title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_376

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: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_377

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

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

tag: genotype

tag: treatment

tag: sequencing batch


title: WT vs Ndrg2KO_ipsilateral coretex 24h after pMCAO_rep2

type: RNA

city: Kanazawa

first: Takumi

last: Nishiuchi

address: 13-1 Takaramachi

country: Japan

institute: Kanazawa University

description: WT vs Ndrg2KO_pMCAO

hyb_protocol: Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) containing fragmented Cydye-labeled cRNA labeled were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequentially by Wash Buffer 1 (6× SSPE, 0.005% N-lauroylsarcosine) and Wash Buffer 2 (0.06× SSPE, 0.005% N-lauroylsarcosine) for 1 min at room temperture.

scan_protocol: Scanned on an Agilent G2565BA scanner. Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

data_processing: Agilent Feature Extraction Software (v 10.7.3.1) was used for background subtraction and LOWESS normalization.

molecule: total RNA

organism: Mus musculus

label_protocol: Total RNA samples (200 ng) from untreated and treated shoots were used to prepare Cy3- or Cy5-labeled cRNA using the Low RNA Input Fluorescent Linear Amplification Kit (Agilent Technologies) following manufacturer's instructions

growth_protocol: Mice were housed in a temparature and humidity controlled room under a 12hours light/dark cycles, with free access to food and water.

extract_protocol: Total RNA extracted using RNeasy following manufacturer's instructions. The quality of total RNA was checked by Agilent tapestation 2200.

treatment_protocol: Mice were deeply anesthetized under isoflurane inhalation. Permanent focal cerebral ischemia was induced by permanent occulusion of the left middle cerebral artery (pMCAO) by electrocoagulation and subsequent disconnection just distal to its crossing of the olfactry tract. Ipsilateral cortices were isolated from WT mice and Ndrg2KO mice 24h after pMCAO.

tag: tissue

value: ipsilateral cortex

tag: strain

tag: age

value: 8 weeks

value: permanent MCAO

tag: time after treatment

value: wildtype


title: Multiome, Ctrl-ATAC

city: Taipei

first: Ya-Ping

last: Yen

address: 128 Academia Road, Section 2, Nankang

department: Institute of molecular biology

country: Taiwan

institute: Academia Sinica

description: Library name: WT-ATAC

library_source: genomic single cell

data_processing:
Raw sequencing data were processed using the standard Cell Ranger ARC pipeline (version 7.0.0, 10X Genomics) for demultiplexing, mapping to the mm10 reference genome, barcode, and UMI (unique molecular identifier) counting, and generating the gene count matrix.
Assembly: mm10
Supplementary files format and content: h5 files for filtered and bigwin/tsv.gz file for ATAC fragment regions, sequenced in Illumina Next-seq 500 plateform

molecule: genomic DNA

source_name: lumbar spinal cord

extract_protocol:
Lumbar segments from the P100~P120 Sun1sfGFP; ChAT-Cre; Mettl14floxed (cKO) and Sun1sfGFP; ChAT-Cre (control) spinal cord were dissected based on morphology and dissociated two at a time in 2 mL pre-chilled lysis buffer with a 7 mL Dounce Homogenizer (pestle A: eight strokes; pestle B: 5 strokes). An additional 3 mL lysis buffer was added, and the entire homogenate was filtered through a 100 µm strainer. Then, 5 mL of 50 % iodixanol was added to create a 10 mL suspension of 25 % iodixanol. The suspension was inverted to mix well before equally splitting into two 15 mL tubes. Iodixanol (40 %, 2 mL) was layered gently at the bottom of the homogenate and centrifuged at 1,000 g for 12 minutes at 4 oC, with a swing bucket centrifuge (brand). The interphase nuclei were transferred to a new 15 mL tube and resuspended with 1:1 volume of 10 X wash buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 1 % BSA, 0.1 % Tween 20, 1 mM DTT, and 1 U/µL RNase inhibitor), followed by centrifuging at 500 g for 10 minutes at 4 oC. The supernatant was discarded and the pellet was resuspended in 800 µL diluted nuclei buffer (20X Nuclei Buffer from Chromium Next GEM Single Cell Multiome ATAC + Gene Expression Kit supplemented with 1 mM DTT, and 1 U/µL RNase inhibitor), before conducting FANS (fluorescence-activated nuclei sorting) using a BD FACS Aria III cell sorter (BD BioSciences, USA). GFPon nuclei were collected in diluted nuclei buffer and centrifuged at 500 g for 7 minutes at 4 oC. Nuclei were adjusted to an appropriate concentration following the manufacturer’s protocol (10x Genomics, 1000285) with diluted nuclei buffer. Then the sorted nuclei from Sun1sfGFP; ChAT-Cre; Mettl14floxed (cKO) and Sun1sfGFP; ChAT-Cre (control) were procced for 10x Genomics Chromium Next GEM single Cell Multiome ATAC+Gene expression experiment.
single-nucleus multiome libraries were prepared following the Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol CG000338 Rev F (10X Genomics, Pleasanton, CA).

value: lumbar spinal cord

value: Cholinergic neurons

value: Ctrl


title: isolate vci_067, replicate 1

city: Boston

first: Peter

last: Culviner

state: MA

address: 677 Huntington Ave

department: IID

country: USA

institute: Harvard School of Public Health

description: Library name: vci_067_1

library_source: transcriptomic

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

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: isolate vci_066, replicate 1

description: Library name: vci_066_1


title: Day 14

city: Buffalo

first: Jianmin

last: Wang

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description:
Library name: GVHD−PBS−T−Day−14
10X Genomics

data_processing:
The demultiplexing, bardoded processing,  gene count and aggregation were make with CellRanger v6.1.2
Assembly: mm10
Supplementary files format and content: Tab separated value files and matrix files.

source_name: Spleen

growth_protocol: Irradiated mice were injected with 0.2x106 purified splenic naïve T cells. Alloreactive T cells (CD45+, H2kb+, H2kd-, TCRβ+) were sorted using a SONY MA900 sorter on day +7 post allo-HCT.

extract_protocol:
T cells (CD45+, H2kb+, H2kd-, TCRβ+) cells were sorted from spleen and single cell libraries were generated using the 10X Genomics platform.  Then live-T cells (CD45+, H2kb+, H2kd-, TCRβ+) cells were isolated using the SONY MA900 cell sorter (Sony Biotechnology).  Single-cell suspensions were pooled together and assessed with AOPI stain using a Cellometer K2 automated cell counter (Nexcelom), to determine concentration, viability and the absence of clumps and debris that could interfere with single cell capture.  Cells were loaded into the Chromium Controller (10X Genomics) where they were partitioned into nanoliter-scale Gel Beads-in-emulsion with a single barcode per cell.  Reverse transcription was performed, and the resulting cDNA is amplified.
Amplified cDNA is separated into full-length and Feature Barcode fractions using SPRISelect beads (Beckman Coulter).  The full-length amplified cDNA was used to generate libraries by enzymatic fragmentation, end-repair, a-tailing, adapter ligation, and PCR to add Illumina compatible sequencing adapters.  Feature barcode derived cDNA was PCR amplified to incorporate Illumina adapter sequences and unique sample indexes.  The resulting libraries were evaluated on D1000 screentape using a TapeStation 4200 (Agilent Technologies) and quantitated using Kapa Biosystems qPCR quantitation kit for Illumina.  They were then pooled, denatured, and diluted to 300 pM with 1% PhiX control library added.  The resulting pool was then loaded into the appropriate NovaSeq Reagent cartridge and sequenced on a NovaSeq6000 following the manufacturer’s recommended protocol (Illumina Inc.).

