title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_268

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').

value: spinal neuron differentiation

value: heterogenous protocol


title: RAM002_day2_Glomeruli_replicate11

status: Public on Apr 30 2025

type: SRA

city: Seattle

first: Shreeram

last: Akilesh

state: WA

address: 1959 NE Pacific St, Box 356100

department: Laboratory Medicine and Pathology

country: USA

institute: University of Washington

library_source: other

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

molecule: other

organism: Homo sapiens

source_name: Kidney

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

tag: tissue

value: Kidney

tag: donor id

tag: roi histology

value: Glomeruli

tag: geomx dsp_probe_set

value: Human NGS Cancer Transcriptome Atlas RNA_1.0

tag: acquisition day


title: RAM007_day2_Glomeruli_replicate7


title: corneal epithelial stem cells, PBS, biol rep 1

city: Suita

first: Xiaoqin

last: Li

state: Osaka

department: Ophthalmology

country: Japan

institute: Osaka University

library_source: transcriptomic

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

molecule: total RNA

source_name: corneal epithelium

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

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

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

value: corneal epithelium

tag: cell type

value: corneal epithelial stem cells

tag: genotype

value: WT

tag: treatment

value: PBS


title: MEF_KO_Infected_24_h_B3

city: Hyderabad

first: Krishnan

middle: Harnivas

last: Harshan

state: Telangana

address: Uppal Rd, IICT Colony

department: Infectious Diseases Group

country: India

institute: CSIR-CCMB

description:
Library name: Sample 36
Column name in raw_count_data_MEF.csv: MEF_KO_Infected_24_h_B3

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

organism: Mus musculus

source_name: MEFs

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

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

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

tag: cell line

value: MEFs

value: Primary Embryonic Fibroblasts

value: CoV-2 infected 24h

value: MAVS KO

tag: batch

value: Batch 3


title: RAM030_day2_Glomeruli_replicate5


title: MEF_KO_Mock_24_h_B3

description:
Library name: Sample 33
Column name in raw_count_data_MEF.csv: MEF_KO_Mock_24_h_B3

value: Mock-infected 24h


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_267

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

library_source: transcriptomic single cell

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

molecule: polyA RNA

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: sequencing batch


title: RAM007_day2_Glomeruli_replicate6


title: RAM030_day2_Glomeruli_replicate4


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_265


title: D53_EPA100_RNA-seq

city: Leiden

first: Thomas

middle: B

last: Kuipers

address: Einthovenweg 20

country: Netherlands

institute: LUMC

description: Passed QC

data_processing:
Alignment of the raw reads and quality control was performed by the sequencing analysis support core (SASC) at the LUMC with FastQC
Reads were aligned to the human genome (Ensembl) using STAR aligner and subset to include only protein coding genes.
We usedthe Bioconductor package DESeq2 to test whether EPA, OA, or PA had an effect on gene expression as compared to the control. DESeq2 fits a generalized linear model assuming the negative binomial distribution for the counts. The model expresses the logarithm of the average of the counts in terms of one or more predictors. In this case, we used three models that had one of the fatty acids, subject identifier, and batch as predictors each.
Lowly expressed genes were removed by determining genes that had at least a count of 1 in half of the counts per fatty acid and control, resulting in 12,938 genes for EPA, 12,949 genes for OA, and 12,971 genes for PA.
We considered genes differentially expressed when the analysis resulted in a false discovery rate (FDR) < 0.05
Assembly: GRCh38
Supplementary files format and content: TSV, gene raw count

source_name: Buffy Coat

growth_protocol: CD4+ T cells were isolated from a buffy coat using magnetic beads and rested for 24h in DMEM supplemented with 5% fetal calf serum (FCS), pen/strep, glutamax, and IL-2 in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using Zymo Quick-RNA Microprep Kit (Zymo). 1μg of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared from 200ng RNA using the Illumina Truseq stranded mRNA library prep (Illumina, 20020594) with a poly A selection.

treatment_protocol: After 24h resting, the cells were exposed to either 100μM eicosapentaenoic, oleic, or palmitic acid diluted in ethanol and dissolved in DMEM supplmented with 2% fatty acid free (FAF) bovine serum albumin (BSA), pen/strep, and glutamax or to the control, ethanol dissolved in DMEM supplmented with 2% FAF BSA, pen/strep, and glutamax for 48 hours.

