title: Donor_A_day1_BCG_H3K18lac

description: Library name: Sample 11

value: Adult Human Peripheral Blood

value: Monocyte


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_835

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: control, replicate 1, scRNAseq, InDrop

city: Nashville

first: Guoqiang

last: Gu

state: TN

address: 2213 Garland Avenue, MRB4, Rm 9415

department: Cell and Developmental Biology

country: USA

institute: Vanderbilt University

description:
Library name: G2S2F2Con
cells were flowed into a microfluidic chip for droplet-formation. The droplets were then used for reverse transcription, library preparation and sequencing (targeting 120 million reads. Novaseq 6000, Illumina)

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

molecule: total RNA

organism: Mus musculus

source_name: islet

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

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

treatment_protocol: None.

tag: tissue

value: islet

tag: strain

value: mixed pancreatic islets


title: Injured 1 day, untreated, HA, 50

city: Villanova

first: Susan

last: Margulies

address: 805 Stoke Road

institute: Emory University

description:
G2HA130118U-1
Count

library_source: transcriptomic

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

organism: Sus scrofa

source_name: brain

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

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

value: brain

tag: brain region

value: hippocampus + amygdala

tag: group name

value: Injured 1 day

tag: survival time_post_injury

value: 1 day

value: untreated

tag: Sex

value: female


title: Donor_B_day1_BCG_H3K18lac

city: Parkville

first: Boris

last: Novakovic

state: Victoria

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

country: Australia

institute: Murdoch Children's Research Institute

description: Library name: Sample 12

library_source: genomic

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

molecule: genomic DNA

source_name: Adult Human Peripheral Blood

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

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

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

tag: donor

tag: chip antibody

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

value: BCG exposed, collected at 24 hours post exposure


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_832


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_833


title: Donor_A_day1_BCG_LDHi_H3K18lac

description: Library name: Sample 15

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


title: microglia, Twi, untreated, P15, sample2

city: Philadelphia

first: F. Chris

last: Bennett

address: 3150 Civic center blvd

institute: UPenn

description:
Library name: G5-1
analysis_id: p15t_3
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds
slingshot_mg0123_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)

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: myeloid

value: Twi

value: unmanipulated

tag: batch


title: Injured 1 day, untreated, FC, 88

description:
G2FA130118U-1
Count

value: frontal cortex


title: Atf4 mut, replicate 1, scRNAseq, InDrop

description:
Library name: G1S1F2Mut
cells were flowed into a microfluidic chip for droplet-formation. The droplets were then used for reverse transcription, library preparation and sequencing (targeting 120 million reads. Novaseq 6000, Illumina)

value: Atf4F/F; Ins1Cre


title: microglia, WT, untreated, P15, sample3

description:
Library name: G6-1
analysis_id: p15w_1
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds

value: WT


title: Donor_D_day1_RPMI_H3K18lac

description: Library name: Sample 10

value: Adult Human Peripheral Blood

value: Monocyte

value: RPMI media only, collected at 24 hours post culture


title: Injured 1 day, untreated, HA, 41

description:
G2HA130116U-2
Count

value: brain

value: hippocampus + amygdala


title: microglia, Twi, untreated, P15, sample1

description:
Library name: G4-1
analysis_id: p15t_2
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds
slingshot_mg0123_seurat_object.rds


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_831

value: spinal neuron differentiation

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_830


title: Donor_C_day1_RPMI_H3K18lac

description: Library name: Sample 9


title: Donor_B_day1_RPMI_H3K18lac

description: Library name: Sample 8


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_829


title: Injured 1 day, untreated, FC, 73

description:
G2FA130116U-2
Count

value: Injured 1 day

value: 1 day

value: untreated

value: female


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_828


title: microglia, WT, untreated, P15, sample2

description:
Library name: F8-1
analysis_id: p15w_3
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds

value: myeloid


title: Donor_A_day1_RPMI_H3K18lac

description: Library name: Sample 7

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


title: Injured 1 day, untreated, HA, 20

description:
G2HA130109U-2
Count


title: microglia, WT, untreated, P15, sample1

description:
Library name: F7-1
analysis_id: p15w_2
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds

value: unmanipulated


title: Donor_3_d6_LPS_H3K18lac

description: Library name: Sample 6

value: LPS exposed for 24 hours, culture for 5 days to macrophage


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_826


title: Donor_1_d6_LPS_H3K18lac

description: Library name: Sample 4


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_825


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_heterozygous_Cell_827


title: Donor_2_d6_LPS_H3K18lac

description: Library name: Sample 5


title: Injured 1 day, untreated, FC, 70

description:
G2FA130109U-2
Count

value: frontal cortex


title: Injured 1 day, untreated, FC, 35

description:
G2FA121219U-2
Count


title: microglia, Twi, untreated, P35, sample7

description:
Library name: C6-2
analysis_id: tu___3
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds
slingshot_mg0123_seurat_object.rds

value: Twi


title: microglia, WT, monocyte_transplanted, P35, sample4

description:
Library name: C7-2
analysis_id: wt___4
Tx_integrated_seurat_object.rds

