES3-D8-1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_694


title: isolate vci_567, replicate 1

description: Library name: vci_567_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_693


title: 2_Eo_DEG_G9_day3_5_VC_GEX


title: 2_Eo_DEG_G9_day3_5_dTAG_GEX


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_692


title: isolate vci_546, replicate 2

description: Library name: vci_546_2


title: isolate vci_546, replicate 1

description: Library name: vci_546_1


title: isolate vci_545, replicate 2

description: Library name: vci_545_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_691


title: 1B_Eo_DEG_G9_day3_GEX


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_690


title: isolate vci_545, replicate 1

description: Library name: vci_545_1


title: rv_eo_deg_day4_dtag_GEX


title: isolate vci_542, replicate 1

description: Library name: vci_542_1


title: rv_eo_deg_day4_control_GEX


title: rv_eo_deg_day4_5_dtag_GEX


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_688


title: isolate vci_542, replicate 2

description: Library name: vci_542_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_687


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_689


title: isolate vci_525, replicate 2

description: Library name: vci_525_2


title: rv_eo_deg_day4_5_control_GEX


title: isolate vci_525, replicate 1

description: Library name: vci_525_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_686


title: rv_eo_deg_day3_5_dtag_GEX


title: isolate vci_505, replicate 1

description: Library name: vci_505_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_685


title: rv_eo_deg_day3_5_control_GEX


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_684


title: isolate vci_499, replicate 1

description: Library name: vci_499_1


title: Camkk2+/+ Stiff 2

city: Madison

first: jianhong

last: ou

state: WI

address: 330 N Orchard Street

institute: Morgridge institute for research

description: HWI-ST1276 (identifier)

data_processing:
RNA-seq reads were trimmed by Trim Galore (v 0.6.7) and counted using salmon (v 1.4.0) for UCSC mm10 annotation.
Assembly: mm10
Supplementary files format and content: csv file of salmon's estimate of the relative abundance of this transcript in units of Transcripts Per Million (TPM)

source_name: bone marrow

growth_protocol: Bone marrow (BM) cells were collected from the femur and tibiae of WT and Camkk2-/- male and female C57Bl/6 mice (8-10 weeks). The BM suspensions were passed through a 70 mm strainer and the red blood cells were lysed using RBC lysis buffer . The BM cells were collected and adjusted to 2´10e6/mL in DMEM conditional media (10% FBS and 30% L929 conditioned medium). BMs were plated in ultra-low attachment multi-well plates at 2´10e6/well. On day 4, half of the medium was refreshed and the cells were ready to use.

extract_protocol:
RNA was extracted using TRIzol reagent and purified by RNeasy mini kit. RNA was extracted and purified as described above. RNA from 2 biological replicates for each experimental point was used for RNA sequencing by Novogene Inc. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand of cDNA was synthesized using random hexamer primers. The second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.rara

treatment_protocol: The collagen-hyaluronic acid hydrogel solution was prepared and neutralized. BMDMs were resuspended in DMEM and mixed with the hydrogel solution at a final concentration of 4´106/mL. Dynamic stiffening was induced 24 hours after cell encapsulation by UV crosslinking using Irgacure 2959 as a photo initiator. After stiffening, the cells were cultured for 48 hours. Then, the hydrogel was digested by collagenase IV (400 U/mL) at 37°C for 1 hour. The detached BMDM were collected and processed for RNA extraction.

value: bone marrow

value: bone marro-derived macrophage

value: stiff hydrogel


title: isolate vci_491, replicate 2

description: Library name: vci_491_2


title: 1A_Eo_DEG_G9_day3_GEX


title: Camkk2+/+ Stiff 1

description: HWI-ST1276 (identifier)


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_682


title: Camkk2+/+/Soft 1/IL4 2

description: HWI-ST1276 (identifier)

value: soft hydrogel/IL4


title: Camkk2+/+/Soft 1/IL4 1

description: HWI-ST1276 (identifier)


title: isolate vci_491, replicate 1

description: Library name: vci_491_1


title: isolate vci_481, replicate 2

description: Library name: vci_481_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_680