value: Buffy Coat

value: CD4+ T cell

value: Eicosapentaenoic Acid

tag: donor

value: Donor 53

value: batch 2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_264

value: spinal neuron differentiation

value: heterogenous protocol


title: D53_OA100_RNA-seq

description: Passed QC

value: Oleic Acid


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_266


title: MEF_KO_Infected_24_h_B1

description:
Library name: Sample 34
Column name in raw_count_data_MEF.csv: MEF_KO_Infected_24_h_B1

value: Batch 1


title: D53_PA100_RNA-seq

description: Passed QC

value: Palmitic Acid


title: MEF_KO_Mock_24_h_B2

description:
Library name: Sample 32
Column name in raw_count_data_MEF.csv: MEF_KO_Mock_24_h_B2

value: Batch 2


title: RAM030_day2_Glomeruli_replicate3

value: Kidney

value: Glomeruli

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: D53_EtOH_RNA-seq

description: Passed QC

value: Ethanol


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_263


title: MEF_KO_Mock_24_h_B1

description:
Library name: Sample 31
Column name in raw_count_data_MEF.csv: MEF_KO_Mock_24_h_B1

value: MEFs

value: Primary Embryonic Fibroblasts

value: MAVS KO


title: RAM003_day2_Glomeruli_replicate2


title: D52_EPA100_RNA-seq

description: Passed QC

value: Buffy Coat

value: CD4+ T cell

value: Donor 52


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_262


title: MEF_KO_Infected_24_h_B2

description:
Library name: Sample 35
Column name in raw_count_data_MEF.csv: MEF_KO_Infected_24_h_B2

value: CoV-2 infected 24h


title: RAM003_day2_Glomeruli_replicate1


title: MEF_WT_Infected_12_h_B3

description:
Library name: Sample 30
Column name in raw_count_data_MEF.csv: MEF_WT_Infected_12_h_B3

value: CoV-2 infected 12h

value: WT

value: Batch 3


title: D52_OA100_RNA-seq

description: Passed QC

value: Oleic Acid

value: batch 2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_261

value: spinal neuron differentiation

value: heterogenous protocol


title: RAM002_day2_Cortex_replicate7

value: Kidney

value: Cortex


title: D52_PA100_RNA-seq

description: Passed QC

value: Palmitic Acid

value: batch 1


title: MEF_WT_Infected_12_h_B1

description:
Library name: Sample 28
Column name in raw_count_data_MEF.csv: MEF_WT_Infected_12_h_B1

value: MEFs

value: Primary Embryonic Fibroblasts

value: Batch 1


title: MEF_WT_Infected_12_h_B2

description:
Library name: Sample 29
Column name in raw_count_data_MEF.csv: MEF_WT_Infected_12_h_B2

value: Batch 2


title: D52_EtOH_RNA-seq

description: Passed QC

value: Buffy Coat

value: CD4+ T cell

value: Ethanol

value: Donor 52


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_259


title: D51_EPA100_RNA-seq

description: Passed QC

value: Eicosapentaenoic Acid

value: Donor 51


title: RAM002_day2_Cortex_replicate6

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: RAM007_day2_Cortex_replicate4


title: D51_OA100_RNA-seq

description: Passed QC

value: Oleic Acid


title: RAM007_day2_Cortex_replicate5


title: MEF_WT_Mock_12_h_B2

description:
Library name: Sample 26
Column name in raw_count_data_MEF.csv: MEF_WT_Mock_12_h_B2

value: Mock-infected 12h

value: WT


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_257

value: spinal neuron differentiation

value: heterogenous protocol


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_258


title: MEF_WT_Mock_12_h_B3

description:
Library name: Sample 27
Column name in raw_count_data_MEF.csv: MEF_WT_Mock_12_h_B3

value: Batch 3


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_256


title: RAM030_day2_Cortex_replicate2

value: Kidney

value: Cortex


title: MEF_KO_Infected_12_h_B3

description:
Library name: Sample 24
Column name in raw_count_data_MEF.csv: MEF_KO_Infected_12_h_B3

value: MEFs

value: Primary Embryonic Fibroblasts

value: CoV-2 infected 12h

value: MAVS KO


title: MEF_WT_Mock_12_h_B1

description:
Library name: Sample 25
Column name in raw_count_data_MEF.csv: MEF_WT_Mock_12_h_B1

value: Batch 1


title: D51_EtOH_RNA-seq

description: Passed QC

value: Buffy Coat

value: CD4+ T cell

value: Ethanol

value: batch 1


title: D51_PA100_RNA-seq

description: Passed QC

value: Palmitic Acid

value: Donor 51


title: RAM030_day2_Cortex_replicate3

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: MEF_KO_Infected_12_h_B2

description:
Library name: Sample 23
Column name in raw_count_data_MEF.csv: MEF_KO_Infected_12_h_B2

value: Batch 2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_255

value: spinal neuron differentiation

value: heterogenous protocol


title: D50_EPA100_RNA-seq

description: Passed QC

value: Eicosapentaenoic Acid

value: Donor 50


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_254


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_260


title: RAM003_day2_Cortex_replicate1

value: Kidney

value: Cortex


title: MEF_KO_Infected_12_h_B1

description:
Library name: Sample 22
Column name in raw_count_data_MEF.csv: MEF_KO_Infected_12_h_B1