value: Spleen

value: Immune cell


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, solvent control 3

city: Barcelona

first: Adria-Jaume

last: Roura

address: Carrer de Baldiri Reixac, 10

country: Spain

institute: IRB Barcelona

data_processing:
Illumina-specific adapters, short reads, and low quality 5′ and 3′ bases were filtered out in the FASTQ format files using Trimmomatic.
The resulting RNA sequencing reads were aligned to a reference mouse genome sequence (mm10) with STAR aligner.
Quantification of mapped reads and summarization by gene was performed using HTSeq-count (version 0.11.1), with paired mode (-p) and reverse stranded mode (-s reverse) enabled, and only reads with MapQ values of 10 or higher were considered.
Low-expressed features were filtered out and an analysis of differentially expressed genes was performed using NOIseq. Only mRNAs encoding protein-coding genes were retained for downstream analysis.
Differential expression analysis was performed using NOIseq methods, with the control state (Vehicle) as the reference group and compared with the RGD, RAE or RGD, anti-PD-1 and combination of RGD+anti-PD-1.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes RPKM values for each sample

source_name: Glioma-associated CD11b+ cells

extract_protocol:
CD11b+ cells were FACS sorted from naive or tumor-bearing hemispheres (pooled from 2 animals per sample at day 21 and from individual mice at day 28) using Cell Sorter BD FACSAriaII. Immediately after sorting, cells were centrifuged and lysed for further isolation of RNA using the RNeasy Plus Mini Kit (Qiagen, Germany) according to manufacturer’s protocol. The integrity and quality of RNA were assessed on an Agilent 2100 Bioanalyzer with an RNA 6000 Pico Kit (Agilent Technologies, CA, USA).
Strand-specific RNA libraries were prepared for sequencing (3 - 4 biological replicates/treatment) using a KAPA Stranded mRNA-Seq Kit (Kapa Biosystems, MA, USA). Poly-A mRNAs were purified from 100 ng of total RNA using poly-T-oligo-magnetic beads (Kapa Biosystems, MA, USA). mRNAs were fragmented and a first-strand cDNA was synthesized using reverse transcriptase and random hexamers. A second-strand cDNA synthesis was performed by removing RNA templates and synthesizing replacement strands, incorporating dUTP in place of dTTP to generate double-stranded (ds) cDNA. dsDNA was then subjected to addition of “A” bases to the 3′ ends and ligation of adapters from NEB, followed by uracil digestion by USER enzyme (NEB, MA, USA). Amplification of fragments with adapters ligated on both ends was performed by PCR using primers containing TruSeq barcodes (NEB, Ipswich, MA, USA). Final libraries were analyzed using Bioanalyzer and Agilent DNA High Sensitivity chips (Agilent Technologies, Santa Clara, CA, USA) to confirm fragment sizes (~300bp). Quantification was performed using a Quantus fluorometer and the QuantiFluor dsDNA System (Promega, Madison, Wisconsin, US).

value: Glioma-associated CD11b+ cells

value: solvent control


title: Appendix 3

type: genomic

city: Jerusalem

first: Ilana

last: Fox-Fisher

address: Faculty of Medicine, The Hebrew University of Jerusalem, Ein Kerem

department: Developmental Biology and Cancer Research

country: Israel

institute: Hebrew University of Jerusalem

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised using standard Illumina protocol

scan_protocol: Arrays were imaged using standard recommended Illumina scanner setting

data_processing: Methylation array data were processed with the minfi package in R. For each sample analyzed on the Illumina Methylation array, CpG sites were filtered out if they were represented by less than 3 beads on the array, if the detection p-value (representing total fluorescence of the relevant probes) was greater than 0.01, or if they mapped to a sex chromosome. Background correction and normalization were performed with the preprocessIllumina function, which removes background calculated based on internal control probes and normalizes all samples to a predetermined control sample.

label: Cy3 and Cy5

source_name: appendix

label_protocol: Standard Illumina Protocol

extract_protocol: A fresh surgical appendix specimen was obtained from a right hemicolectomy surgery due to carcinoma of the colon. The appendix tissue was verified by a pathologist that it was not cancerous. The appendix was placed in 10 mL of ice-cold HBSS. Mucosal and muscle layers were separated with fine curved iris scissors. Mucosal strips were thoroughly rinsed in a petri dish containing fresh HBSS and then transferred to a 50ml tube containing 50 mL of HBSS, 0.15% dithiothreitol (75mg/50ml). Tubes were placed on an orbital plate at room temperature and were stirred at 0.3g for 30 minutes until residual mucus and free additional debris were dissolved. The solution was moved to a new 50 ml tube, 10 ml of pre-warmed (37ᵒC) PBS 20mM ph7.2 EDTA was added and warmed for 10 min at 37ᵒC and mixed every 2 minutes, PBS/EDTA removed. 10 ml of cold PBS was added and then shaken vigorously. For at least 10 minutes until crypts structures are seen. Centrifuge the crypts:  1000 rpm 7 min at 4ᵒC. supernatant is removed and resuspended with 5ml cold PBS and transferred to a new 15ml tube and centrifuged for 2 minutes in 200g at 4ᵒC. the supernatant was removed and re-suspended in 1ml Tryp LE + 0.5mg/ml DNaseI and incubated at 37°C for 10-30 minutes until single cells were seen under a microscope. Tryp LE was stopped by adding PBS 0.5% BSA (up to 10-15ml). centrifuge:300g 5 minutes at 4ᵒC. cells were then stained with CD326+, CD45-, CD31-, CD235- for flow cytometry sorting

value: appendix

value: Healthy appendix epithelial cells


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, solvent control 2


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, RGD 2

value: RGD peptide


title: isolate vci_066, replicate 2

description: Library name: vci_066_2


title: Day 7

description:
Library name: PBS−T−cells−Day7
10X Genomics


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_375

value: spinal neuron differentiation

value: homogenous protocol


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_378


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_380


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_379


title: isolate vci_064, replicate 2

description: Library name: vci_064_2


title: Nude mice, glioma-associated CD11b+ cells, tumour bearing mouse, solvent control 1


title: OM_UW.

city: Stanford

first: Jennifer

middle: Brigitta

last: Parker

state: CA

address: 257 Campus Drive

department: Surgery

institute: Stanford University

description: Library name: Oral Unwounded

data_processing:
Bulk RNA-seq data were extracted from the sequencer as demultiplexed fastq files and transferred to the Stanford SCG server. Individual fastq files were aligned to the mm10 reference genome using TopHat (v2.0.13), resulting in 23 counts matrices (n = 3 biological replicates for each of the  experimental groups except FUS for which n =2). These data were read into R using the base read.delimn fuction, were merged into a single matrix using cbind, and then were annotated according to sample name, replicate, and condition. To compute the top differentially expressed genes between each pair of conditions, CPM normalization was first performed on the counts matrices using the cpm function. A gene threshold of at least 2 samples with at least 0.5 cpm was employed. PCA was performed using prcomp, and the log-transformed PCA data were plotted using autoplot. Differentially expressed genes between groups were determined using DESeq2, with its functions calcNormFactors, esimateCommonDisp, estimageGLMTrededDisp, estimatedTagwiseDisp, DESeq, and lfcShrink. Volcano plots of the resulting resLFC objects were then generated using EnhancedVolcano (v1.13.2). The Biological Coefficient of Variation was calculated using plotBCV. EnrichR analysis were performed on the top 200 genes up-regulated following treatment with either XX or YY
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, spatial files

molecule: cytoplasmic RNA

source_name: Skin/Oral Mucosa

extract_protocol:
Mouse oral mucosa and facial wounds were harvested at listed timepoints. Wounds were mechanically digested with sharp dissecting scissors. Tissue was then added to an enzymatic digestion consisting of Collagenase II (ThermoFisher, Cat:17101015) and IV (ThermoFisher, Cat:17104019) in DMEM-F12 (GIBCOTM, Fischer Scientific, Hampton, NH). Samples were added to an orbital shaker at 150 rpm for 90 minutes at 37ºC. FACS buffer was added to quench the digest and samples were filtered through 70 µm cell strainers. Samples were then centrifuged at 1500 for 5 minutes at 4°C. For samples that were sorted, cells were counted and resuspended in FACS buffer. Primary antibodies were applied, and cells were stained in the dark with gentle agitation for 30 min. Cells were then washed thoroughly in FACS buffer. A BD II FACS Aria machine was used for FACS sorting analysis. For lineage negative (Lin-) FACS analysis, the following primary antibodies were used: Tie2, CD45, CD31, CD324, CD326, Ter119.
Samples were submitted to external company for bulk RNAseq prep. The relevant protocols were followed per manufacturer’s guidelines.

value: Skin/Oral Mucosa

value: Fibroblast (Lin -)

value: Wnt1ER mTmG


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_374


title: F_UW.

description: Library name: Face Unwounded


title: C57BL6 mice, GL261 glioma cells, tumour bearing mouse, RAE 3

description: C57BL6 mice_GL261_normalized_counts.csv

value: GL261 human glioblastoma

value: RAE peptide


title: OMPOD7.

description: Library name: Oral Wounded Day 7


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_373


title: C57BL6 mice, GL261 glioma cells, tumour bearing mouse, RGD 3

description: C57BL6 mice_GL261_normalized_counts.csv


title: isolate vci_064, replicate 1

description: Library name: vci_064_1


title: isolate vci_063, replicate 2

description: Library name: vci_063_2


title: FPOD7.