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_681


title: Camkk2+/+ /Soft 1

description: HWI-ST1276 (identifier)

value: soft hydrogel


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_679


title: isolate vci_478, replicate 2

description: Library name: vci_478_2


title: Camkk2-/- Stiff 2

description: HWI-ST1276 (identifier)


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_678


title: Camkk2+/+ /Soft 2

description: HWI-ST1276 (identifier)


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_677


title: isolate vci_481, replicate 1

description: Library name: vci_481_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_676


title: Camkk2-/- Stiff 1

description: HWI-ST1276 (identifier)


title: Camkk2-/-/Soft 1/IL4 2

description: HWI-ST1276 (identifier)


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_675


title: isolate vci_499, replicate 2

description: Library name: vci_499_2


title: isolate vci_476, replicate 2

description: Library name: vci_476_2


title: isolate vci_478, replicate 1

description: Library name: vci_478_1


title: Camkk2-/-/Soft 1/IL4 1

description: HWI-ST1276 (identifier)


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_674


title: isolate vci_476, replicate 1

description: Library name: vci_476_1


title: Camkk2-/-/Soft 2

description: HWI-ST1276 (identifier)


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_673


title: isolate vci_472, replicate 1

description: Library name: vci_472_1


title: Camkk2-/-/Soft 1

description: HWI-ST1276 (identifier)


title: isolate vci_472, replicate 2

description: Library name: vci_472_2


title: isolate vci_461, replicate 2

description: Library name: vci_461_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_683


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_672


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_671


title: isolate vci_461, replicate 1

description: Library name: vci_461_1


title: PS19_TPPU, replicate 1, snRNAseq

city: HOUSTON

first: chuangye

last: Qi

state: Texas

address: One plaza

department: Huffington Center

institute: Baylor College of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using CellRanger
removing ambient RNA by CellBender
removing doublets by Scrublet
cell cluster umap analysis by Scanpy and scVI
Assembly: mm10
Supplementary files format and content: hdf5 matrix files

source_name: hippocampus

extract_protocol:
For snRNA-seq, single nucleus suspensions were isolated from about 50mg frozen mouse hippocampus following 10x genomics recommendation.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: hippocampus

value: female

value: 9.5 months old

value: TPPU 3mg/kg  for 12 weeks


title: PS19_TPPU, replicate 2, snRNAseq

description: 10x Genomics

value: male


title: isolate vci_456, replicate 2

description: Library name: vci_456_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_670


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_669


title: PS19, replicate 2, snRNAseq

description: 10x Genomics

value: Vehicle (10%PEG-400 in H2O)


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_668

value: spinal neuron differentiation


title: isolate vci_456, replicate 1

description: Library name: vci_456_1


title: PS19, replicate 1, snRNAseq

description: 10x Genomics


title: WT_TPPU, replicate 2, snRNAseq

description: 10x Genomics


title: isolate vci_455, replicate 2

description: Library name: vci_455_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_667


title: isolate vci_455, replicate 1

description: Library name: vci_455_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_666


title: WT_TPPU, replicate 1, snRNAseq

description: 10x Genomics


title: WT, replicate 2, snRNAseq

description: 10x Genomics


title: isolate vci_453, replicate 2

description: Library name: vci_453_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_665


title: isolate vci_449, replicate 2

description: Library name: vci_449_2


title: isolate vci_453, replicate 1

description: Library name: vci_453_1


title: WT, replicate 1, snRNAseq

description: 10x Genomics


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_663


title: Male CANA 7

city: New York

first: Shoshana

last: Yakar

state: NY

address: 345E 24th Street

institute: New York University

description: Cell culture males.xlsx

data_processing:
sequence reads were assembled and mapped to the mouse reference genome (Ensembl Mus_musculus GRCm38.90) using HISAT2 v.2.1.0.13,
Counts quantification was determined using HTSeq-counts v0.6.0
Differential expression analysis was performed by DESeq2 R/Bioconductor package
Assembly: Ensembl Mus_musculus GRCm38.90
Supplementary files format and content: HTSeq-counts v0.6.0 (.xlsx file)

source_name: Primary osteoblast cells (differentiated bone marrow MSCs)

growth_protocol: Bone marrow MSCs cultured for 7-days in a-modified minimum essential medium (aMEM, CAT#) containing 10% fetal calf serum (FBS), penicillin/sterptomycin and fungizone.