value: WT


title: Donor_3_d1_LPS_H3K18lac

description: Library name: Sample 3

value: Adult Human Peripheral Blood

value: Monocyte

value: LPS exposed, collected at 24 hours post exposure


title: microglia, Twi, monocyte_transplanted, P35, sample3

description:
Library name: C8-2
analysis_id: tt___3
Tx_integrated_seurat_object.rds

value: brain


title: Injured 1 day, untreated, HA, 65

description:
G2HA121219U-2
Count

value: hippocampus + amygdala


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_824

value: spinal neuron differentiation

value: homogenous protocol


title: Injured 1 day, untreated, HA, 9

description:
G2HA121128U-1
Count

value: Injured 1 day

value: 1 day


title: microglia, Twi, monocyte_transplanted, P35, sample2

description:
Library name: C5-2
analysis_id: tt___2
Tx_integrated_seurat_object.rds


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_823


title: Injured 1 day, untreated, FC, 64

description:
G2FA121128U-1
Count

value: untreated

value: female


title: microglia, Twi, untreated, P35, sample6

description:
Library name: C4-2
analysis_id: tu___2
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds
slingshot_mg0123_seurat_object.rds

value: myeloid


title: Donor_2_d1_LPS_H3K18lac

description: Library name: Sample 2

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


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_822


title: Donor_1_d1_LPS_H3K18lac

description: Library name: Sample 1


title: microglia, Twi, untreated, P35, sample5

description:
Library name: C3-2
analysis_id: tu___1
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds
slingshot_mg0123_seurat_object.rds

value: unmanipulated


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_821


title: Injured 1 day, untreated, FC, 22

description:
G2FA111130U-1
Count

value: frontal cortex


title: microglia, Twi, monocyte_transplanted, P35, sample1

description:
Library name: A6-2
analysis_id: tt___1
Tx_integrated_seurat_object.rds

value: Twi


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_820


title: Injured 1 day, untreated, FC, 56

description:
G2FA111118U-1
Count


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_819


title: female healthy control, recovery_replicate 1

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

description: Library name: 0730sHF2

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

value: peripheral blood mononuclear cells

tag: disease state

value: healthy control

tag: time point_in_exercise

value: T2 (recovery)


title: female GWI patient, recovery_replicate 23

description: Library name: 1930sGF2

value: GWI patient


title: Injured 1 day, untreated, HA, 54

description:
G2HA111104U-1
Count

value: brain


title: female healthy control, maximal exertion_replicate 1

description: Library name: 0729sHF1

value: T1 (maximal exertion)


title: microglia, WT, monocyte_transplanted, P35, sample3

description:
Library name: A5-2
analysis_id: wt___3
Tx_integrated_seurat_object.rds

value: WT


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_818

value: spinal neuron differentiation

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_817


title: Injured 1 day, untreated, FC, 66

description:
G2FA111104U-1
Count

value: Injured 1 day

value: 1 day


title: microglia, WT, monocyte_transplanted, P35, sample1

description:
Library name: A3-2
analysis_id: wt___1
Tx_integrated_seurat_object.rds


title: female GWI patient, recovery_replicate 22

description: Library name: 1927sGF2

value: female


title: Injured 1 day, untreated, HA, 76

description:
G2HA111111U-1
Count

value: hippocampus + amygdala

value: untreated


title: Injured 1 day, untreated, HA, 71

description:
G2HA111026U-2
Count


title: microglia, WT, untreated, P35, sample4

description:
Library name: A2-2
analysis_id: wu___2
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds

value: myeloid

value: unmanipulated


title: female GWI patient, recovery_replicate 21

description: Library name: 1924sGF2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_815

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').


title: Injured 1 day, untreated, FC, 36

description:
G2FA111026U-2
Count

value: frontal cortex


title: microglia, WT, untreated, P35, sample3

description:
Library name: A1-2
analysis_id: wu___1
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds


title: microglia, WT, untreated, P35, sample5

description:
Library name: C2-2
analysis_id: wu___3
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_814


title: female healthy control, baseline_replicate 1

description: Library name: 0728sHF0

value: peripheral blood mononuclear cells

value: T0 (baseline)


title: female GWI patient, recovery_replicate 20

description: Library name: 1921sGF2

value: T2 (recovery)


title: microglia, WT, untreated, P35, sample2

description:
Library name: W4
analysis_id: p35w_4
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds


title: female GWI patient, recovery_replicate 24

description: Library name: 1933sGF2

value: GWI patient


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_813


title: Injured 1 day, untreated, HA, 72

description:
G2HA111130U-1
Count

value: brain


title: female GWI patient, recovery_replicate 18

description: Library name: 1915sGF2


title: Sham, untreated, FC, 122

description:
G4FA110902B
Count

value: Naive

value: 0 days


title: microglia, WT, untreated, P35, sample1

description:
Library name: W3
analysis_id: p35w_3
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds

value: WT


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_812

value: spinal neuron differentiation

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_811


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_810


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_816


title: Sham, untreated, HA, 118

description:
G4HA130603I-3
Count


title: Sham, untreated, FC, 116

description:
G4FA110513-2
Count


title: microglia, Twi, untreated, P35, sample2

description:
Library name: T2
analysis_id: p35t_2
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds
slingshot_mg0123_seurat_object.rds

value: Twi


title: female GWI patient, recovery_replicate 15

description: Library name: 1903sGF2

value: female


title: microglia, Twi, untreated, P35, sample3

description:
Library name: T3
analysis_id: p35t_3
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds
slingshot_mg0123_seurat_object.rds


title: female GWI patient, recovery_replicate 17

description: Library name: 1912sGF2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_809


title: Injured CsA treated, treated, HA, 4

description:
G1HA121214U-1
Count

value: hippocampus + amygdala

value: Injured CsA treated

value: 30 hours

value: Cyclosporine A treated


title: Sham, untreated, HA, 121

description:
G4HA130610I-3
Count

value: untreated


title: microglia, Twi, untreated, P35, sample1

description:
Library name: T1
analysis_id: p35t_1
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds
slingshot_mg0123_seurat_object.rds

value: myeloid

value: unmanipulated


title: female GWI patient, recovery_replicate 14

description: Library name: 0744sGF2

value: peripheral blood mononuclear cells

value: T2 (recovery)


title: Sham, untreated, FC, 124

description:
G4FA110606-2
Count

value: brain

value: frontal cortex


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_808


title: female GWI patient, recovery_replicate 19

description: Library name: 1918sGF2

value: GWI patient


title: Sham, untreated, FC, 113

description:
G4FA130610I-3
Count

value: Naive

value: 0 days


title: microglia, Twi, untreated, P35, sample4

description:
Library name: T4
analysis_id: p35t_4
Tx_integrated_seurat_object.rds
noTx_integrated_seurat_object.rds
globoid_subsetting_seurat_object.rds
slingshot_mg0123_seurat_object.rds


title: female GWI patient, recovery_replicate 16

description: Library name: 1909sGF2


title: BRI-1895_TCR_Library

city: Boston

first: Cody

last: Nelson

state: MA

address: 221 Longwood Ave

institute: Brigham and Women's Hospital

description: Library name: BRI-1895

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10, hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD4 T cells

extract_protocol:
Live CD4+CD19-CXCR5+. Cells were stained with TotalSeq-C Hashtags (Biolegened) and pooled in a single sample before loading.
scRNA-seq, bulkRNAseq; Cells were resuspended in 0.4% BSA in PBS at a concentration of 2,000 cells per μl, then loaded onto a single lane (Chromium chip K, 10X Genomics) followed by encapsulation in a lipid droplet (Single Cell 5′kit V2, 10X Genomics) followed by cDNA and library generation according to the manufacturer’s protocol. 5’ mRNA library was sequenced to an average of 50,000 reads per cell, V(D)J library and HTO (Cell Hashing antibodies) library sequenced to an average of 5,000 reads per cell, all using Illumina Novaseq.

value: CD4 T cells

value: Mouse CD4 T  cell

value: Blood and LN


title: female GWI patient, recovery_replicate 13

description: Library name: 0741sGF2

value: female


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_806

value: spinal neuron differentiation

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_807


title: BRI-1893_GEX_HTO_Library

description: Library name: BRI-1893_Hashing


title: Sham, untreated, HA, 110

description:
G4HA110831B
Count

value: hippocampus + amygdala


title: female GWI patient, recovery_replicate 12

description: Library name: 0738sGF2


title: Sham, untreated, HA, 123

description:
G4HA130603I-2
Count

value: untreated


title: female GWI patient, recovery_replicate 11

description: Library name: 0735sGF2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_804


title: Sham, untreated, FC, 108

description:
G4FA130603I-2
Count


title: NW_rep1

city: Shanghai

first: Jiajun

last: Cui

address: No.131, Dong'an Road, Xuhui District, Shanghai, China

country: China

institute: Obstetrics and Gynecology Hospital of Fudan University

description: Library name: Sample5

data_processing:
WGBS reads were filtered and trimmed with “fastp”. Quality control was conducted by FastQC. Genomic feature annotation was done using the Bioconductor package annotatr. Duplicate reads were removed by the command deduplicate_bismark from Bismark. Methylation calling was performed by Bismark Methylation Extractor.
Assembly: NCBI37/mm9
Supplementary files format and content: Bismark Coverage