description: Library name: Face Wounded Day 7


title: C57BL6 mice, naive 3

description: C57BL6 mice_GL261_normalized_counts.csv

value: naive


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_372


title: isolate vci_062, replicate 1

description: Library name: vci_062_1

value: bacterial


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_371


title: isolate vci_063, replicate 1

description: Library name: vci_063_1

value: Clinical Isolate


title: C57BL6 mice, GL261 glioma cells, tumour bearing mouse, RGD 2

description: C57BL6 mice_GL261_normalized_counts.csv


title: isolate vci_061, replicate 2

description: Library name: vci_061_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_369


title: C57BL6 mice, GL261 glioma cells, tumour bearing mouse, RAE 2

description: C57BL6 mice_GL261_normalized_counts.csv


title: OUS6

description: Library name: OUS6

growth_protocol: Briefly, a solution of 2mg/mL collagen I (Advanced Biomatrix, Cat:5005), 0.8x MEM (ThermoFisher, Cat:11430030) in 16mM HEPES (Sigma, CAT: 83264), and suspended mouse primary fibroblasts derived from either facial skin or oral mucosa (concentration 500,000 cells/mL) in DMEM (ThermoFisher, Cat: 10569010) were pipetted into cruciform-shaped PDMS (DOW, Cat:2646340) molds and allowed to gelate before removing the mold. Hydrogels were constrained by metal pins and medium containing DMEM + Glutamax media (ThermoFisher, Cat:10569010) enriched with 10% fetal bovine serum (ThermoFisher, Cat:10082147), 1% Antibiotic-Antimycotic (ThermoFisher Cat:15240062). Strain was achieved through movement of metal anchor pins in each of the four arms of the hydrogel. Strain quantification was confirmed by Fiji analysis of TiO2 dye marks on the central region of each hydrogel. Media containing small molecule mechanotransduction inhibitors to FAK (PF573228 [10uM], Tocris, Cat: 3239) Axl ([10nM] MedChem express) were added depending on the experimental condition. Media was replaced every other day. Hydrogels were kept for 72 hours.

extract_protocol:
Gels were digested with collagenase and cells frozen in lysis buffer before being sent off to Admera for bulk-rna seq library generation and sequencing.
Admera constructed bulk-rna seq libraries via manufacturers instructions.

value: Fibroblast

value: Wildtype

value: Unstretched Gel


title: OUS5

description: Library name: OUS5


title: isolate vci_061, replicate 1

description: Library name: vci_061_1


title: isolate vci_060, replicate 1

description: Library name: vci_060_1


title: isolate vci_060, replicate 2

description: Library name: vci_060_2


title: FUS5

description: Library name: FUS5


title: FUS4

description: Library name: FUS4


title: C57BL6 mice, GL261 glioma cells, tumour bearing mouse, solvent control 2

description: C57BL6 mice_GL261_normalized_counts.csv

value: solvent control


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_366


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_370


title: OUS4

description: Library name: OUS4


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_367


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_368


title: C57BL6 mice, GL261 glioma cells, tumour bearing mouse, solvent control 3

description: C57BL6 mice_GL261_normalized_counts.csv


title: AXLO3

description: Library name: AXLO3

value: Stretched Gel + AXL  inhibitor


title: isolate vci_059, replicate 2

description: Library name: vci_059_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_365


title: C57BL6 mice, GL261 glioma cells, tumour bearing mouse, RAE 1

description: C57BL6 mice_GL261_normalized_counts.csv


title: C57BL6 mice, GL261 glioma cells, tumour bearing mouse, solvent control 1

description: C57BL6 mice_GL261_normalized_counts.csv


title: isolate vci_058, replicate 2

description: Library name: vci_058_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_364


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_363


title: isolate vci_058, replicate 1

description: Library name: vci_058_1


title: AXLO1

description: Library name: AXLO1


title: AXLF3

description: Library name: AXLF3


title: C57BL6 mice, naive 1

description: C57BL6 mice_GL261_normalized_counts.csv


title: C57BL6 mice, naive 2

description: C57BL6 mice_GL261_normalized_counts.csv


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_362


title: Nude mice, U87MG glioma cells, tumour bearing mouse, RAE 3

source_name: U-87 MG

value: U-87 MG

value: U-87 MG human glioblastoma


title: isolate vci_057, replicate 2

description: Library name: vci_057_2


title: AXLF2

description: Library name: AXLF2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_361

value: spinal neuron differentiation


title: isolate vci_057, replicate 1

description: Library name: vci_057_1


title: isolate vci_059, replicate 1

description: Library name: vci_059_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_360

value: homogenous protocol


title: FAKO3

description: Library name: FAKO3

value: Skin/Oral Mucosa

value: Stretched Gel + FAK inhibitor


title: isolate vci_056, replicate 2

description: Library name: vci_056_2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_359


title: AXLF1

description: Library name: AXLF1


title: isolate vci_056, replicate 1

description: Library name: vci_056_1


title: Nude mice, naive 3


title: AXLO2

description: Library name: AXLO2


title: Nude mice, U87MG glioma cells, tumour bearing mouse, solvent control 3


title: C57BL6 mice, GL261 glioma cells, tumour bearing mouse, RGD 1

description: C57BL6 mice_GL261_normalized_counts.csv

value: RGD peptide


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_358


title: Nude mice, U87MG glioma cells, tumour bearing mouse, RAE 2


title: isolate vci_053, replicate 2

description: Library name: vci_053_2


title: FAKF3

description: Library name: FAKF3


title: FAKO1

description: Library name: FAKO1


title: Nude mice, U87MG glioma cells, tumour bearing mouse, RGD 2


title: isolate vci_055, replicate 2

description: Library name: vci_055_2


title: Nude mice, U87MG glioma cells, tumour bearing mouse, solvent control 2


title: Nude mice, U87MG glioma cells, tumour bearing mouse, RAE 1


title: isolate vci_049, replicate 2

description: Library name: vci_049_2


title: FAKF1

description: Library name: FAKF1


title: FAKO2

description: Library name: FAKO2


title: isolate vci_049, replicate 1

description: Library name: vci_049_1


title: OS5

description: Library name: OS5

value: Stretched Gel


title: OS4

description: Library name: OS4


title: FAKF2

description: Library name: FAKF2


title: isolate vci_052, replicate 2

description: Library name: vci_052_2


title: Nude mice, U87MG glioma cells, tumour bearing mouse, RGD 3


title: isolate vci_048, replicate 1

description: Library name: vci_048_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_352


title: isolate vci_048, replicate 2

description: Library name: vci_048_2


title: Nude mice, U87MG glioma cells, tumour bearing mouse, solvent control 1


title: Nude mice, naive 2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_356


title: Nude mice, naive 1


title: FS3

description: Library name: FS3


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_357


title: isolate vci_052, replicate 1

description: Library name: vci_052_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_354


title: Nude mice, U87MG glioma cells, tumour bearing mouse, RGD 1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_353


title: OS6

description: Library name: OS6


title: Replicate-2B

city: Charlottesville

first: Araceli

middle: E

last: Santiago

state: VA

address: 409 Lane Road

department: Pediatrics

institute: University of Virginia

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Escherichia coli

source_name: Bacteria

growth_protocol: Bacterial strains used in this study were routinely propagated in Luria broth (LB) (American Bioanalytical, Natick, MA) from a fresh agar plate and grown overnight at 37°C. When needed, kanamycin (kan) was added to a final concentration of 50 ug/mL . For RNAseq, bacterial strains were cultured in Dulbecco’s modified Eagle’s medium with 0.4% glucose (DMEM high glucose) (Gibco, Grand Island, NY).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Bacteria

value: mutant

value: Strain  042


title: isolate vci_046, replicate 1

description: Library name: vci_046_1

value: bacterial

value: Clinical Isolate


title: Replicate-1B


title: Replicate-2A

value: WT


title: FS1

description: Library name: FS1

value: Fibroblast

value: Wildtype


title: isolate vci_045, replicate 2

description: Library name: vci_045_2


title: OM_POD7 scRNA-seq

description:
Library name: Oral Mucosa POD7
four hashes per tube; Green Fibroblasts: TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11 ; Red Fibroblasts: TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; Red all other cells: TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; Green all other cells: TotalSeq-B-0304 MouseHashTag4--M1-42_30-F20

data_processing:
FASTQs were demultiplexed, and files then aligned to mm10 reference genome using Space Ranger (10x Genomics, v.2.0.1).
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, spatial files

source_name: Oral Mucosa

extract_protocol:
Mouse oral mucosa and facial wounds were harvested at listed timepoints. Wounds were mechanically digested with sharp dissecting scissors. Tissue was then added to an enzymatic digestion consisting of Collagenase II (ThermoFisher, Cat:17101015) and IV (ThermoFisher, Cat:17104019) in DMEM-F12 (GIBCOTM, Fischer Scientific, Hampton, NH). Samples were added to an orbital shaker at 150 rpm for 90 minutes at 37ºC. FACS buffer was added to quench the digest and samples were filtered through 70 µm cell strainers. Samples were then centrifuged at 1500 for 5 minutes at 4°C. For samples that were sorted, cells were counted and resuspended in FACS buffer. Primary antibodies were applied, and cells were stained in the dark with gentle agitation for 30 min. Cells were then washed thoroughly in FACS buffer. A BD II FACS Aria machine was used for FACS sorting analysis. For lineage negative (Lin-) FACS analysis, the following primary antibodies were used: Tie2, CD45, CD31, CD324, CD326, Ter119.
scRNAseq  Stanford Genomics Facility (SGF) using the 10x Genomics Visium platform. The relevant protocols were followed per manufacturer’s guidelines.