value: MEFs

value: Primary Embryonic Fibroblasts

value: CoV-2 infected 12h


title: RAM003_day2_Medulla_replicate2

value: Medulla


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_253


title: D50_OA100_RNA-seq

description: Passed QC

value: Buffy Coat

value: CD4+ T cell

value: Oleic Acid


title: MEF_KO_Mock_12_h_B3

description:
Library name: Sample 21
Column name in raw_count_data_MEF.csv: MEF_KO_Mock_12_h_B3

value: Mock-infected 12h

value: MAVS KO

value: Batch 3


title: RAM003_day2_Medulla_replicate1

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: D50_PA100_RNA-seq

description: Passed QC

value: Palmitic Acid

value: batch 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_252

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', 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'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').

value: spinal neuron differentiation

value: heterogenous protocol


title: D50_EtOH_RNA-seq

description: Passed QC

value: Ethanol

value: Donor 50


title: RAM002_day2_RCC_replicate3

value: Kidney

value: RCC


title: MEF_KO_Mock_12_h_B1

description:
Library name: Sample 19
Column name in raw_count_data_MEF.csv: MEF_KO_Mock_12_h_B1

value: MEFs

value: Primary Embryonic Fibroblasts

value: Batch 1


title: D49_EPA100_RNA-seq

description: Passed QC

value: Buffy Coat

value: CD4+ T cell

value: Eicosapentaenoic Acid

value: Donor 49


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_251


title: RAM002_day2_RCC_replicate1


title: MEF_KO_Mock_12_h_B2

description:
Library name: Sample 20
Column name in raw_count_data_MEF.csv: MEF_KO_Mock_12_h_B2

value: Mock-infected 12h

value: MAVS KO

value: Batch 2


title: RAM002_day2_RCC_replicate2

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: D49_OA100_RNA-seq

description: Passed QC

value: Oleic Acid

value: batch 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_249

value: spinal neuron differentiation

value: heterogenous protocol


title: RAM002_day1_Glomeruli_replicate11

value: Kidney

value: Glomeruli


title: D49_PA100_RNA-seq

description: Passed QC

value: Palmitic Acid


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_248


title: RAM002_day1_Glomeruli_replicate10


title: RAM002_day1_Glomeruli_replicate9


title: D49_EtOH_RNA-seq

description: Passed QC

value: Ethanol


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_247


title: D48_EPA100_RNA-seq

description: Passed QC

value: Donor 48


title: HEepG2-shPCCB-2-Input

city: Shanghai

first: Liu

last: Fangfang

address: No. 555, Zuchongzhi Road, Pudong New Area, Shanghai, China

country: China

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

description:
Library name: Sample16
Column name in TSS_reads_2000_BT_anno_short.csv: KD2input

library_source: genomic

data_processing:
ChIP–seq reads were aligned to the UCSC hg38 reference genome (Illumina iGenomes) using Bowtie2 (v2.2.6), and uniquely mapped reads were retained.
SAMtools (v0.1.19) was used for BAM conversion, sorting, and removal of PCR duplicates. Read density profiles were generated using ngs.plot (v2.61).
Peak calling was performed with MACS2 (v2.1.1) at a false discovery rate (FDR) of 0.01.
Assembly: hg38
Supplementary files format and content: bigWig,csv

molecule: genomic DNA

growth_protocol: HepG2 cells were maintained in DMEM supplemented containing 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were cultured in an incubator containing 5% CO2 at 37 oC with suitable humidity.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. ChIP-seq was performed as previously described using MNase digestion, with the Drosophila genome included as a spike-in control for normalization. For each sample, 30 µg of chromatin was incubated overnight at 4°C with antibodies against Kpm, Kac, or Kpr.
ChIP-seq libraries were constructed according to the manufacturer’s instructions using the SimpleChIP® Plus Enzymatic Chromatin IP Kit (Cell Signaling Technology). The libraries were sequenced on an Illumina HiSeq 2500 platform using 50 bp single-end reads.

treatment_protocol: Cells were cultured in low-glucose DMEM for two days.

value: hepatocellular carcinoma

value: PCCB konckdown

value: shPCCB

tag: antibody


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_246


title: HEepG2-shPCCB-1-Input

description:
Library name: Sample15
Column name in TSS_reads_2000_BT_anno_short.csv: KD1input


title: HEepG2-shPCCB-2-Kac

description:
Library name: Sample14
Column name in TSS_reads_2000_BT_anno_short.csv: KD2Kac

value: Kac (PTM, #PTM-105RM)