source_name: sperm

extract_protocol:
The cauda epididymis was dissected from the mice, placed in pre-warmed M2 medium (Sigma, N7167), and gently squeezed to release the caudal fluid into the media. The sperm containing media was incubated at 37°C for 30 minutes and then transferred to a fresh tube through cell filter. Sperm cells were collected by centrifugation at 800xg for 5 minutes, followed by a wash with 1X PBS and centrifugation step. After removing the supernatant, all samples were treated with somatic lysis buffer (SLB: 0.1% SDS, 0.5% Triton-X-100 in DEPC water) on ice for 20 minutes, followed by centrifugation at 1000xg for 5 minutes. The treated sperm was washed twice with 1X PBS and centrifuged at 4000xg for 3 minutes. The sperm DNA was extracted using TIANamp Micro DNA Kit.
A total of 100 ng of genomic DNA was fragmented to 350 bp using Hieff® Smearase (YEASEN, 12907ES24). Subsequently, the DNA was bisulfite converted with EpiArt DNA Methylation Bisulfite Kit (Vazyme, EM101-01), and the WGBS library was prepared using EpiArt DNA Methylation Library Kit for Illumina V3 (Vazyme, NE103-01) following the manufacturer’s instructions. The libraries were purified using VAHTS DNA Clean Beads (Vazyme, N411-01). In each group, the WGBS libraries of 3 mice sperm were pooled into a sequencing library in equal proportions and then sequenced on the Illumina NovaSeq 6000 in paired-end mode (PE150).

value: sperm

tag: age

value: 16 weeks old

value: male

value: nicotine-exposed followed by normal feeding mice


title: N_rep2

description: Library name: Sample4

value: 11 weeks old

value: nicotine-exposed mice


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_803

tag: cell line


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_805

tag: cell type


title: female GWI patient, recovery_replicate 9

description: Library name: 0727sGF2

value: peripheral blood mononuclear cells

value: GWI patient

value: T2 (recovery)


title: Sham, untreated, HA, 95

description:
G4HA140515U-3
Count

value: brain

value: Sham

value: 8 days


title: female GWI patient, recovery_replicate 8

description: Library name: 0724sGF2

value: female


title: N_rep1

description: Library name: Sample3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_802

value: spinal neuron differentiation

tag: genotype


title: Sham, untreated, FC, 42

description:
G4FA140515U-3
Count

value: frontal cortex

tag: treatment


title: C_rep2

description: Library name: Sample2

value: normal feeding mice


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_801

value: homogenous protocol

tag: sequencing batch


title: C_rep1

description: Library name: Sample1

tag: tissue

value: sperm


title: Sham, untreated, HA, 94

description:
G4HA120604F-2
Count

value: hippocampus + amygdala

value: 4 days

value: untreated


title: NW_rep2

description: Library name: Sample6

value: 16 weeks old

tag: strain

value: male

value: nicotine-exposed followed by normal feeding mice


title: female GWI patient, recovery_replicate 6

description: Library name: 0718sGF2

value: peripheral blood mononuclear cells

value: GWI patient


title: Sham, untreated, HA, 117

description:
G4HA110902B
Count

value: brain

tag: brain region

value: Naive

value: 0 days


title: Sham, untreated, HA, 96

description:
G4HA140522U
Count

tag: group name

value: Sham

value: 8 days

value: female


title: female GWI patient, recovery_replicate 5

description: Library name: 0715sGF2

value: T2 (recovery)


title: female GWI patient, recovery_replicate 10

description: Library name: 0732sGF2


title: female GWI patient, recovery_replicate 4

description: Library name: 0712sGF2


title: Flt3-pos_GEX

city: Barcelona

first: Daniel

last: Fernandez-Perez

state: Choose State

address: Carrer Baldiri Reixac 12

department: Aging and Metabolism

country: Spain

institute: IRB Barcelona

description:
Library name: Flt3-pos_GEX
10xGenomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software 7.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrices

source_name: Bone marrow

extract_protocol:
Following euthanasia, bone marrow was harvested from the femur, tibia, pelvis, and sternum through mechanical crushing, ensuring the retrieval of most HSCs. The collected bone marrow cells were then sieved through a 100-μm strainer and cleansed with a cold 'Easy Sep' buffer containing PBS with 2% fetal bovine serum (FBS), followed by lysis of red blood cells using RBC lysis buffer (Biolegend, Catalog no. 420302). At first, mature lineage cells were selectively depleted through the Lineage Cell Depletion Kit, mouse (Miltenyi Biotec, Catalog no. 130-110-470), while the resulting Lin- (lineage-negative) fraction was then enriched for c-Kit expression using CD117 MicroBeads (Miltenyi Biotec, Catalog no: 130-091-224). These cKit-enriched cells were washed, blocked with FcX and stained with following fluorescently labeled antibodies: APC anti-mouse CD117, clone ACK2 (Biolegend catalog no. 105812), PE/Cy7 anti-mouse Ly6a (Sca-1) (Biolegend, catalog no. 108114); Pacific Blue anti-mouse Lineage Cocktail (Biolegend, catalog no. 133310); PE anti-mouse CD201 (EPCR) (Biolegend, catalog no. 141504); PE/Cy5 anti-mouse CD150 (SLAM) (Biolegend, catalog no. 115912); APC/Cyanine7 anti-mouse CD48 (Biolegend, catalog no. 103432).
Single-cell library using Chromium Single Cell 3’ Reagent Kits (v3) was performed following the manufacturer’s guidelines (10X Genomics). We multiplexed samples coming from different mouse replicates with Biolegend TotalSeq™ anti-mouse hashing antibodies in a single 10X reaction. Following the reverse transcription of mRNA and first-strand cDNA amplification, 100 ng of the cDNA libraries were used as templates to amplify LARRY barcodes by nested PCR similar to the protocol described in (Weinreb et al. 2020). The first PCR used forward primer CTGAGCAAAGACCCCAACGAGAA together with the corresponding 10x Genomics dual index TruSeq reverse primer using the following programs 1, 98 C, 3 min; 2, 98 C, 20 s; 3, 58 C, 15 s; 4, 72 C, 20 s; 5, repeat steps 2–4 08 times; 6, 72 C, 3 min; 7, 4 C, hold. The PCR products were then purified with a 0.8:1 ratio of Ampure XP beads. Purified PCR products were then subjected to a second PCR using the forward primer GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC TGC TAG GAG AGA CCA TAT GGG ATC and the corresponding 10x dual index Truseq reserve primer, following program 1, 98 C, 3 min; 2, 98 C, 20 s; 3, 58 C, 15 s; 4, 72 C, 20 s; 5, repeat steps 2–4 08 times; 6, 72 C, 3 min; 7, 4 C, hold. The final PCR products were then purified by a 0.8:1 ratio of Ampure XP bead: PCR products, were indexed using the 10x dual index TruSeq kit, and sequenced using Illumina NovaSeq or NextSeq.