value: Oral Mucosa

value: Wnt1ER mTmG


title: F_POD7 scRNA-seq

description:
Library name: Facial POD7
four hashes per tube; Green Fibroblasts: TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11 ; Red Fibroblasts: TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; Red all other cells: TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; Green all other cells: TotalSeq-B-0304 MouseHashTag4--M1-42_30-F19

source_name: Skin

value: Skin


title: Replicate-1A


title: Hi-C in 6KO+sh1A+DS+TSA 0h

city: Saitama

first: Kei

last: Fukuda

state: Japan

address: 2-1 Hrosawa, Wakoshi

institute: RIKEN

description:
Library name: Hi-C_6KO_sh1A_DS_TSA0
Hi-C_6KO_sh1A_DS

library_source: genomic

data_processing:
4DN Hi-C pipeline (v43, https://github.com/4dn-dcic/docker-4dn-hic).
Assembly: mm10
Supplementary files format and content: .hic

source_name: 6KO iMEFs

growth_protocol: We used previously established Setdb1, Suv39h1/2, Ehmt1, Ehmt2, Ring1b KO iMEFs to analysis the role of uH2A in heterochromatin maintenance (Fukuda et al., 2023). Mouse embryonic fibroblasts were maintained in Dulbecco's modified Eagle's medium (Nacalai tesque, 08458-16) containing 10% fetal bovine serum (Biosera, FB1061), MEM Non-Essential medium and 2-Mercaptoethanol (Nacalai tesque, 21417-52).

extract_protocol:
2x10^6 fixed cells were sujected to Hi-C analysis
Hi-C experiments were performed as previously described (Ikeda et al., 2018; Kadota et al., 2020), based on DpnII enzyme (4-bps cutter) using 2×10^6 fixed cells. Hi-C libraries were subject to paired-end sequencing (150 base pair (bp) read length) using HiSeq X Ten. Detailed protocol for HiC-seq library preparation is available at Protocols.io (https://www.protocols.io/view/iconhi-c-protocol-ver-1-0-4mjgu4n).

treatment_protocol: Ring1a knockdown by shRNA. We produced a lentiviral vector expressing shRNA targeting Ring1a by transfecting 293FT cells with shRNA vector, psPax2, and pMD2.G using PEI. Two days later, we collected the culture supernatant and then used it to transduce 5KO-Ring1b KO iMEFs at MOI=2. Following selection with 7 μg/ml BSD for 3 days, we collected the cells. TSA treatment. Six knockout (6KO) iMEFs treated with DS3201 and shRing1A were exposed to 2 μM TSA for 2 hours and 6 hours, followed by Western blotting, H3K27ac ChIP-seq, and in situ Hi-C analysis.

value: 6KO iMEFs

value: MEF

value: Ring1a shRNA + DS3201

tag: batch


title: F_POD2 scRNA-seq

description:
Library name: Facial POD2
four hashes per tube; Green Fibroblasts: TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11 ; Red Fibroblasts: TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; Red all other cells: TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; Green all other cells: TotalSeq-B-0304 MouseHashTag4--M1-42_30-F17


title: OM_POD1 scRNA-seq

description:
Library name: Oral Mucosa POD1
four hashes per tube; Green Fibroblasts: TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11 ; Red Fibroblasts: TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; Red all other cells: TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; Green all other cells: TotalSeq-B-0304 MouseHashTag4--M1-42_30-F18


title: isolate vci_044, replicate 2

description: Library name: vci_044_2


title: Input ChIP-seq in 6KO+sh1A+DS+TSA

description: Library name: Input_6KO_sh1A_DS_TSA

data_processing:
Trim adapter and low quality reads using Trim_galore
Map reads on mouse genome by Bowtie2
Remove PCR duplicates by Picard
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
ChIP DNA was extracted by Native ChIP protocol
Native ChIP and crosslinked ChIP. Native ChIP assays were performed as described previously (Fukuda et al. 2023). Antibody against H3K27ac (D5E5, CST) was used. The ChIP DNA was fragmented by Picoruptor (Diagenode) for 10 cycles of 30 seconds on, 30 seconds off. Then, ChIP library was constructed by KAPA Hyper Prep Kit (KAPA BIOSYSTEMS) and SeqCap Adapter Kit A (Roche) according to manufacturer instructions. The concentration of the ChIP-seq library was quantified by KAPA Library quantification kit (KAPA BIOSYSTEMS). ChIP sequencing was performed on a HiSeq X platform (Illumina). We performed two biological replicates for ChIP-seq.

value: RIng1a shRNA +DS +TSA


title: isolate vci_047, replicate 1

description: Library name: vci_047_1


title: Hi-C in 6KO+sh1A+DS+TSA 6h

description:
Library name: Hi-C_6KO_sh1A_DS_TSA6
Hi-C_6KO_sh1A_DS_TSA

value: Ring1a shRNA + DS3201 + TSA


title: OM_POD2 scRNA-seq

description:
Library name: Oral Mucosa POD2
four hashes per tube; Green Fibroblasts: TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11 ; Red Fibroblasts: TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; Red all other cells: TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; Green all other cells: TotalSeq-B-0304 MouseHashTag4--M1-42_30-F16


title: isolate vci_043, replicate 2

description: Library name: vci_043_2


title: FS2

description: Library name: FS2

value: Skin/Oral Mucosa

value: Stretched Gel


title: OM_POD4 scRNA-seq

description:
Library name: Oral Mucosa POD4
four hashes per tube; Green Fibroblasts: TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11 ; Red Fibroblasts: TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; Red all other cells: TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; Green all other cells: TotalSeq-B-0304 MouseHashTag4--M1-42_30-F15


title: isolate vci_046, replicate 2

description: Library name: vci_046_2


title: isolate vci_043, replicate 1

description: Library name: vci_043_1


title: H3K27ac ChIP-seq in 6KO+sh1A+DS+TSA

description: Library name: H3K27ac_6KO_sh1A_DS_TSA


title: F_POD4 scRNA-seq

description:
Library name: Facial POD4
four hashes per tube; Green Fibroblasts: TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11 ; Red Fibroblasts: TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; Red all other cells: TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; Green all other cells: TotalSeq-B-0304 MouseHashTag4--M1-42_30-F14


title: isolate vci_042, replicate 2

description: Library name: vci_042_2


title: isolate vci_042, replicate 1

description: Library name: vci_042_1


title: F_UW scRNA-seq

description:
Library name: Facial Unwounded
four hashes per tube; Green Fibroblasts: TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11 ; Red Fibroblasts: TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; Red all other cells: TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; Green all other cells: TotalSeq-B-0304 MouseHashTag4--M1-42_30-F13


title: Total RNA-Seq, shEXOSC3

city: Pittsburgh

first: Da

last: Yang

state: PA

address: 3501 Terrace

department: School of Pharmacy

institute: University of Pittsburgh

data_processing:
Reads were aligned using STAR.
Gene expression quantification and differential expression analysis were done by cuffdiff.
bw files were generated by STAR bedGraph output.
Assembly: hg38
Supplementary files format and content: Total_RNA_Seq_DEG, tab-delimited text files include gene expression and differential expression analysis results.
Supplementary files format and content: bw files showing the read distribution across the genome.

source_name: Mammary gland/Breast

growth_protocol: MCF-7 cells stably expressing shCtrl or shEXOSC3 RNA cells at low passage numbers (< 5) were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen). 10 µg total RNA was treated with RNase-free DNase I (Promega) for 30 min at 37 °C and RNA cleanup was performed using the RNA Clean & Concentrator-5 columns (Zymo). 1 µg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using KAPA RNA Hyper RiboErase HMR (96 rxn) following manufacturer's protocols.

treatment_protocol: Cells at exponential phase were washed twice with ice-cold PBS solution.

value: Mammary gland/Breast

tag: disease

value: Adenocarcinoma

value: Human epithelial cell

value: EXOSC3 knockdown


title: male healthy control, recovery_replicate 20

city: Fort Lauderdale

first: Lubov

last: Nathanson

state: Florida

address: 3321 College Ave.