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_245


title: HEepG2-shPCCB-1-Kpr

description:
Library name: Sample11
Column name in TSS_reads_2000_BT_anno_short.csv: KD1Kpr

value: Kpr (PTM, #PTM-230)


title: HEepG2-shPCCB-1-Kac

description:
Library name: Sample13
Column name in TSS_reads_2000_BT_anno_short.csv: KD1Kac


title: RAM007_day1_Glomeruli_replicate8


title: D48_OA100_RNA-seq

description: Passed QC

value: Buffy Coat

value: CD4+ T cell


title: RAM007_day1_Glomeruli_replicate7

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: HEepG2-shPCCB-2-Kpr

description:
Library name: Sample12
Column name in TSS_reads_2000_BT_anno_short.csv: KD2Kpr


title: RAM007_day1_Glomeruli_replicate6


title: HEepG2-shPCCB-2-Kpm

description:
Library name: Sample10
Column name in TSS_reads_2000_BT_anno_short.csv: KD2Kpm

value: Kpm


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_243


title: HEepG2-shPCCB-1-Kpm

description:
Library name: Sample9
Column name in TSS_reads_2000_BT_anno_short.csv: KD1Kpm


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_242


title: RAM030_day1_Glomeruli_replicate5


title: RAM030_day1_Glomeruli_replicate4


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_244


title: HEepG2-shNT-2-Input

description:
Library name: Sample8
Column name in TSS_reads_2000_BT_anno_short.csv: NT2input

value: shNT


title: D47_EPA100_RNA-seq

description: Passed QC

value: Eicosapentaenoic Acid

value: Donor 47

value: batch 1


title: D48_PA100_RNA-seq

description: Passed QC


title: D47_OA100_RNA-seq

description: Passed QC

value: Oleic Acid


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_241

value: spinal neuron differentiation

value: heterogenous protocol


title: RAM030_day1_Glomeruli_replicate3

value: Kidney

value: Glomeruli


title: D47_PA100_RNA-seq

description: Passed QC

value: Palmitic Acid


title: HEepG2-shNT-1-Input

description:
Library name: Sample7
Column name in TSS_reads_2000_BT_anno_short.csv: NT1input

value: hepatocellular carcinoma


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_240


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_250


title: RAM003_day1_Glomeruli_replicate2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_239


title: D48_EtOH_RNA-seq

description: Passed QC

value: Ethanol

value: Donor 48


title: HEepG2-shNT-2-Kac

description:
Library name: Sample6
Column name in TSS_reads_2000_BT_anno_short.csv: NT2Kac

value: Kac (PTM, #PTM-105RM)


title: D47_EtOH_RNA-seq

description: Passed QC

value: Buffy Coat

value: CD4+ T cell


title: RAM003_day1_Glomeruli_replicate1

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: HEepG2-shNT-1-Kac

description:
Library name: Sample5
Column name in TSS_reads_2000_BT_anno_short.csv: NT1Kac

value: shNT


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_238


title: D46_OA100_RNA-seq

description: Passed QC

value: Donor 46


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_237


title: D46_EPA100_RNA-seq

description: Passed QC

value: Eicosapentaenoic Acid


title: HEepG2-shNT-1-Kpr

description:
Library name: Sample3
Column name in TSS_reads_2000_BT_anno_short.csv: NT1Kpr

value: Kpr (PTM, #PTM-230)


title: D46_PA100_RNA-seq

description: Passed QC

value: batch 1


title: HEepG2-shNT-2-Kpm

description:
Library name: Sample2
Column name in TSS_reads_2000_BT_anno_short.csv: NT2Kpm

value: Kpm


title: D46_EtOH_RNA-seq

description: Passed QC


title: RAM007_day1_Cortex_replicate5

value: Cortex


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_236

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', 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'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', 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'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', 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'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').

value: spinal neuron differentiation

value: heterogenous protocol


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_235


title: D53_EPA100

description: Passed QC

data_processing:
Alignment of the raw reads and quality control was performed by the sequencing analysis support core (SASC) at the LUMC with FastQC and the ChIP-seq pipeline from BioWDL.
Cutadapt to perform adapter clipping.
Reads are mapped to a reference genome (Encode GRCh38) using BWA aligner, and MACS2 was used to perform the peakcalling.
These peak files were then processed using R. Using DiffBind, reads in the BAM files were counted for each peak.
The read counts per peak for each sample were merged to create one table containing all peaks and read counts of all the samples combined.
De novo motif analysis was then performed using HOMER.
Assembly: GRCh38
Supplementary files format and content: TSV, peak read count

extract_protocol:
Post-exposure 1*10^5 cells were taken from each exposure and ATAC-sequencing libraries were generated using the Omni-ATAC protocol.
Barcoded libraries were sequenced to a read depth of 30 million 150 base pair paired-end reads using the Novaseq 6000 (Illumina).