extract_protocol:
RNA was extracted from osteoblast cultures (10 days) using Qiagen RNeasy plus mini kit (Qiagen, cat# 74204). RNA quality was assessed using RNA ScreenTape on a 4200 TapeStation
Illumina TruSeq Stranded Total RNA library prep with Ribozero Gold

treatment_protocol: At day 8 cells were cultured in osteoblast induction media containing: aMEM, 10%FBS,  penicillin/streptomycin, fungizone, dexamethasone (Sigma Cat # D8893), ß-glycerol phosphate (Sigma Cat # 50020), and ascorbic acid (Sigma cat# A4403-100MG).

value: Primary cells

value: osteoblast

value: Male

value: 9 months old

value: Canagliflozine (180 ppm) diet


title: isolate vci_449, replicate 1

description: Library name: vci_449_1

value: bacterial

value: Clinical Isolate


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_664

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_662


title: isolate vci_446, replicate 2

description: Library name: vci_446_2


title: Male CANA 3

description: Cell culture males.xlsx

value: Primary osteoblast cells (differentiated bone marrow MSCs)


title: Male CANA 4

description: Cell culture males.xlsx


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_661


title: Male CANA 1

description: Cell culture males.xlsx


title: isolate vci_446, replicate 1

description: Library name: vci_446_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_660


title: isolate vci_444, replicate 2

description: Library name: vci_444_2


title: Male Control 4

description: Cell culture males.xlsx

value: Control diet


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_659


title: isolate vci_444, replicate 1

description: Library name: vci_444_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_658


title: Male Control 3

description: Cell culture males.xlsx


title: Male Control 2

description: Cell culture males.xlsx


title: isolate vci_439, replicate 2

description: Library name: vci_439_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_657


title: isolate vci_439, replicate 1

description: Library name: vci_439_1


title: Male Control 1

description: Cell culture males.xlsx


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_656


title: isolate vci_436, replicate 2

description: Library name: vci_436_2


title: Female CANA 4

description: Cell culture females.xlsx

value: Female


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_655


title: isolate vci_436, replicate 1

description: Library name: vci_436_1


title: Female CANA 3

description: Cell culture females.xlsx


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_654


title: isolate vci_430, replicate 2

description: Library name: vci_430_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_653


title: isolate vci_430, replicate 1

description: Library name: vci_430_1


title: Female Control 3

description: Cell culture females.xlsx


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_652


title: Female Control 2

description: Cell culture females.xlsx


title: isolate vci_417, replicate 2

description: Library name: vci_417_2


title: isolate vci_423, replicate 1

description: Library name: vci_423_1


title: Female Control 1

description: Cell culture females.xlsx


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_651


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_649


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_650


title: Gata2 KO_rep4

first: Kathrin

last: Bernt

state: PA

address: 3501 Civic Center Boulevard,

institute: Children's Hospital of philadelphia

data_processing:
StarAligner
Kallisto
DEseq2
R, EnhancedVolcano, GSEA
htseq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Bone marrow

growth_protocol: Cells were grown in IMDM medium supplemented with 15% heat inactivated FBS, 1% Penicillin/Streptomycin, 1% L-Glutamine, murine IL-3, murine IL-6 (10ng/mL), and murine SCF (20ng/mL).

extract_protocol:
Murine MA9 Gata2 f/f and Gata2 -/- (Gata2 KO) leukemias were subjected to RNA extraction. RNA was purified using Qiagen Rneasy nini or micro kits according to manufacturer's instructions
Library prep was performed using PolyA selected mRNA species (eukaryotic) and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina®. Samples were sequenced using Illumina NovaSeq6000, 65bp paired-end reads, multiplexed.

value: Bone marrow

value: AML

value: MA9 leukemia

value: Gata2 -/-


title: isolate vci_417, replicate 1

description: Library name: vci_417_1


title: Gata2 KO_rep3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_648


title: isolate vci_414, replicate 2

description: Library name: vci_414_2


title: Gata2 KO_rep2


title: Gata2 KO_rep1


title: isolate vci_409, replicate 2

description: Library name: vci_409_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_646


title: Gata2 f/f_rep4

value: Gata2 f/f


title: isolate vci_414, replicate 1

description: Library name: vci_414_1


title: Female CANA 1

description: Cell culture females.xlsx


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_647

value: spinal neuron differentiation


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_644


title: isolate vci_409, replicate 1

description: Library name: vci_409_1


title: isolate vci_423, replicate 2

description: Library name: vci_423_2


title: Gata2 f/f_rep2


title: Gata2 f/f_rep3


title: isolate vci_403, replicate 2

description: Library name: vci_403_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_R495X_Cell_645