department: INIM

institute: Nova Southeastern University

description: Library name: 2988sHM2

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)

tag: Sex

value: male


title: OM_UW scRNA-seq

description:
Library name: Oral Mucosa Unwounded
four hashes per tube; Green Fibroblasts: TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11 ; Red Fibroblasts: TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; Red all other cells: TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; Green all other cells: TotalSeq-B-0304 MouseHashTag4--M1-42_30-F12

value: Oral Mucosa

value: Wnt1ER mTmG


title: H3K27ac ChIP-seq in 6KO+sh1A+DS

description: Library name: H3K27ac_6KO_sh1A_DS

value: 6KO iMEFs

value: RIng1a shRNA +DS


title: isolate vci_045, replicate 1

description: Library name: vci_045_1

value: bacterial

value: Clinical Isolate


title: isolate vci_044, replicate 1

description: Library name: vci_044_1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_KO_Cell_355

value: spinal neuron differentiation

value: homogenous protocol


title: Total RNA-Seq, shCtrl

value: Scramble shRNA overexpression


title: F_POD1 scRNA-seq

description:
Library name: Facial POD1
four hashes per tube; Green Fibroblasts: TotalSeq-B-0301 MouseHashTag1--M1-42_30-F11 ; Red Fibroblasts: TotalSeq-B-0302 MouseHashTag2--M1-42_30-F11; Red all other cells: TotalSeq-B-0303 MouseHashTag3--M1-42_30-F11; Green all other cells: TotalSeq-B-0304 MouseHashTag4--M1-42_30-F11

value: Skin


title: isolate vci_041, replicate 2

description: Library name: vci_041_2


title: male healthy control, recovery_replicate 19

description: Library name: 2976sHM2


title: male healthy control, recovery_replicate 18

description: Library name: 2964sHM2


title: isolate vci_040, replicate 2

description: Library name: vci_040_2


title: isolate vci_041, replicate 1

description: Library name: vci_041_1


title: male healthy control, recovery_replicate 17

description: Library name: 2952sHM2


title: F_POD4

description: Library name: Facial POD4

data_processing:
FASTQs were demultiplexed, and files then aligned to mm10 reference genome using Space Ranger (10x Genomics, v.2.0.1).
Downstream analyses were conducted with Seurat, applying the spatial data vignette.
Assembly: mm10
Supplementary files format and content: Tab-separated values files, matrix files, spatial files
Library strategy: Spatial Transcriptomics

extract_protocol:
Tissue was flashfrozen per 10x's Visium Tissue Preprataion Protocol (CG000240)
Visiun was then performed at the Stanford Genomics Facility (SGF) using the 10x Genomics Visium platform. The relevant protocols were followed per manufacturer’s guidelines.

value: Wildtype


title: isolate vci_040, replicate 1

description: Library name: vci_040_1


title: male healthy control, recovery_replicate 16

description: Library name: 2844sHM2


title: isolate vci_039, replicate 2

description: Library name: vci_039_2


title: OM_UW

description: Library name: Oral Mucosa Unwounded

value: Unwounded


title: male healthy control, recovery_replicate 15

description: Library name: 2832sHM2


title: isolate vci_039, replicate 1

description: Library name: vci_039_1


title: male healthy control, recovery_replicate 14

description: Library name: 2820sHM2


title: F_UW

description: Library name: Facial Unwounded


title: male healthy control, recovery_replicate 13

description: Library name: 2808sHM2


title: isolate vci_038, replicate 2

description: Library name: vci_038_2


title: CIA+LPS

city: Omaha

first: Aaron

middle: D

last: Schwab

state: NE

address: 42nd and Emile St.

institute: University of Nebraska Medical Center

description:
Library name: Sample 4
10x Genomices

data_processing:
The Cell Ranger Count tool, which uses STAR, was utilized to align the reads to the mouse reference transcriptome. Aligned reads were filtered for valid cell barcodes and unique molecular identifiers (UMIs) and observed cell barcodes were retained. The default estimated cell count was used for this experiment.  The resulting analysis files for each sample were then aggregated using the Cell Ranger aggr pipeline, which performed a between-sample normalization step and merged all samples into one. The aggregated cell-by-gene count matrix was then used as the input for downstream analysis. The aggregated matrix was analyzed using the Loupe Browser (v.6.4; 10X Genomics) that allows easy visualization and analysis of Chromium single-cell 5′ and 3′ gene expression data and visualize UMAP plots, as well as normalized and annotated cell clustering and projection. To find the Differential Expression or Marker genes, we used the “globally distinguished” from the Significant Feature Comparison option to distinguish a cluster from every other cluster by using the p-value threshold (p<0.05) and log2fold-change (FC) > 1 (upregulated) or < -1 (downregulated) to filter for significant genes.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lung

extract_protocol:
Cells were processed for RNAseq in FACS buffer (2% fetal bovine serum + 0.1% NaN3 in phosphate buffered saline (PBS); all reagents purchased from Sigma unless otherwise specified). Single cell suspensions generated from whole lungs were quantified and viability tested using a LUNA-FLTM Dual Fluorescence Cell Counter (Logos Biosystems, Annandale, VA). Single cells were isolated using a 10x Chromium controller per manufacturer’s suggested protocol (10x Genomics, Pleasanton, CA). Following cell capture, the gel beads in emulsion/sample solution were recovered and placed into strip tubes. Reverse transcription was performed on a thermocycler (C100 TouchTM Thermal cycler, Bio-Rad, Hercules, CA) per recommended protocol followed by cDNA amplification. Amplified products were solid phase reversible immobilization (SPIR) bead-purified and evaluated by Fragment Analyzer (Agilent, Santa Clara, CA).
Twenty-five percent of the cDNA volume was subjected to fragmentation and double-sided SPRIselect (Beckman /Coulter, Indianapolis, IN) was used for PCR purification. PCR products were purified, quantified, and library size distribution determined by fragment Analyzer. Libraries were sequenced per the manufacturer’s suggested parameters on a NextSeq500 sequences to an average depth of 50,000 reads per cell.

value: Lung

value: 6-8 weeks old

value: Male

value: CIA+LPS


title: isolate vci_038, replicate 1

description: Library name: vci_038_1


title: LPS

description:
Library name: Sample 3
10x Genomices

value: Sham+LPS


title: CIA

description:
Library name: Sample 2
10x Genomices

value: CIA+Saline


title: OM_POD4

description: Library name: Oral Mucosa POD4

value: Oral Mucosa


title: male healthy control, recovery_replicate 11

description: Library name: 2784sHM2

value: peripheral blood mononuclear cells

value: healthy control

value: T2 (recovery)

value: male


title: isolate vci_035, replicate 2

description: Library name: vci_035_2

value: bacterial

value: Clinical Isolate


title: male healthy control, recovery_replicate 12

description: Library name: 2796sHM2


title: Sham

description:
Library name: Sample 1
10x Genomices

value: Sham+Saline


title: SM,susceptible,Xoo,rep1

city: Hyderabad

first: Ramesh

middle: Venkata

last: Sonti

state: Telangana

address: Habsiguda

country: India

institute: CSIR-Centre for Cellular and Molecular Biology

hyb_protocol: The normalized cRNA was fragmented (into 50-200 bp fragments), hybridized to rice gene chips, washed, stained, and scanned as per Affymetrix protocols.

scan_protocol: The arrays were scanned on an Affymetrix GeneChip Scanner 3000.

data_processing: The data was analyzed using the Transcriptome Analysis Console (TAC) provided by Affymetrix. The ‘.cel’ files were provided as input and data were normalized using PLIER.  The results were compared between Xoo-treated plants vs mock-treated plants. At the same time, we compared mock-treated plants and Xoo-treated plants of both varieties. Transcripts showing differential expression of > 1.5 fold with a false discovery rate (FDR) value below 0.05 were considered significantly differentially expressed.

label: biotin

organism: Oryza sativa

source_name: Leaf

label_protocol: 8 µg of total RNA isolated from water or Xoo inoculated leaveswere converted to cDNA using an Affymetrix (Santa Clara, CA) one-cycle labeling kitfollowing the manufacturer’s instructions. The synthesized double-stranded cDNA was column purified and was further subjected to RNA amplification using an Affymetrix IVT labeling kit. The amplified RNA (cRNA) generated in this manner was quantitated by using a NanoDrop® ND-1000 UV-Vis Spectrophotometer (NanoDrop Technologies, Wilmington, DE).

growth_protocol: Seeds were germinated on Petri plates with a germination towel. 5-day old seedlings were transferred to pots. Experiments were conducted in 60-day-old rice plants in the greenhouse.

extract_protocol: After 24hr a 2mm leaf piece from the site of clip-inoculation was collected and frozen immediately into liquid nitrogen. 15 such leaf pieces were collected for each treatment in each set. Total RNA was isolated from the harvested pieces using TRI-REAGENT (Sigma).

treatment_protocol: Xoo strain BXO43 was cultured overnight on peptone-sucrose (PS) media. 60-day-old rice plant leaves were clip-inoculated with scissors dipped in water or Xoo (O.D. = 1.0).