value: Donor 53


title: RAM007_day1_Cortex_replicate4

value: Kidney


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_234


title: RAM030_day1_Cortex_replicate3


title: D53_OA100

description: Passed QC

value: Oleic Acid


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_233


title: Young_Chow.049

first: Robert

last: Kleemann

address: Sylviusweg 71

institute: The Netherlands Organisation for Applied Scientific Research

description: Library name: 105170-001-049

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the ensembl reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files (.tsv) contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package (https://bioconductor.org/packages/release/bioc/html/DESeq2.html).

source_name: Hippocampus

growth_protocol: Male Ldlr-/-.Leiden mice were obtained from an internal breeding stock of TNO Metabolic Health Research (Leiden, the Netherlands) and housed in the Pre-clinical Imaging Center (PRIME) of Radboud university medical center (Nijmegen, the Netherlands). The animals in this study are part of a larger study which is comparable to a previous longitudinal study in C57BL/6J mice, and approved by an independent Animal Welfare Body (approval number TNO-458) and the Veterinary Authority of Radboud university medical center (approval number 2017-0063-004). All procedures performed on these animals were in accordance with European Union regulations and guidelines on animal research. All animals were group-housed (2-4 mice per cage) in Digitally Ventilated Cages (Techniplast SPA, Buguggiate, Italy) and cages from different groups were randomized over shelves in a clean-conventional animal room (relative humidity 50-60%, temperature 21°C, 12-hour light/dark cycle). The animals received unlimited food and water throughout the study. Until the start of the study all mice were fed a standardized chow diet (Sniff R/M-H diet, Sniff Spezialdiäten GmbH, Soest, Germany).

extract_protocol:
Brain tissue was collected in 1 ml cold Trizol (Invitrogen, Paisley, UK) and homogenized using a dispersing machine (ultra-Turrax; IKA Werke GmbH & Co. KG, Staufen, Germany). After chloroform extraction and isopropyl alcohol precipitation, total RNA was dissolved in 25 μl RNase-free diethylpyrocarbonate (DEPC)-treated water. The RNA concentration of the tissue was measured with a Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific Inc, Wilmington, DE, USA).
mRNA was isolated from total RNA with oligo-dT magnetic beads. Next, cDNA was synthesized and subsequently ligated with sequencing adapters and amplified by PCR and was processed into tagged random sequence libraries (NEBNext Ultra II Directional RNA Library Prep Kit for Illumina, NEB #E7760S/L , Biolabs) and sample quality was checked for proper size distribution (300-500 bp peak, Fragment Analyzer). The mixed (multiplex) sample libraries were sequenced on an Illumina NovaSeq6000 v1.5 sequencer (Illumina, San Diego) with a paired-read 150-cycle sequencing protocol at GenomeScan BV (Leiden, the Netherlands), resulting in ~20-70 million read counts per sample. Clustering and DNA sequencing using the NovaSeq6000 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: At the start of the experiment the animals were 10-12 weeks old (corresponding to young adults). One group of chow-fed mice (Young-Chow = yC, n=15) was euthanized at 3 months of age as a younger lean (healthy) reference. Then, from 2.5 to 8 months of age, one aging group (Aging-Chow = aC, n=15 ) remained on the standardized chow diet and another aging group (HFD, n=17) was fed an obesity-inducing energy-dense high-fat diet (HFD). These 2 groups were sacrificed around 8 months of age. RNAseq analysis was performed on Hippocampi isolated from the right hemispheres of fresh brains at sacrifice.

value: Hippocampus

value: yC

tag: treatmdescript

tag: animalnr


title: Young_Chow.048

description: Library name: 105170-001-048


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_232


title: RAM003_day1_Cortex_replicate1


title: RAM030_day1_Cortex_replicate2


title: D53_EtOH

description: Passed QC

value: Buffy Coat

value: Ethanol


title: D53_PA100

description: Passed QC

value: CD4+ T cell

value: Palmitic Acid


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_231


title: Young_Chow.042

description: Library name: 105170-001-042


title: RAM002_day1_Cortex_replicate6

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: RAM002_day1_Cortex_replicate7


title: Young_Chow.041

description: Library name: 105170-001-041


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_230


title: RAM003_day1_Medulla_replicate2

value: Medulla


title: D52_EPA100

description: Passed QC

value: Eicosapentaenoic Acid

value: Donor 52


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_229


title: HEepG2-shNT-2-Kpr

description:
Library name: Sample4
Column name in TSS_reads_2000_BT_anno_short.csv: NT2Kpr

value: hepatocellular carcinoma

value: shNT

value: Kpr (PTM, #PTM-230)