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_643


title: isolate vci_403, replicate 1

description: Library name: vci_403_1


title: Gata2 f/f_rep1


title: isolate vci_400, replicate 2

description: Library name: vci_400_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_641


title: mMA9_Gata2 KO_input

library_source: genomic

data_processing:
BWA Alignment
MACS2 peak calling
IGV 2.8.0
Assembly: mm10
Supplementary files format and content: bigwig file

extract_protocol:
MA9 leukemia cells were collected from bone marrow of primary animals and transduced with Cre or MIT as control, then sorted for GFP and tdTomato. After 7-9 days in culture ChIP was performed. Briefly, samples were crosslinked, lysed, sonicated and immunoprecipated with the indicated antibody overnight. After a series of washes they were reverse crosslinked overnight and DNA extracted.
Library prep was performed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®, Illumina NovaSeq 6000, 2x100bp paired-end reads, multiplexed

tag: antibody


title: isolate vci_395, replicate 2

description: Library name: vci_395_2


title: isolate vci_400, replicate 1

description: Library name: vci_400_1


title: mMA9_Gata2 ff_input

tag: cell line


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_642

tag: cell type


title: isolate vci_395, replicate 1

description: Library name: vci_395_1

tag: genotype


title: mMA9_Gata2 KO-input

tag: treatment


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_638

tag: sequencing batch


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_639


title: isolate vci_392, replicate 2

description: Library name: vci_392_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_640


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_637


title: mMA9_Gata2 ff_H3K4m1-treat

tag: tissue


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_636


title: isolate vci_389, replicate 2

description: Library name: vci_389_2


title: isolate vci_379, replicate 2

description: Library name: vci_379_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_635


title: mMA9_Gata2 KO_H3K27ac-treat


title: isolate vci_379, replicate 1

description: Library name: vci_379_1


title: mMA9_Gata2 ff_H3K27ac-treat


title: mMA9_Gata2 KO_Gata2_treat_rep2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_633


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_634


title: mMA9_Gata2 KO_Gata2_treat_rep1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_632


title: isolate vci_373, replicate 2

description: Library name: vci_373_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_631


title: isolate vci_366, replicate 2

description: Library name: vci_366_2


title: mMA9_Gata2 ff_Gata2_treat_rep1


title: mMA9_Gata2 ff-input


title: mMA9_Gata2 KO_H3K4m1-treat


title: isolate vci_392, replicate 1

description: Library name: vci_392_1


title: D14_Olig2

city: Toronto

first: Maryam

last: Faiz

address: 1 Kings College Circle

country: Canada

institute: University of Toronto

data_processing:
Fastq files were first demultiplexed with Kallisto29 (RRID:SCR_016582)(v0.48.0) and Bustools30 (RRID:SCR_018210)(V 0.41.0) using supplied whitelists (Data S1) with the -BDWTA option and aligning to GRCm38.96 with Cre sequence appended to the end. Bustools30 was then used to generate gene count tables. Cells were plotted based upon UMI counts per barcode, thresholds were selected based on inflection point of UMI count per barcode plots. These thresholds produced read and gene count distributions that were comparable between all treatment groups (Supplemental Figure 1A, Supplemental Figure 5A). Gene count tables were made into S4 objects, scaled, normalized and dimensions reduced (PCA then UMAP) using the Seurat31 package (RRID:SCR_016341) (v4.1). Clusters identified as microglia and as vascular and leptomeningeal cells (VLMCs) (Supplemental Figure 1B-C [cluster 8], Supplemental Figure 5B-C [cluster 6 and 8]) were removed prior to further analysis.
Assembly: Mus_musculus.GRCm39.cdna.all.fa.gz appended with the Cre sequence
Supplementary files format and content: Fastq files were first demultiplexed with Kallisto29 (RRID:SCR_016582)(v0.48.0) and Bustools30 (RRID:SCR_018210)(V 0.41.0) using supplied whitelists (Data S1) with the -BDWTA option and aligning to GRCm38.96 with Cre sequence appended to the end. Bustools30 was then used to generate gene count tables. Cells were plotted based upon UMI counts per barcode, thresholds were selected based on inflection point of UMI count per barcode plots. These thresholds produced read and gene count distributions that were comparable between all treatment groups (Supplemental Figure 1A, Supplemental Figure 5A). Gene count tables were made into S4 objects, scaled, normalized and dimensions reduced (PCA then UMAP) using the Seurat31 package (RRID:SCR_016341) (v4.1). Clusters identified as microglia and as vascular and leptomeningeal cells (VLMCs) (Supplemental Figure 1B-C [cluster 8], Supplemental Figure 5BC [cluster 6 and 8]) were removed prior to further analysis. For each sample a counts.barcodes.txt, counts.genes.txt and counts.mtx is provided