tag: Stage

value: 60-day old


title: SM,susceptible,Xoo,rep3


title: isolate vci_035, replicate 1

description: Library name: vci_035_1


title: male healthy control, recovery_replicate 10

description: Library name: 2772sHM2


title: p53 CUT&RUN IDH2-R172K p53 Off Replicate 3

city: Chapel Hill

first: John

middle: P.

last: Morris IV

state: NC

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

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

institute: University of North Carolina at Chapel Hill

data_processing:
Fastq files were trimmed to remove Ns using TrimGalore 0.6.7.
Bowtie2 2.3.4.1 was used to align reads to the mouse mm10 genome.
Samtools generate aligned sorted BAM files and reads with mapping quality scores <10 were filtered out.
BAM files were converted to bigwig format for visualization using
TMM on 200 bp window high abundance regions (peaks) was performed using csaw to generate scale factors for normalization of samples. The effective library size was calculated using these scale factors, divided by a million, and the reciprocal was supplied to --scaleFactor in csaw to generate bigwig files which were then averaged using wiggletools mean.
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: Liver Tumor

growth_protocol: NPsh p53 restoration cells were grown on sterile tissue culture plates coated with PureCol Collagen I (Advanced BioMatrix in DMEM containing tet-free Fetal Bovine Serum (Gemini) and 1% Penicillin Streptomycin in 5% CO2 at 37C.

extract_protocol:
Monolayer cells were detached using TrypLE, washed with CUT&RUN wash buffer, and adhered to Concanavelin A beads. CUT&RUN was performed according to the Cell Signaling Technology manufacturers protocol.
DNA was purified and libraries were prepped using the Hyperprep Kit with KAPA Library Amplification Primer Mix and KAPA Unique Dual-Indexed Adapter Kit. Qubit was used to measure library concentrations and a TapeStation was used to confirm library integrity before pooling and sequencing on a Nextseq500.

treatment_protocol: IDH2-WT or IDH2-R172K were stably transduced into NPsh cells. Cells were grown either on doxycycline 1 ug/mL or removed from doxycycline for 6 days before collection for CUT&RUN.

value: Liver Tumor

value: IDH2 -R172K Overexpression

value: 1 ug/mL Doxycycline


title: SM,susceptible,mock,rep2


title: isolate vci_033, replicate 1

description: Library name: vci_033_1


title: male healthy control, recovery_replicate 9

description: Library name: 2760sHM2


title: SM,susceptible,Xoo,rep2


title: SM,susceptible,mock,rep3


title: SM210,resistant,Xoo,rep1


title: SM210,resistant,Xoo,rep2


title: SM210,resistant,Xoo,rep3


title: Input ChIP-seq in 6KO+sh1A+DS

description: Library name: Input_6KO_sh1A_DS

value: 6KO iMEFs

value: MEF

value: RIng1a shRNA +DS


title: isolate vci_032, replicate 2

description: Library name: vci_032_2


title: p53 CUT&RUN IDH2-R172K p53 Off Replicate 1


title: p53 CUT&RUN IDH2-R172K p53 On Replicate 3

value: 6 days Off Doxycycline


title: male healthy control, recovery_replicate 7

description: Library name: 2736sHM2


title: isolate vci_032, replicate 1

description: Library name: vci_032_1


title: p53 CUT&RUN IDH2-R172K p53 On Replicate 2


title: male healthy control, recovery_replicate 6

description: Library name: 2724sHM2


title: SM210,resistant,mock,rep2


title: male healthy control, recovery_replicate 8

description: Library name: 2748sHM2


title: isolate vci_030, replicate 2

description: Library name: vci_030_2


title: SM210,resistant,mock,rep3


title: SM,susceptible,mock,rep1


title: p53 CUT&RUN IDH2-WT p53 Off Replicate 3

value: IDH2 Wildtype Overexpression


title: male healthy control, recovery_replicate 5

description: Library name: 2712sHM2


title: male healthy control, recovery_replicate 4

description: Library name: 2700sHM2


title: isolate vci_030, replicate 1

description: Library name: vci_030_1


title: isolate vci_029, replicate 1

description: Library name: vci_029_1


title: isolate vci_029, replicate 2

description: Library name: vci_029_2


title: male healthy control, recovery_replicate 3

description: Library name: 2688sHM2


title: isolate vci_028, replicate 2

description: Library name: vci_028_2


title: p53 CUT&RUN IDH2-WT p53 Off Replicate 2


title: p53 CUT&RUN IDH2-WT p53 Off Replicate 1


title: male healthy control, recovery_replicate 1

description: Library name: 2664sHM2


title: isolate vci_028, replicate 1

description: Library name: vci_028_1


title: Heat stress Rep3

city: Tokyo

first: Nobuhiro

last: Suzuki

state: 東京都

address: 7-1, Kioicho, Chiyoda

institute: Sophia University

description: Biological replicate 3 of 4. heat stressed shoot, sampled immediately after 30min treatment

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

organism: Arabidopsis thaliana

source_name: Heat stressed shoot

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Arabidopsis plants were grown on peat pellet under 21oC, 16/8 h light/dark cycle, 50mmolm-2s-1 in a growth chamber.

extract_protocol: Total RNA was extracted using TRIzol reagent and purified using Qiagen RNeasy mini kit.

treatment_protocol: Fouteen-day-old plants were subjected to heat stress (40oC) in a growth chamber or irradiated with microwave (23W) using a Start SYNTH for 1h

tag: ecotype

value: Columbia 0

value: shoot

value: Heat stress


title: isolate vci_027, replicate 2

description: Library name: vci_027_2

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


title: Heat stress Rep4

description: Biological replicate 4 of 4. heat stressed shoot, sampled immediately after 30min treatment


title: male healthy control, maximal exertion_replicate 20

description: Library name: 5275sHM1

value: peripheral blood mononuclear cells

value: healthy control

value: T1 (maximal exertion)


title: p53 CUT&RUN IDH2-WT p53 On Replicate 2


title: p53 CUT&RUN IDH2-R172K p53 On Replicate 1


title: SM210,resistant,mock,rep1


title: Heat stress Rep1

description: Biological replicate 1 of 4. heat stressed shoot, sampled immediately after 30min treatment


title: Microwave Rep3

description: Biological replicate 3 of 4. microwave irradiated shoot, sampled immediately after 30min treatment

source_name: Microwave irradiated shoot

value: Microwave


title: isolate vci_027, replicate 1

description: Library name: vci_027_1

source_name: bacterial

value: bacterial

value: Clinical Isolate


title: male healthy control, maximal exertion_replicate 19

description: Library name: 2987sHM1

value: male


title: Microwave Rep1

description: Biological replicate 1 of 4. microwave irradiated shoot, sampled immediately after 30min treatment


title: Heat stress Rep2

description: Biological replicate 2 of 4. heat stressed shoot, sampled immediately after 30min treatment


title: Microwave Rep4

description: Biological replicate 4 of 4. microwave irradiated shoot, sampled immediately after 30min treatment


title: male healthy control, recovery_replicate 2

description: Library name: 2676sHM2

value: T2 (recovery)


title: isolate vci_026, replicate 2

description: Library name: vci_026_2


title: p53 CUT&RUN IDH2-WT p53 On Replicate 1

value: Liver Tumor


title: Microwave Rep2

description: Biological replicate 2 of 4. microwave irradiated shoot, sampled immediately after 30min treatment


title: isolate vci_026, replicate 1

description: Library name: vci_026_1


title: male healthy control, maximal exertion_replicate 17

description: Library name: 2951sHM1


title: p53 CUT&RUN IDH2-WT p53 On Replicate 3


title: male healthy control, maximal exertion_replicate 16

description: Library name: 2843sHM1


title: male healthy control, maximal exertion_replicate 15

description: Library name: 2831sHM1


title: B6_12M_20M_PBMCs_CMO

city: Philadelphia

first: Makarand

middle: V

last: Risbud

address: 1025 Walnut Street

department: Orthopaedic Surgery

institute: Thomas Jefferson University

description:
B6_12M_PBMCs_CMO (Sample 5)
B6_20M_PBMCs_CMO (Sample 6)
10X Genomics scRNA-seq CMO
B6_12M_barcodes.tsv.gz
B6_12M_features.tsv.gz
B6_12M_matrix.mtx.gz
B6_20M_barcodes.tsv.gz
B6_20M_features.tsv.gz
B6_20M_matrix.mtx.gz

data_processing:
Raw data were aligned to the mouse reference transcriptome (mm10-2020-A) and underwent preprocessing with Cell Ranger Multi v7.0.1. According to the authors ' recommended workflow, downstream processing was conducted using Seurat v4.3.0
Data were further analyzed and visualized using the scType and clusterProfiler packages in R.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CMO