value: Bone marrow

value: LSK cells

tag: group


title: female GWI patient, recovery_replicate 3

description: Library name: 0709sGF2

tag: Sex


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_799

value: spinal neuron differentiation

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_798


title: Flt3-pos_HTO

description:
Library name: Flt3-pos_HTO
10xGenomics

library_source: other

molecule: protein


title: Flt3-neg_LARRY

description:
Library name: Flt3-neg_LARRY
10xGenomics


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_796


title: female GWI patient, recovery_replicate 2

description: Library name: 0706sGF2


title: female GWI patient, recovery_replicate 1

description: Library name: 0703sGF2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_800


title: Flt3-neg_HTO

description:
Library name: Flt3-neg_HTO
10xGenomics


title: Flt3-neg_GEX

description:
Library name: Flt3-neg_GEX
10xGenomics


title: female GWI patient, maximal exertion_replicate 25

description: Library name: 1932sGF1

value: T1 (maximal exertion)


title: Flt3-pos_LARRY

description:
Library name: Flt3-pos_LARRY
10xGenomics


title: Sham, untreated, FC, 85

description:
G4FA120604F-2
Count

value: frontal cortex

tag: survival time_post_injury

value: 4 days

value: untreated


title: female GWI patient, recovery_replicate 7

description: Library name: 0721sGF2

value: peripheral blood mononuclear cells


title: Sham, untreated, FC, 52

description:
G4FA120514F-2
Count


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_797


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_795


title: D6-rep1_LARRY

description:
Library name: D6-rep1_LARRY
10xGenomics

source_name: exvivo HSC PVA culture

growth_protocol: Ex-vivo cultures of HSCs were done under self-renewing F12-PVA-based conditions as described previously ((Wilkinson et al. 2019)). To this end, cell-culture activated 96-well flat-bottom plates were coated with a layer of 100 ng/ml fibronectin (Bovine Fibronectin Protein, CF Catalog: 1030-FN) for 30 minutes at room temperature. Following the sorting process, HSCs were transferred into 200 µl of complete HSC media supplemented with 100ng/ml recombinant mouse TPO and 10ng/ml recombinant mouse SCF (PeproTech Recombinant Murine TPO Catalogue Number: 315-14; PeproTech Recombinant Murine SCF, Catalogue Number: 250-03) and grown at 37°C with 5% CO2. During lentiviral library transduction, the first media change took place 24 hours post-transduction. All other protocol steps followed the guidelines provided in (Wilkinson et al. 2020)