title: RAM003_day1_Medulla_replicate1


title: D52_PA100

description: Passed QC

value: batch 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_228

value: spinal neuron differentiation

value: heterogenous protocol


title: D52_OA100

description: Passed QC

value: Oleic Acid


title: RAM003_day1_Medulla_replicate3

value: Kidney


title: Young_Chow.040

description: Library name: 105170-001-040

value: Hippocampus

value: yC


title: HEepG2-shNT-1-Kpm

description:
Library name: Sample1
Column name in TSS_reads_2000_BT_anno_short.csv: NT1Kpm

value: Kpm


title: RAM002_day1_RCC_replicate3

value: RCC


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_TARDBP_M337V_Cell_227


title: Young_Chow.047

description: Library name: 105170-001-047


title: Young_Chow.013

description: Library name: 105170-001-013


title: RAM002_day1_RCC_replicate2


title: D51_EPA100

description: Passed QC

value: Buffy Coat

value: CD4+ T cell

value: Donor 51


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_226


title: Young_Chow.012

description: Library name: 105170-001-012


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_225


title: RAM002_day1_RCC_replicate1

value: Human NGS Cancer Transcriptome Atlas RNA_1.0


title: D51_OA100

description: Passed QC


title: I2_DMSO_C_VNS

city: Jackson

first: Lavanya

last: Challagundla

state: MS

address: 2500 North State Street

department: Cell and Molecular Biology

institute: University of Mississippi Medical Center

data_processing:
The study involved two rounds of alignment: the first round aligned reads against a database of mature miRNA sequences, miRbase (version 22.1), the second round aligned unaligned reads to the human reference genome (vGRCh38.p14) obtained from the Ensembl database. These alignments were crucial for identifying and quantifying miRNAs in the samples. I n the first round, the alignment was performed using Bowtie (version 1.2.2) with stringent criteria. Unaligned reads were separated for the second round of alignment to the reference genome. The resulting SAM files were sorted and converted into BAM files using the “samtools view” option (samtools version 1.18). The “samtools idxstats” command was used to record the count of each miRNA in every sample. A customized Python script (python/3.11.5) combined all the mature miRNA-based count files into one file, with 2656 miRNAs as rows and samples as columns. Unaligned reads from the previous step were aligned to the Human Reference Genome (vGRCh38.p14). Only regions within the coordinates provided by miRBase (in the form of a .BED file) were annotated after mapping. A tagged BAM file was generated using the “tagBAM” utility from Bedtools software (version 2.27.1). For each of the 2656 miRNAs per sample, the “samtools view” command was applied to the counts file to retain only the unique miRNA counts. The same customized Python script used previously was also employed for genome-based count files, creating one file that combined counts from all the samples. Another custom python script added the counts from both miRBase and reference genome-based alignments. This final count represented the known miRNAs found in each sample and was used for downstream differential expression analysis.
Assembly: Human Reference Genome (vGRCh38.p14)
Supplementary files format and content: miRNA  Count Data

source_name: Foreskin

extract_protocol:
The Revvity Nextflex Small RNA NGS Kit v4 was employed to construct small RNA libraries from total RNA samples following the manufacturer's protocols. The procedure included adapter ligation, reverse transcription, and PCR amplification, culminating in size selection to enrich for small RNA species. Libraries were quantified, pooled (n=24), and sequenced on an Illumina platform to generate high-throughput sequencing data for downstream analysis. Library was sequenced with NextSeq 2000 P3 (50 cycle) fl
The Revvity Nextflex Small RNA NGS Kit v4 was employed to construct small RNA libraries from total RNA samples following the manufacturer's protocols. The procedure included adapter ligation, reverse transcription, and PCR amplification, culminating in size selection to enrich for small RNA species. Libraries were quantified, pooled (n=24), and sequenced on an Illumina platform to generate high-throughput sequencing data for downstream analysis. Library was sequenced with NextSeq 2000 P3 (50 cycle) fl