source_name: Peripheral Blood

extract_protocol:
Whole blood was collected from 12M and 20M SM/J and BL6 mice via intracardiac puncture and diluted into an equal volume of Dulbecco’s PBS + 2% FBS (StemCell Technologies, 07905). According to the manufacturer’s specifications, blood was layered on top of Lymphoprep™ (StemCell Technologies, 07851) in a 15 mL tube and centrifuged at 800 rcf for 20 minutes at room temperature. The mononuclear cells were washed twice with PBS + 2% FBS, and platelets were removed with an additional centrifugation at 120 rcf for 10 minutes. To facilitate removal of any remaining RBCs, a lysis step was performed (Biolegend, 420302). Briefly, lysis buffer (1X) was added to the cell suspension and incubated for 5 minutes, with periodic inversion. Cells were then centrifuged at 350 rcf for 10 minutes, and PBMCs were washed twice with PBS + 2% FBS.
Libraries were constructed according to manufacturer's specification for the 10X Genomics 3' single-cell gene expression analysis, with multiplexing

value: Peripheral Blood

value: PMBCs

value: mixed sample (12-month-old, 20-month-old)


title: SMJ_12M_20M_PBMCs_scRNA

description:
SMJ_12M_PBMCs_scRNA (Sample 3)
SMJ_20M_PBMCs_scRNA (Sample 4)
10X Genomics scRNA-seq
SMJ_12M_barcodes.tsv.gz
SMJ_12M_features.tsv.gz
SMJ_12M_matrix.mtx.gz
SMJ_20M_barcodes.tsv.gz
SMJ_20M_features.tsv.gz
SMJ_20M_matrix.mtx.gz

data_processing:
Raw data were aligned to the mouse reference transcriptome (mm10-2020-A) and underwent preprocessing with Cell Ranger Multi v7.0.1. According to the authors ' recommended workflow, downstream processing was conducted using Seurat v4.3.0
Data were further analyzed and visualized using the scType and clusterProfiler packages in R.
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files

value: SM/J


title: isolate vci_025, replicate 2

description: Library name: vci_025_2

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


title: Control Rep3

description: Biological replicate 3 of 4. Control shoot, untreated

source_name: Shoot

value: Control


title: male healthy control, maximal exertion_replicate 14

description: Library name: 2819sHM1


title: isolate vci_024, replicate 2

description: Library name: vci_024_2


title: Mouse IgG Control

value: IDH2 Wildtype Overexpression

value: Combined Dox On Dox Off


title: Control Rep4

description: Biological replicate 4 of 4. Control shoot, untreated

value: Columbia 0

value: shoot


title: Control Rep1

description: Biological replicate 1 of 4. Control shoot, untreated


title: Control Rep2

description: Biological replicate 2 of 4. Control shoot, untreated


title: B6_12M_20M_PBMCs_scRNA

description:
B6_12M_PBMCs_scRNA (Sample 1)
B6_20M_PBMCs_scRNA (Sample 2)
10X Genomics scRNA-seq
B6_12M_barcodes.tsv.gz
B6_12M_features.tsv.gz
B6_12M_matrix.mtx.gz
B6_20M_barcodes.tsv.gz
B6_20M_features.tsv.gz
B6_20M_matrix.mtx.gz


title: male healthy control, maximal exertion_replicate 18

description: Library name: 2963sHM1

value: peripheral blood mononuclear cells

value: healthy control


title: isolate vci_025, replicate 1

description: Library name: vci_025_1


title: SMJ_12M_20M_PBMCs_CMO

description:
SMJ_12M_PBMCs_CMO (Sample 7)
SMJ_20M_PBMCs_CMO (Sample 8)
10X Genomics scRNA-seq CMO
SMJ_12M_barcodes.tsv.gz
SMJ_12M_features.tsv.gz
SMJ_12M_matrix.mtx.gz
SMJ_20M_barcodes.tsv.gz
SMJ_20M_features.tsv.gz
SMJ_20M_matrix.mtx.gz


title: RPK;Pdk1;AlbCreER_tumor_7 technical rep2

city: Munich

first: Ursula

last: Ehmer

address: Ismaninger Str. 22

department: Internal Medicine II

country: Germany

institute: Klinikum rechts der Isar, TU München

description: AGCGGG

data_processing:
R version 4.02
Bioconductor version 3.12
DESeq2 version 1.30.1
no trimming
gene annotation M25
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: matrix column names for each technical replicate are listed under description

source_name: tumor

extract_protocol:
liver samples and liver tumors were isolated using the Maxwell 16 LEV simplyRNA Kit (Promega) according to the manufacturer’s instructions
Reverse transcription was carried out for individual samples using the Maxima RT polymerase with oligo-dT primers consisting of a sample barcode, unique molecular identifiers (UMIs) and an adaptor. Ends of cDNAs were extended by a template switch oligo (TSO) and full-length cDNA was amplified with primers binding to the TSO-site and the adaptor. For fragmentation of cDNA, NEB Ultra II FS kit was used, followed by end repair and A-tailing, to which a TruSeq adapter was ligated. Finally, 3’-end-fragments were amplified using primers with Illumina P5 and P7 overhangs

value: tumor

value: tamoxifen


title: Microglia, 5xFAD negative, Csf1 treated, CD11c negative 1

city: Freiburg im Breisgau

first: Marco

last: Prinz

state: Baden-Württemberg

address: Breisacher Str. 64, C/O Institut für Neuropathologie

department: Institut für Neuropathologie

institute: Universitätsklinikum Freiburg

description:
Library name: plate_12_Csf1_Pool_1_1_12_S16_scRNAseq
mCEL-Seq2

data_processing:
Analysis of all datasets was performed according to the following initial pipeline: The count matrices were analyzed with R Studio (version 2022.07.1 Build 554) using the Seurat package (version 5). For quality control, duplets were excluded by selecting cells with <4000 nFeatures and ambient noise was filtered by selecting cells with >200 nFeatures. The data was normalized using the “NormalizeData” function with the “LogNormalize” method, variable features were found using “FindVariableFeatures” function with the ‘variance stabilizing transformation’ method and selecting the top 4000 features. Data was scaled using “ScaleData” function and then reduced in dimensions using principal component analysis (PCA) with the “RunPCA” function.
Reads were processed using STARsolo with the Gencode M26 reference. Barcode filtering applied standard thresholds without sample-specific optimization. Processed gene expression matrices are unique per sample.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Index sorting was done using a MoFlo Astrios EQ at the Lighthouse Core Facility. The following antibodies and dyes were used: 1:500 Fixable Viability Dye in eFluor780 (Thermofisher 65-0865-14); 1:200 for all antibodies used for the dump channel in APC-Cy7 (CD3 clone 145-2C11, BioLegend  #100330, Gr1 cloneRB6-8C5, BioLegend  #108423, CD19 clone 1D3, BD #557655); 1:100 for CD45 in BV786 (clone 30-F11, BD #564225); 1:100 for CD11b in BV605 (clone M1/70, BioLegend #101257); 1:100 for CD11c in PE-Cy7 (clone N418, eBioscience #25-0114-82); 1:100 for Clec7a in APC (clone 17-5859-80 eBioscience #bg1fpj).  Single cortical microglia were sorted into 384-well plates. Gating strategy is provided in Suppl. Figure 3a. Cells were spun down and stored at –80°C until further processing. RNA from single cells was isolated and transcribed into cDNA.
For RNA sequencing, the mCEL-Seq2 protocol was used as previously established.

value: Brain

value: Microglia

value: Cx3cr1-CreERT2 R26-Confetti

value: mCSF

tag: library type

value: mRNA

tag: sample group


title: male healthy control, maximal exertion_replicate 12

description: Library name: 2795sHM1

value: T1 (maximal exertion)