extract_protocol:
Following euthanasia, bone marrow was harvested from the femur, tibia, pelvis, and sternum through mechanical crushing, ensuring the retrieval of most HSCs. The collected bone marrow cells were then sieved through a 100-μm strainer and cleansed with a cold 'Easy Sep' buffer containing PBS with 2% fetal bovine serum (FBS), followed by lysis of red blood cells using RBC lysis buffer (Biolegend, Catalog no. 420302). At first, mature lineage cells were selectively depleted through the Lineage Cell Depletion Kit, mouse (Miltenyi Biotec, Catalog no. 130-110-470), while the resulting Lin- (lineage-negative) fraction was then enriched for c-Kit expression using CD117 MicroBeads (Miltenyi Biotec, Catalog no: 130-091-224). These cKit-enriched cells were washed, blocked with FcX and stained with following fluorescently labeled antibodies: APC anti-mouse CD117, clone ACK2 (Biolegend catalog no. 105812), PE/Cy7 anti-mouse Ly6a (Sca-1) (Biolegend, catalog no. 108114); Pacific Blue anti-mouse Lineage Cocktail (Biolegend, catalog no. 133310); PE anti-mouse CD201 (EPCR) (Biolegend, catalog no. 141504); PE/Cy5 anti-mouse CD150 (SLAM) (Biolegend, catalog no. 115912); APC/Cyanine7 anti-mouse CD48 (Biolegend, catalog no. 103432).
For scRNA sequencing and subsequent plating, cells were pipetted up and down gently a few times to be dissociated into single cells and transferred to a 1.5 mL microtube. The well was then washed with prewarmed PBS to collect all the possible remaining cells. Cells were then concentrated by centrifugation at 800 g for 8 minutes. Washed cells were then blocked with FcX, and stained with the E-SLAM stem cell antibodies panel, to confirm expansion of E-SLAM cells. Live cells were then sorted based on fluorescent reporter expression. Part of the sample as specified in text was then taken for constructing a single-cell library using Chromium Single Cell 3’ Reagent Kits (v3) following the manufacturer’s guidelines (10X Genomics). The remaining part was then plated back for further expansion in culture. To minimize the impact of batch effects on sequencing, we multiplexed different conditions leveraging the unique barcode pattern of our libraries together with Biolegend TotalSeq™ anti-mouse hashing antibodies, enabling the simultaneous preparation of libraries representing all experimental conditions in a single reaction for each day of sampling. Following the reverse transcription of mRNA and first-strand cDNA amplification, 100 ng of the cDNA libraries were used as templates to amplify LARRY barcodes by nested PCR similar to the protocol described in (Weinreb et al. 2020). The first PCR used forward primer CTGAGCAAAGACCCCAACGAGAA together with the corresponding 10x Genomics dual index TruSeq reverse primer using the following programs 1, 98 C, 3 min; 2, 98 C, 20 s; 3, 58 C, 15 s; 4, 72 C, 20 s; 5, repeat steps 2–4 08 times; 6, 72 C, 3 min; 7, 4 C, hold. The PCR products were then purified with a 0.8:1 ratio of Ampure XP beads. Purified PCR products were then subjected to a second PCR using the forward primer GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATC TGC TAG GAG AGA CCA TAT GGG ATC and the corresponding 10x dual index Truseq reserve primer, following program 1, 98 C, 3 min; 2, 98 C, 20 s; 3, 58 C, 15 s; 4, 72 C, 20 s; 5, repeat steps 2–4 08 times; 6, 72 C, 3 min; 7, 4 C, hold. The final PCR products were then purified by a 0.8:1 ratio of Ampure XP bead: PCR products, were indexed using the 10x dual index TruSeq kit, and sequenced using Illumina NovaSeq or NextSeq.

value: exvivo HSC PVA culture

value: LSK + LK cells

value: WT, Dnmt3aR878H, Npm1cA, Dnmt3aR878H+Npm1cA

tag: timepoint


title: female GWI patient, maximal exertion_replicate 24

description: Library name: 1929sGF1

value: GWI patient


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_793

value: Control


title: D6-rep1_GEX

description:
Library name: D6-rep1_GEX
10xGenomics


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_794


title: female GWI patient, maximal exertion_replicate 23

description: Library name: 1926sGF1


title: D30-rep1_LARRY

description:
Library name: D30-rep1_LARRY
10xGenomics


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_791


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_792


title: D30-rep1_HTO

description:
Library name: D30-rep1_HTO
10xGenomics


title: female GWI patient, maximal exertion_replicate 22

description: Library name: 1923sGF1


title: PLC/PRF/5-shBAP18

city: Shenyang

first: Chunyu

last: Wang

state: Liaoning

address: No.77 Puhe Road, Shenyang North New Area, School of Life Sciences, China Medical University

department: Cell biology

institute: China medical university

data_processing:
Raw reads were first filtered with minimum average read quality score=7 and minimum read length=500bp. Ribosomal RNA were discarded after mapping to rRNA database. Next, full-length, non-chemiric (FLNC) transcripts were determined by searching for primer at both ends of reads. Clusters of FLNC transcripts were obtained after mapping to reference genome with mimimap2, and consensus isoforms were obtained after polishing within each cluster by pinfish. Consensus sequences were mapped to reference genome using minimap2. Mapped reads were further collapsed by cDNA_Cupcake package with min-coverage=85% and min-identity=90%. 5’ difference was not considered when collapsing redundant transcripts.
Assembly: hg38
Supplementary files format and content: Excel file includes read counts and CPM values for each Sample.

source_name: liver

growth_protocol: Cells were cultured with MEM containing 10% FBS serum, in a humidified incubator at 37 °C and 5% CO2.

extract_protocol:
Total RNA was harvested by Trizol RNA isolater, and 1 µg total RNA was prepared for cDNA libraries.
The cDNA libraries were prepared using cDNA-PCR Sequencing Kit (SQK-PCS109).

value: liver

value: transfection of lentivirus-delivered shBAP18.


title: female GWI patient, maximal exertion_replicate 20

description: Library name: 1917sGF1

value: female


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_789


title: Abdomen_Pdgfra+Krt5lineage+

city: Suita

first: Takashi

last: Shimbo

state: Osaka

address: 2-2 Yamadaoka

country: Japan

institute: Osaka university

data_processing:
Sequencing outputs were demultiplexed using cellranger (6.1.2) mkfastq
Fastq files were aligned to Mus musculus mm10 reference using cellranger (6.1.2) count or multi
Assembly: Mouse reference, mm10
Supplementary files format and content: Processed data files are gzipped cellranger count output directory (sample_feature_bc_matrix or filtered_feature_bc_matrix).