source_name: prmary glial cells

extract_protocol:
For Ai14 reprogramming, LV-hGFAP::Sox10-P2A-Cre, LV-hGFAP::Olig2-P2A-Cre, LV-hGFAP::Nkx6.2-P2A-Cre, and control LV-hGFAP::BFP-T2A-Cre were used. For Ai14;Aldh1l1-CreERT2 reprogramming, LV-hGFAP::Sox10-P2A-zsGreen, LV-hGFAP::Olig2-P2A-zsGreen, LV-hGFAP::Nkx6.2-P2A-zsGreen and control LV-hGFAP::zsGreen were used. A multiplicity of infection (MOI) of 100 was used for all experiments. Virus-containing astrocyte media was placed on the cells and left overnight. Viral media was replaced with fresh astrocyte media one day post transduction (DPT). Three DPT, cells were switched to OPC differentiation media2 [DMEM/F12/Glutamax (Gibco Catalogue No.  11330032), 1X N2 (Gibco Catalogue No. 17502048), 1X B27 without vitamin A (Gibco Catalogue No. 17504044), 200 ng/ml SHH (R&D Systems Catalogue No.  464-SH), 20 ng/ml FGF (R&D Systems Catalogue No. 3139-FB), 4 ng/ml PDGF (Sigma Catalogue No. SRP3228)]. At 10 DPT, the cells were switched to OL differentiation media2 [DMEM/F12/Glutamax, 1X N2, 1X B27 without vitamin A, 40 ng/ml T3 (T2877 Catalogue No. Sigma), 200 ng/ml SHH, 100 ng/ml Noggin (R&D Systems Catalogue No. 1967-NG), 10 µM cAMP (Sigma Catalogue No. A9501), 100 ng/ml IGF (R&D Systems Catalogue No. 791-MG), 10 ng/ml NT3 (Sigma Catalogue No. SRP6007)].
At 14DPT, LV-hGFAP::Sox10-P2A-Cre, LV-hGFAP::Olig2-P2A-Cre, LV-hGFAP::Nkx6.2-P2A-Cre, and control LV-hGFAP::BFP-T2A-Cre cultures were processed using the BD Rhapsody System (BD Biosciences) and then sequenced. For single-cell isolation, an average of 9813.75 viable cells were captured in wells at cell load (Table S1). The BD Rhapsody scanner reported an average multiplet rate of 10.13% and an average number of wells with viable cells and a bead of 7081.5 (Table S1). Detailed metrics for each sample can be found in Table S1. Samples were down-sampled to 2500 cells and carried through and converted to cDNA using the BD Rhapsody WTA Reagent Kit (Becton Dickinson Canada, Catalogue No. 633802). Each cell was sequenced at approximately 100 million reads per cell (at least 2x150 bp paired-end reads) on a Novaseq (Donnelly Sequencing Centre, University of Toronto).
In addition, LV-GFAP::Sox10 and control LV-GFAP::Cre cultures were collected prior to transduction, at 3DPT and 8DPT, and processed using the BD Rhapsody System (BD Biosciences) and then sequenced. For single-cell isolation, an average of 10263.8 viable cells were captured in wells at cell load (Table S2). The BD Rhapsody scanner reported an average multiplet rate of 6.86% and an average number of wells with viable cells and a bead of 7785 (Table S2). Detailed metrics for each sample can be found in Table S2. Samples were down-sampled to 2500 cells and carried through and converted to cDNA using the BD Rhapsody WTA Reagent Kit (Becton Dickinson Canada, Catalogue No. 633802). Each cell was sequenced at approximately 100 million reads per cell (at least 2x150 bp paired-end reads) on a Novaseq (Donnelly Sequencing Centre, University of Toronto).
In addition, LV-GFAP::Sox10 and control LV-GFAP::Cre cultures were collected prior to transduction, at 3DPT and 8DPT, and processed using the BD Rhapsody System (BD Biosciences) and then sequenced. For single-cell isolation, an average of 10263.8 viable cells were captured in wells at cell load (Table S2). The BD Rhapsody scanner reported an average multiplet rate of 6.86% and an average number of wells with viable cells and a bead of 7785 (Table S2). Detailed metrics for each sample can be found in Table S2.