value: male


title: Microglia, 5xFAD negative, Csf1 treated, CD11c negative 2

description:
Library name: plate_12_Csf1_Pool_2_13_24_S17_scRNAseq
mCEL-Seq2

tag: cell type


title: isolate vci_023, replicate 2

description: Library name: vci_023_2

value: bacterial

tag: genotype

value: Clinical Isolate


title: isolate vci_024, replicate 1

description: Library name: vci_024_1


title: RPK;Pdk1;AlbCreER_tumor_6 technical rep2

description: AGACCT

tag: treatment


title: male healthy control, maximal exertion_replicate 13

description: Library name: 2807sHM1


title: Microglia, 5xFAD negative, PBS control, CD11c negative 3

description:
Library name: plate_10_PBS_Pool_2_13_24_S15_scRNAseq
mCEL-Seq2

value: PBS


title: isolate vci_023, replicate 1

description: Library name: vci_023_1


title: Microglia, 5xFAD negative, PBS control, CD11c negative 2

description:
Library name: plate_10_PBS_Pool_1_1_12_S14_scRNAseq
mCEL-Seq2


title: male healthy control, maximal exertion_replicate 11

description: Library name: 2783sHM1


title: RPK;Pdk1;AlbCreER_tumor_5 technical rep2

description: TATTGT


title: male healthy control, maximal exertion_replicate 10

description: Library name: 2771sHM1


title: isolate vci_022, replicate 2

description: Library name: vci_022_2


title: Microglia, 5xFAD negative, PBS control, CD11c negative 1

description:
Library name: plate_9_PBS_Pool_1_1_12_S13_scRNAseq
mCEL-Seq2


title: Microglia, 5xFAD positive, Csf1 treated, CD11c positive 4

description:
Library name: plate_8_Csf1_Pool_2_13_24_S12_scRNAseq
mCEL-Seq2

value: Cx3cr1-CreERT2 R26-Confetti FAD


title: isolate vci_022, replicate 1

description: Library name: vci_022_1


title: RPK;Pdk1;AlbCreER_tumor_4 technical rep2

description: CTATAT


title: male healthy control, maximal exertion_replicate 9

description: Library name: 2759sHM1


title: Microglia, 5xFAD positive, Csf1 treated, CD11c positive 3

description:
Library name: plate_8_Csf1_Pool_1_1_12_S11_scRNAseq
mCEL-Seq2


title: isolate vci_021, replicate 2

description: Library name: vci_021_2


title: RPK;Pdk1;AlbCreER_tumor_2 technical rep2

description: GGTGGC


title: male healthy control, maximal exertion_replicate 7

description: Library name: 2735sHM1


title: isolate vci_021, replicate 1

description: Library name: vci_021_1


title: Microglia, 5xFAD positive, Csf1 treated, CD11c positive 2

description:
Library name: plate_7_Csf1_Pool_2_13_24_S10_scRNAseq
mCEL-Seq2


title: male healthy control, maximal exertion_replicate 8

description: Library name: 2747sHM1


title: RPK;AlbCreER_tumor_8 technical rep2

description: CGCCCT


title: RPK;Pdk1;AlbCreER_tumor_1 technical rep2

description: GCCCTC


title: isolate vci_020, replicate 2

description: Library name: vci_020_2


title: Microglia, 5xFAD positive, Csf1 treated, CD11c negative 4

description:
Library name: plate_6_Csf1_Pool_2_13_24_S8_scRNAseq
mCEL-Seq2


title: Microglia, 5xFAD positive, Csf1 treated, CD11c positive 1

description:
Library name: plate_7_Csf1_Pool_1_1_12_S9_scRNAseq
mCEL-Seq2


title: RPK;AlbCreER_tumor_7 technical rep2

description: ACGGGG


title: isolate vci_019, replicate 2

description: Library name: vci_019_2


title: male healthy control, maximal exertion_replicate 6

description: Library name: 2723sHM1


title: male healthy control, maximal exertion_replicate 5

description: Library name: 2711sHM1


title: RPK;AlbCreER_tumor_6 technical rep2

description: TTTTGA


title: Microglia, 5xFAD positive, Csf1 treated, CD11c negative 2

description:
Library name: plate_5_Csf1_Pool_2_13_24_S6_scRNAseq
mCEL-Seq2


title: RPK;AlbCreER_tumor_5 technical rep2

description: TATGAA


title: RPK;Pdk1;AlbCreER_tumor_3 technical rep2

description: ACTTAT


title: Microglia, 5xFAD positive, Csf1 treated, CD11c negative 3

description:
Library name: plate_6_Csf1_Pool_1_1_12_S7_scRNAseq
mCEL-Seq2


title: isolate vci_018, replicate 2

description: Library name: vci_018_2


title: male healthy control, maximal exertion_replicate 4

description: Library name: 2699sHM1


title: isolate vci_019, replicate 1

description: Library name: vci_019_1


title: male healthy control, maximal exertion_replicate 3

description: Library name: 2687sHM1


title: Microglia, 5xFAD positive, PBS control, CD11c positive 2

description:
Library name: plate_4_PBS_Pool_2_13_24_S4_scRNAseq
mCEL-Seq2


title: male healthy control, maximal exertion_replicate 1

description: Library name: 2663sHM1


title: isolate vci_018, replicate 1

description: Library name: vci_018_1


title: Microglia, 5xFAD positive, PBS control, CD11c positive 1

description:
Library name: plate_4_PBS_Pool_1_1_12_S3_scRNAseq
mCEL-Seq2


title: RPK;AlbCreER_tumor_3 technical rep2

description: ACAATA


title: p53 CUT&RUN IDH2-R172K p53 Off Replicate 2

value: Liver Tumor

value: IDH2 -R172K Overexpression

value: 1 ug/mL Doxycycline


title: Microglia, 5xFAD positive, Csf1 treated, CD11c negative 1

description:
Library name: plate_5_Csf1_Pool_1_1_12_S5_scRNAseq
mCEL-Seq2


title: RPK;AlbCreER_tumor_4 technical rep2

description: CATTAT


title: male healthy control, maximal exertion_replicate 2

description: Library name: 2675sHM1

value: peripheral blood mononuclear cells

value: healthy control


title: isolate vci_017, replicate 1

description: Library name: vci_017_1


title: male healthy control, baseline_replicate 20

description: Library name: 5267sHM0

value: T0 (baseline)


title: Microglia, 5xFAD positive, PBS control, CD11c negative 2

description:
Library name: plate_1_PBS_Pool_2_13_24_S2_scRNAseq
mCEL-Seq2

value: Brain


title: RPK;AlbCreER_tumor_2 technical rep2

description: GGGTCG

value: tumor

value: tamoxifen


title: RPK;AlbCreER_tumor_1 technical rep2

description: GCCAGG


title: isolate vci_016, replicate 2

description: Library name: vci_016_2


title: isolate vci_016, replicate 1

description: Library name: vci_016_1


title: Microglia, 5xFAD positive, PBS control, CD11c negative 1

description:
Library name: plate_1_PBS_Pool_1_1_12_S1_scRNAseq
mCEL-Seq2

value: Microglia


title: isolate vci_015, replicate 2

description: Library name: vci_015_2


title: male healthy control, baseline_replicate 18

description: Library name: 2974sHM0


title: male healthy control, baseline_replicate 19

description: Library name: 2986sHM0


title: RPK_tumor_AAV_4 technical rep2

description: AGATTA

value: AAV-Cre


title: isolate vci_015, replicate 1

description: Library name: vci_015_1


title: RPK_tumor_AAV_5 technical rep2

description: CTTTAA


title: male healthy control, baseline_replicate 17

description: Library name: 2950sHM0


title: male healthy control, baseline_replicate 16

description: Library name: 2924sHM0


title: RPK_tumor_AAV_3 technical rep2

description: GTGCGC


title: scRNAseq, Microglia, late stage AD, LPS treated, CD11c negative

description:
Library name: P5_LS_LPS_neg_1_scRNAseq
mCEL-Seq2

tag: disease stage

value: late stage AD

value: Antibiotic cocktail

value: mRNA


title: scRNAseq, Microglia, late stage AD, LPS treated, CD11c positive

description:
Library name: P5_LS_LPS_pos_2_scRNAseq
mCEL-Seq2

tag: tissue


title: scRNAseq, Microglia, late stage AD, Abx treated, CD11c positive

description:
Library name: P5_LS_Abx_pos_4_scRNAseq
mCEL-Seq2

value: LPS


title: isolate vci_017, replicate 2

description: Library name: vci_017_2

value: bacterial

value: Clinical Isolate


title: isolate vci_014, replicate 2

description: Library name: vci_014_2


title: RPK_tumor_AAV_2 technical rep2

description: GCCGTG


title: male healthy control, baseline_replicate 14

description: Library name: 2830sHM0

value: male


title: scRNAseq, Microglia, late stage AD, Abx treated, CD11c negative

description:
Library name: P5_LS_Abx_neg_3_scRNAseq
mCEL-Seq2

value: Cx3cr1-CreERT2 R26-Confetti FAD


title: male healthy control, baseline_replicate 15

description: Library name: 2842sHM0


title: RPK_tumor_AAV_1 technical rep2

description: CGCGCA


title: isolate vci_013, replicate 2

description: Library name: vci_013_2


title: scRNAseq, Microglia, late stage AD, untreated, CD11c positive

description:
Library name: P4_LSN_pos_8_scRNAseq
mCEL-Seq2

value: Untreated


title: isolate vci_013, replicate 1

description: Library name: vci_013_1


title: male healthy control, baseline_replicate 13

description: Library name: 2818sHM0

value: peripheral blood mononuclear cells


title: control_liver_5 technical rep2

description: CGCTGC

source_name: liver

value: liver


title: male healthy control, baseline_replicate 12

description: Library name: 2806sHM0

value: healthy control

value: T0 (baseline)