value: Foreskin

value: Human Foreskin Fibroblasts

value: Fibroblasts

value: Diploid Human-Male

value: Coilin 2 siRNA with DMSO treatment


title: D51_PA100

description: Passed QC

value: Palmitic Acid

value: batch 1


title: I2_DMSO_A_VNS


title: Young_Chow.014

description: Library name: 105170-001-014


title: I2_DMSO_B_VNS


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_222

value: spinal neuron differentiation

value: heterogenous protocol


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_223


title: Aged_Chow.046

description: Library name: 105170-001-046

value: Hippocampus

value: aC


title: D51_EtOH

description: Passed QC

value: Ethanol


title: D50_OA100

description: Passed QC

value: Oleic Acid

value: Donor 50


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_221


title: D50_EPA100

description: Passed QC

value: Buffy Coat

value: CD4+ T cell

value: Eicosapentaenoic Acid


title: D52_EtOH

description: Passed QC

value: Donor 52


title: Aged_Chow.039

description: Library name: 105170-001-039R


title: D50_PA100

description: Passed QC


title: Aged_Chow.038

description: Library name: 105170-001-038


title: N_LPS_B_SI

value: Foreskin

value: Human Foreskin Fibroblasts

value: Control siRNA with 2ug/uL LPS treatment


title: Young_Chow.011

description: Library name: 105170-001-011

value: yC


title: D50_EtOH

description: Passed QC


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_220


title: N_LPS_A_SI

value: Fibroblasts

value: Diploid Human-Male


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_224

value: spinal neuron differentiation


title: Young_Chow.004

description: Library name: 105170-001-004


title: N_DMSO_C_VNS

value: Control siRNA DMSO treatment


title: W_LPS_C_SI

value: WRAP53 siRNA with 2ug/uL LPS treatment


title: D49_EPA100

description: Passed QC

value: Donor 49

value: batch 1


title: Aged_Chow.037

description: Library name: 105170-001-037

value: Hippocampus

value: aC


title: Aged_Chow.036

description: Library name: 105170-001-036


title: N_LPS_C_SI


title: Aged_Chow.045

description: Library name: 105170-001-045


title: Aged_Chow.024

description: Library name: 105170-001-024


title: W_LPS_B_SI


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_217

value: heterogenous protocol


title: D49_OA100

description: Passed QC

value: Buffy Coat

value: CD4+ T cell

value: Oleic Acid


title: W_LPS_A_SI

value: Foreskin


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_215


title: D49_EtOH

description: Passed QC

value: Ethanol


title: Aged_Chow.021

description: Library name: 105170-001-021


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_219


title: W_DMSO_C_VNS

value: Human Foreskin Fibroblasts

value: WRAP53 siRNA with DMSO treatment


title: D48_EPA100

description: Passed QC

value: Eicosapentaenoic Acid

value: Donor 48


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_214

value: spinal neuron differentiation


title: Aged_Chow.003

description: Library name: 105170-001-003


title: Aged_Chow.002

description: Library name: 105170-001-002


title: D48_OA100

description: Passed QC


title: Aged_Chow.022

description: Library name: 105170-001-022


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_213


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_218


title: N_DMSO_B_VNS

value: Fibroblasts

value: Diploid Human-Male

value: Control siRNA DMSO treatment


title: D48_PA100

description: Passed QC

value: Palmitic Acid

value: batch 1


title: W_DMSO_B_VNS


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_212


title: Aged_Chow.001

description: Library name: 105170-001-001

value: Hippocampus

value: aC


title: D48_EtOH

description: Passed QC

value: Buffy Coat


title: W_DMSO_A_VNS


title: D49_PA100

description: Passed QC

value: CD4+ T cell

value: Donor 49


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_211

value: heterogenous protocol


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_216


title: High Fat Diet.035

description: Library name: 105170-001-035

value: HFD

value: High Fat Diet


title: IA_LPS_C_SI

value: Foreskin

value: Human Foreskin Fibroblasts

value: Coilin A siRNA with 2ug/uL LPS treatment


title: D47_EPA100

description: Passed QC

value: Eicosapentaenoic Acid

value: Donor 47


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_210

value: spinal neuron differentiation


title: High Fat Diet.034

description: Library name: 105170-001-034


title: IA_LPS_A_SI

value: Fibroblasts

value: Diploid Human-Male


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_209


title: D47_PA100

description: Passed QC

value: Palmitic Acid

value: batch 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_208


title: High Fat Diet.032

description: Library name: 105170-001-032

value: Hippocampus


title: IA_DMSO_C_VNS

value: Coilin A siRNA with DMSO treatment


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_207


title: High Fat Diet.031

description: Library name: 105170-001-031


title: High Fat Diet.028

description: Library name: 105170-001-028


title: IA_DMSO_A_VNS


title: D46_OA100

description: Passed QC

value: Buffy Coat

value: CD4+ T cell

value: Oleic Acid

value: Donor 46


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_206

value: heterogenous protocol


title: D46_PA100

description: Passed QC


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_203


title: D46_EtOH

description: Passed QC

value: Ethanol


title: High Fat Diet.025

description: Library name: 105170-001-025

value: HFD

value: High Fat Diet


title: IA_LPS_B_SI

value: Foreskin

value: Human Foreskin Fibroblasts

value: Coilin A siRNA with 2ug/uL LPS treatment


title: High Fat Diet.026

description: Library name: 105170-001-026


title: D47_EtOH

description: Passed QC

value: Donor 47


title: D47_OA100

description: Passed QC


title: I2_LPS_A_SI

value: Fibroblasts

value: Diploid Human-Male

value: Coilin 2 siRNA with 2ug/uL LPS treatment


title: I2_LPS_B_SI


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_202

value: spinal neuron differentiation


title: IA_DMSO_B_VNS

value: Coilin A siRNA with DMSO treatment


title: N_DMSO_A_VNS

value: Control siRNA DMSO treatment


title: D46_EPA100

description: Passed QC

value: Buffy Coat

value: CD4+ T cell

value: Eicosapentaenoic Acid

value: batch 1


title: ALET-HIV5,SR9011 5 uM

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

address: C.P. 6128, succursale Centre-ville

country: Canada

institute: Université de Montréal

description:
SR8
RNA-Seq (rRNA-depleted stranded (HMR))