value: prmary glial cells


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_629

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: isolate vci_361, replicate 2

description: Library name: vci_361_2

data_processing:
See publication for complete details. Paired end reads were demultiplexed by their inline barcodes using cutadapt and a custom demultiplexer script.
Reads were mapped with bowtie2 to H37Rv reference.
Non-unique reads were removed with picard.
Reads were mapped to H37Rv regions with a custom script, removing low mapq reads. Reported values are log2 transformed and library depth normalized.
Assembly: NC_000962.3
Supplementary files format and content: 2D csvs with gene IDs and sample names

extract_protocol:
Crosslinks were reversed by incubating at 70°C. Cells were lysed in Trizol using bead beating tubes. RNA was extracted by adding chloroform and removing the aqueous upper layer. RNA was precipitated onto carboxylate-modified magnetic beads with isopropanol-GuHCl and beads were washed with ethanol. RNA was resuspended into tris-buffered water. See publication for full details.
RNA library preps were prepared for Illumina sequencing using a custom protocol, see publication for complete details. Briefly, cDNA was barcoded using random primers with inline barcodes and an Illumina sequencing adapter. Barcoded, single-stranded cDNA was pooled and a second adapter was added using a splint ligation. Reads corresponding to rRNA were depleted using Taq polymerase's endonuclease activity, combined with a library of guides. Libraries were amplified and sequenced on either a MiSeq or NovaSeq instrument.


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_628


title: D14_Nkx6.2


title: isolate vci_361, replicate 1

description: Library name: vci_361_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_627


title: D14_Sox10


title: D8_Control

value: Cre


title: isolate vci_359, replicate 1

description: Library name: vci_359_1


title: isolate vci_358, replicate 2

description: Library name: vci_358_2


title: D14_Control


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_624


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_626


title: isolate vci_373, replicate 1

description: Library name: vci_373_1


title: isolate vci_358, replicate 1

description: Library name: vci_358_1


title: mMA9_Gata2 ff_Gata2_treat_rep2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_630


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_623


title: D3_Sox10


title: isolate vci_366, replicate 1

description: Library name: vci_366_1


title: isolate vci_355, replicate 1

description: Library name: vci_355_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_621


title: isolate vci_350, replicate 2

description: Library name: vci_350_2


title: isolate vci_359, replicate 2

description: Library name: vci_359_2


title: isolate vci_350, replicate 1

description: Library name: vci_350_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_620


title: Input

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

institute: Fudan University Shanghai Cancer Center

data_processing:
mapping to mouse genome mm10 use bowtie2
Call pake use MACS2
Assembly: mm10
Supplementary files format and content: bedgraph
Library strategy: CUT & Tag-seq

source_name: liver

growth_protocol: Primary hepatocytes were seeded in collagen I conjugated 6-well plates (2.5 x 10 ^ 6 cells/well) and cultured in Medium 199 with 10% FBS.

extract_protocol:
CUT & Tag for primary hepatocytes was performed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) following their protocol.
Libraries were constructed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903) following their protocol.

treatment_protocol: After cell attachment, hepatocytes were transduced with adenovirus in appropriate MOI (MOI = 10 for overexpression adenovirus) for 12 h, and then hepatocytes were starved for another 12 h before harvested. For FoxO1 and input samples, genomic DNA were extracted from hepatocytes transduced with control adenovirus.