source_name: skin

extract_protocol:
Freshly collected skins were minced using scissors, and suspended  in digestion buffer (RPMI with 5%v/v  fetal bovine serum, 0.3mg/mL Liberase TM (Merck) and 5U/mL DNase1) and incubated 37°C for 30minutes twice. The samples were resuspended in another digestion buffer (TrypLE Select Enzyme(Thermo Fisher Scientific) with 5U/mL DNase1) and incubated 37°C for 15minutes. The obtained cell suspensions were filtered through a 70µm cell strainer, washed in Minimum Essential Medium alpha (Thermo Fisher Scientific) with 2%v/v FBS.
Isolated skin cells were individually labeled using the 3' CellPlex Kit Set A (10x Genomics). SYTOX negative target cells from each individual were sorted using the BD FACS Aria III system (BD Biosciences).Library preparation was performed according to the 10x Genomics protocol "Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) with Feature Barcode technology for Cell Multiplexing".

value: skin

tag: region

value: Abdomen

tag: gate

value: eGFP+tdTomato+


title: Abdomen_Pdgfra+Krt5lineage-

value: eGFP+tdTomato-


title: female GWI patient, maximal exertion_replicate 19

description: Library name: 1914sGF1

tag: disease state

tag: time point_in_exercise

value: T1 (maximal exertion)


title: isolate g2g_050, replicate 1

first: Peter

last: Culviner

address: 677 Huntington Ave

department: IID

institute: Harvard School of Public Health

description: Library name: g2g_050_1

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

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, maximal exertion_replicate 18

description: Library name: 1911sGF1


title: Back_Pdgfra+Krt5lineage+

value: Back


title: isolate g2g_050, replicate 2

description: Library name: g2g_050_2


title: female GWI patient, maximal exertion_replicate 17

description: Library name: 1908sGF1

value: peripheral blood mononuclear cells


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_787

tag: cell line

value: spinal neuron differentiation

value: homogenous protocol


title: Back_Pdgfra+Krt5lineage-


title: female GWI patient, maximal exertion_replicate 16

description: Library name: 1905sGF1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_786

tag: cell type


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_785

tag: genotype


title: isolate g2g_049, replicate 1

description: Library name: g2g_049_1


title: isolate g2g_049, replicate 2

description: Library name: g2g_049_2


title: Head_Pdgfra+Krt5lineage+

value: Head


title: female GWI patient, maximal exertion_replicate 15

description: Library name: 1902sGF1

value: GWI patient


title: female GWI patient, maximal exertion_replicate 21

description: Library name: 1920sGF1


title: D30-rep1_GEX

description:
Library name: D30-rep1_GEX
10xGenomics

value: exvivo HSC PVA culture

value: LSK + LK cells

value: WT, Dnmt3aR878H, Npm1cA, Dnmt3aR878H+Npm1cA


title: isolate g2g_048, replicate 2

description: Library name: g2g_048_2


title: Head_Pdgfra+Krt5lineage-


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_790

value: Control

tag: treatment


title: PLC/PRF/5-shControl

value: liver

value: WT

value: transfection of control lentivirus.


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_783

tag: sequencing batch


title: female GWI patient, maximal exertion_replicate 14

description: Library name: 0743sGF1

tag: tissue

value: female


title: isolate g2g_048, replicate 1

description: Library name: g2g_048_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_788


title: female GWI patient, maximal exertion_replicate 13

description: Library name: 0740sGF1

value: T1 (maximal exertion)


title: isolate g2g_047, replicate 2

description: Library name: g2g_047_2

value: bacterial


title: female GWI patient, maximal exertion_replicate 12

description: Library name: 0737sGF1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_781


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_782


title: CLP3

city: Wuhan

first: Jianmin

last: Ling

address: 1095 Jiefang Dadao, Wuhan 430000, China

department: Emergency

institute: Huazhong university of science and technology

data_processing: fasto, HISAT2, DESeq2

growth_protocol: Mouse BV2 cell lines were cultured in DMEM supplemented with 10 % fetal bovine serum and 1% penicillin/streptomycin at 37 °C with 5% CO2 in a humidified atmosphere.Two-month-old male SPF C57BL/6 mice (20–22 grams) were obtained from Shulaibao Biotechnology Co., Ltd. (Wuhan, China). The mice were housed under a 12-hour light/dark cycle with free access to standard rodent food and water. The room temperature was maintained at 18–22 °C, with a humidity level of 50–60%. Five mice were housed per cage.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using  VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Cells were treated LPS (1 ng/mL) treatment for 12 h. DMSO served as the vehicle control for the treatment conditions. 24h after Sham/CLP surgery, the hippocampus were collected.