data_processing:
Raw Count Matrix was obtained from the standard workflow used at The McGill University and Génome Québec Innovation Centre.
Features with at least one count per million (CPM) were kept prior to transformation.
Raw Counts were transformed into log2-CPM values using the voom method from the limma Bioconductor R package.
Assembly: GRCh38.96
Supplementary files format and content: Comma-separated text file includes raw counts for each sample.
Supplementary files format and content: Comma-separated text file includes log-CPM values for each sample.

source_name: Memory CD4+ T cells

growth_protocol: N/Ap

extract_protocol:
All Prep DNA/RNA/miRNA Universal Kit, Qiagen.
cDNA libraries and RNA-seq were performed by The McGill University and Génome Québec Innovation Centre, Montreal, QC. 100 bp paired-end sequencing was performed on an Illumina-NovaSeq (depth was above 150 million reads).

treatment_protocol: Cells were activated via the T cell receptor (TCR) using immobilized CD3 and soluble CD28 Abs (BD Biosciences), and cultured in RPMI 1640 media (cat# 11875119, GIBCO) containing 10% FBS (Sigma) and 1% Penicillin/Streptomycin (Gibco) in presence of DMSO (control), SR9011 (5mM), or SR8278 (10mM) for 18 hours.

tag: subject

tag: hiv status

value: Uninfected

value: Memory CD4+ T cells


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_205

value: heterogenous protocol


title: I2_LPS_C_SI

tag: tissue

value: Foreskin


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_201


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_204


title: High Fat Diet.033

description: Library name: 105170-001-033

value: Hippocampus

value: HFD

value: High Fat Diet


title: ALET-HIV5,DMSO

description:
SR7
RNA-Seq (rRNA-depleted stranded (HMR))

value: DMSO


title: ALET-HIV2,SR8278 10 uM

description:
SR3
RNA-Seq (rRNA-depleted stranded (HMR))


title: W_LPS_C

data_processing:
The raw reads were aligned using the STAR aligner (STAR-2.7.11a) to the Human reference genome (GRCh38.p14) with corresponding annotation GTF files. The alignment was performed with default parameters, and uniquely mapped reads were retained for downstream analysis FeatureCounts (2.0.2) was used to generate the count data.
The differential expression analysis was conducted using the DESeq2 package in R (4.3.1)
Assembly: Human (GRCh38.p14)
Supplementary files format and content: The gene-level count data, obtained from FeatureCounts

source_name: W

extract_protocol:
RNA was extracted using TRIzol Reagent along with Pure Link RNA Mini Kit (Invitrogen) according to manufacturer instructions and assessed for quality control parameters of minimum concentration and fidelity (i.e. 18S and 28S bands, RIS >8).
Libraries were developed using the Illumina TruSeq mRNA Stranded Library Prep Kit , quantified with a Qubit fluorimeter (Invitrogen), and assessed for quality and size using the QIAxcel Advanced System
Samples were pooled into a single library (n=24 pooled samples per library) and sequenced using the NextSeq 1000/2000 P3  (200 cycles) flow cell on the  Illumina NextSeq 2000 platform.

value: W


title: ALET-HIV5,SR8278 10 uM

description:
SR9
RNA-Seq (rRNA-depleted stranded (HMR))


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_200


title: W_LPS_B


title: High Fat Diet.018

description: Library name: 105170-001-018


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_199


title: W_LPS_A


title: High Fat Diet.020

description: Library name: 105170-001-020


title: ST050,SR8278 10 uM

description:
SR24
RNA-Seq (rRNA-depleted stranded (HMR))


title: High Fat Diet.015

description: Library name: 105170-001-015


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_198


title: High Fat Diet.010

description: Library name: 105170-001-010


title: W_DMSO_C


title: High Fat Diet.019

description: Library name: 105170-001-019


title: ST050,SR9011 5 uM

description:
SR23
RNA-Seq (rRNA-depleted stranded (HMR))


title: High Fat Diet.009

description: Library name: 105170-001-009


title: ST050,DMSO

description:
SR22
RNA-Seq (rRNA-depleted stranded (HMR))


title: W_DMSO_B


title: High Fat Diet.007

description: Library name: 105170-001-007


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_196