value: liver

value: primary hepatocytes

value: mouse primary hepatpcytes

value: WT

value: fasted


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_619

first: Eva

last: Hedlund

value: homogenous protocol


title: FoxO1


title: isolate vci_347, replicate 2

first: Peter

last: Culviner

description: Library name: vci_347_2

value: bacterial

value: Clinical Isolate


title: D0

value: untreated


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_618


title: D3_Control


title: isolate vci_347, replicate 1

description: Library name: vci_347_1


title: D8_Sox10


title: Fasted_AZ191_3

city: Shanghai

first: Hong

last: Zhang

address: 600 Yishan Road

department: Shanghai Diabetes Institute

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
The cleaned reads were aligned to the index file of the mm10 genome generated by HISAT2 version 2.0.5. Read counts for each gene were calculated by HTSeq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 μg of total RNA was used for the construction of sequencing libraries.
Libraries were constructed using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme)

treatment_protocol: After cell attachment, hepatocytes were starved for another 12 h following vehicle or AZ191 treatments.

value: AZ191, fasted


title: isolate vci_355, replicate 2

description: Library name: vci_355_2


title: Fasted_AZ191_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_625

city: Stockholm

address: Svante Arrhenius v. 16C

institute: Stockholm University


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_616


title: Fasted_AZ191_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_617


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_622


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_615


title: isolate vci_344, replicate 2

city: Boston

address: 677 Huntington Ave

institute: Harvard School of Public Health

description: Library name: vci_344_2


title: isolate vci_344, replicate 1

description: Library name: vci_344_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_614


title: Fasted_Vehicle_2

value: vehicle, fasted


title: DYRK1B

value: Flag-DYRK1B, fasted


title: Fasted_Vehicle_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_612


title: isolate vci_343, replicate 1

description: Library name: vci_343_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_613


title: isolate vci_343, replicate 2

description: Library name: vci_343_2


title: Fed_AZ191_3

value: AZ191, fed


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_611


title: isolate vci_341, replicate 2

description: Library name: vci_341_2


title: Fed_AZ191_2


title: isolate vci_346, replicate 1

description: Library name: vci_346_1


title: isolate vci_346, replicate 2

description: Library name: vci_346_2


title: Fed_AZ191_1


title: isolate vci_341, replicate 1

description: Library name: vci_341_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_609


title: isolate vci_340, replicate 2

description: Library name: vci_340_2


title: Fasted_Vehicle_3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_608


title: isolate vci_340, replicate 1

description: Library name: vci_340_1


title: Fed_Vehicle_2

value: vehicle, fed


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_607

value: spinal neuron differentiation


title: isolate vci_338, replicate 2

description: Library name: vci_338_2


title: isolate vci_338, replicate 1

description: Library name: vci_338_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_606


title: Fed_Vehicle_1


title: oocyte-3,rep3

city: Hefei

first: Tie

last: Chang

address: Huangshan Road

institute: University of Science and Technology of China

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).
We aligned reads of all samples to the mus musculus（ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/） reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/, version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. HISAT2 allows multiple alignments per read (up to 20 by default) and a maximum of two mismatch when mapping the reads to the reference. HISAT2 build a database of potential splice junctions and confirms these by comparing the previously unmapped reads against the database of putative junctions.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Mus_musculus.GRCm38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: oocyte

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: oocyte


title: Fed_Vehicle_3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_605


title: oocyte-3,rep2


title: isolate vci_337, replicate 2

description: Library name: vci_337_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_604


title: isolate vci_336, replicate 2

description: Library name: vci_336_2


title: oocyte-3,rep1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_610


title: oocyte-2,rep3


title: isolate vci_336, replicate 1

description: Library name: vci_336_1


title: oocyte-2, rep2


title: isolate vci_337, replicate 1

description: Library name: vci_337_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_602


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_600


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_601


title: isolate vci_334, replicate 2

description: Library name: vci_334_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_599


title: isolate vci_333, replicate 1

description: Library name: vci_333_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_598


title: oocyte-1, rep2

value: fresh


title: isolate vci_334, replicate 1

description: Library name: vci_334_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_597


title: oocyte-1, rep1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_596