value: brain

value: CLP


title: isolate g2g_047, replicate 1

description: Library name: g2g_047_1

value: Clinical Isolate


title: CLP2


title: female GWI patient, maximal exertion_replicate 11

description: Library name: 0734sGF1

value: peripheral blood mononuclear cells


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_780

value: spinal neuron differentiation

value: homogenous protocol


title: female GWI patient, maximal exertion_replicate 10

description: Library name: 0731sGF1

value: GWI patient


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_784


title: CLP1


title: female GWI patient, maximal exertion_replicate 9

description: Library name: 0726sGF1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_778


title: Sham4

value: Sham


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_779


title: isolate g2g_046, replicate 2

description: Library name: g2g_046_2


title: female GWI patient, maximal exertion_replicate 8

description: Library name: 0723sGF1


title: isolate g2g_045, replicate 2

description: Library name: g2g_045_2


title: Sham3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_777


title: Sham2


title: CLP4


title: female GWI patient, maximal exertion_replicate 7

description: Library name: 0720sGF1


title: isolate g2g_045, replicate 1

description: Library name: g2g_045_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_776


title: isolate g2g_044, replicate 2

description: Library name: g2g_044_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_775


title: isolate g2g_044, replicate 1

description: Library name: g2g_044_1


title: female GWI patient, maximal exertion_replicate 6

description: Library name: 0717sGF1


title: isolate g2g_043, replicate 1

description: Library name: g2g_043_1


title: L3

source_name: cells

value: cells

value: tumor

value: LPS


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_774

value: Control


title: female GWI patient, maximal exertion_replicate 5

description: Library name: 0714sGF1


title: isolate g2g_046, replicate 1

description: Library name: g2g_046_1


title: L4

value: WT


title: Sham1


title: female GWI patient, maximal exertion_replicate 4

description: Library name: 0711sGF1


title: isolate g2g_041, replicate 1

description: Library name: g2g_041_1


title: female GWI patient, maximal exertion_replicate 3

description: Library name: 0708sGF1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_772


title: L1


title: isolate g2g_040, replicate 2

description: Library name: g2g_040_2


title: L2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_773


title: S4

value: no


title: female GWI patient, maximal exertion_replicate 2

description: Library name: 0705sGF1

value: female


title: female GWI patient, maximal exertion_replicate 1

description: Library name: 0702sGF1

value: T1 (maximal exertion)


title: isolate g2g_040, replicate 1

description: Library name: g2g_040_1

value: bacterial


title: isolate g2g_039, replicate 2

description: Library name: g2g_039_2


title: female GWI patient, baseline_replicate 24

description: Library name: 1931sGF0

value: T0 (baseline)


title: S3


title: isolate g2g_039, replicate 1

description: Library name: g2g_039_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_769


title: S2


title: female GWI patient, baseline_replicate 23

description: Library name: 1928sGF0


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_768


title: S1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_767


title: female GWI patient, baseline_replicate 21

description: Library name: 1922sGF0


title: isolate g2g_038, replicate 1

description: Library name: g2g_038_1


title: isolate g2g_038, replicate 2

description: Library name: g2g_038_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_766


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

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

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

tag: mouse age

value: 18-20 months

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


title: female GWI patient, baseline_replicate 22

description: Library name: 1925sGF0

value: peripheral blood mononuclear cells


title: isolate g2g_037, replicate 2

description: Library name: g2g_037_2

value: Clinical Isolate


title: female GWI patient, baseline_replicate 20

description: Library name: 1919sGF0

value: GWI patient


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_770

value: spinal neuron differentiation

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_765


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


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_Control_Cell_771


title: isolate g2g_037, replicate 1

description: Library name: g2g_037_1


title: female GWI patient, baseline_replicate 19

description: Library name: 1916sGF0


title: isolate g2g_036, replicate 1

description: Library name: g2g_036_1


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


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_764


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

value: 4hrs post 100ng/mL LPS


title: female GWI patient, baseline_replicate 18

description: Library name: 1913sGF0


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_763


title: isolate g2g_035, replicate 1

description: Library name: g2g_035_1


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


title: female GWI patient, baseline_replicate 17

description: Library name: 1910sGF0


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_762


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


title: isolate g2g_034, replicate 2

description: Library name: g2g_034_2


title: female GWI patient, baseline_replicate 16

description: Library name: 1907sGF0


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_761


title: isolate g2g_034, replicate 1

description: Library name: g2g_034_1


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

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


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_760


title: isolate g2g_033, replicate 2

description: Library name: g2g_033_2


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

value: WT


title: female GWI patient, baseline_replicate 15

description: Library name: 1904sGF0


title: female GWI patient, baseline_replicate 14

description: Library name: 1901sGF0


title: isolate g2g_033, replicate 1

description: Library name: g2g_033_1


title: female GWI patient, baseline_replicate 13

description: Library name: 0742sGF0


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_759


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

value: 24hrs post 5μg/mL β-Glucan


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_757


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


title: female GWI patient, baseline_replicate 11

description: Library name: 0736sGF0

value: female


title: female GWI patient, baseline_replicate 12

description: Library name: 0739sGF0


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


title: isolate g2g_031, replicate 2

description: Library name: g2g_031_2


title: female GWI patient, baseline_replicate 10

description: Library name: 0733sGF0


title: isolate g2g_032, replicate 1

description: Library name: g2g_032_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_755


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