title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_140

description: The rows in 'counts.txt' and 'rpkms.txt' are genes and the columns are the cell ids ('Cell_001', 'Cell_002', 'Cell_003', 'Cell_004', 'Cell_005', 'Cell_006', 'Cell_007', 'Cell_008', 'Cell_009', 'Cell_010', 'Cell_011', 'Cell_012', 'Cell_013', 'Cell_014', 'Cell_015', 'Cell_016', 'Cell_017', 'Cell_018', 'Cell_019', 'Cell_020', 'Cell_021', 'Cell_022', 'Cell_023', 'Cell_024', 'Cell_025', 'Cell_026', 'Cell_027', 'Cell_028', 'Cell_029', 'Cell_030', 'Cell_031', 'Cell_032', 'Cell_033', 'Cell_034', 'Cell_035', 'Cell_036', 'Cell_037', 'Cell_038', 'Cell_039', 'Cell_040', 'Cell_041', 'Cell_042', 'Cell_043', 'Cell_044', 'Cell_045', 'Cell_046', 'Cell_047', 'Cell_048', 'Cell_049', 'Cell_050', 'Cell_051', 'Cell_052', 'Cell_053', 'Cell_054', 'Cell_055', 'Cell_056', 'Cell_057', 'Cell_058', 'Cell_059', 'Cell_060', 'Cell_061', 'Cell_062', 'Cell_063', 'Cell_064', 'Cell_065', 'Cell_066', 'Cell_067', 'Cell_068', 'Cell_069', 'Cell_070', 'Cell_071', 'Cell_072', 'Cell_073', 'Cell_074', 'Cell_075', 'Cell_076', 'Cell_077', 'Cell_078', 'Cell_079', 'Cell_080', 'Cell_081', 'Cell_082', 'Cell_083', 'Cell_084', 'Cell_085', 'Cell_086', 'Cell_087', 'Cell_088', 'Cell_089', 'Cell_090', 'Cell_091', 'Cell_092', 'Cell_093', 'Cell_094', 'Cell_095', 'Cell_096', 'Cell_097', 'Cell_098', 'Cell_099', 'Cell_100', 'Cell_101', 'Cell_102', 'Cell_103', 'Cell_104', 'Cell_105', 'Cell_106', 'Cell_107', 'Cell_108', 'Cell_109', 'Cell_110', 'Cell_111', 'Cell_112', 'Cell_113', 'Cell_114', 'Cell_115', 'Cell_116', 'Cell_117', 'Cell_118', 'Cell_119', 'Cell_120', 'Cell_121', 'Cell_122', 'Cell_123', 'Cell_124', 'Cell_125', 'Cell_126', 'Cell_127', 'Cell_128', 'Cell_129', 'Cell_130', 'Cell_131', 'Cell_132', 'Cell_133', 'Cell_134', 'Cell_135', 'Cell_136', 'Cell_137', 'Cell_138', 'Cell_139', 'Cell_140', 'Cell_141', 'Cell_142', 'Cell_143', 'Cell_144', 'Cell_145', 'Cell_146', 'Cell_147', 'Cell_148', 'Cell_149', 'Cell_150', 'Cell_151', 'Cell_152', 'Cell_153', 'Cell_154', 'Cell_155', 'Cell_156', 'Cell_157', 'Cell_158', 'Cell_159', 'Cell_160', 'Cell_161', 'Cell_162', 'Cell_163', 'Cell_164', 'Cell_165', 'Cell_166', 'Cell_167', 'Cell_168', 'Cell_169', 'Cell_170', 'Cell_171', 'Cell_172', 'Cell_173', 'Cell_174', 'Cell_175', 'Cell_176', 'Cell_177', 'Cell_178', 'Cell_179', 'Cell_180', 'Cell_181', 'Cell_182', 'Cell_183', 'Cell_184', 'Cell_185', 'Cell_186', 'Cell_187', 'Cell_188', 'Cell_189', 'Cell_190', 'Cell_191', 'Cell_192', 'Cell_193', 'Cell_194', 'Cell_195', 'Cell_196', 'Cell_197', 'Cell_198', 'Cell_199', 'Cell_200', 'Cell_201', 'Cell_202', 'Cell_203', 'Cell_204', 'Cell_205', 'Cell_206', 'Cell_207', 'Cell_208', 'Cell_209', 'Cell_210', 'Cell_211', 'Cell_212', 'Cell_213', 'Cell_214', 'Cell_215', 'Cell_216', 'Cell_217', 'Cell_218', 'Cell_219', 'Cell_220', 'Cell_221', 'Cell_222', 'Cell_223', 'Cell_224', 'Cell_225', 'Cell_226', 'Cell_227', 'Cell_228', 'Cell_229', 'Cell_230', 'Cell_231', 'Cell_232', 'Cell_233', 'Cell_234', 'Cell_235', 'Cell_236', 'Cell_237', 'Cell_238', 'Cell_239', 'Cell_240', 'Cell_241', 'Cell_242', 'Cell_243', 'Cell_244', 'Cell_245', 'Cell_246', 'Cell_247', 'Cell_248', 'Cell_249', 'Cell_250', 'Cell_251', 'Cell_252', 'Cell_253', 'Cell_254', 'Cell_255', 'Cell_256', 'Cell_257', 'Cell_258', 'Cell_259', 'Cell_260', 'Cell_261', 'Cell_262', 'Cell_263', 'Cell_264', 'Cell_265', 'Cell_266', 'Cell_267', 'Cell_268', 'Cell_269', 'Cell_270', 'Cell_271', 'Cell_272', 'Cell_273', 'Cell_274', 'Cell_275', 'Cell_276', 'Cell_277', 'Cell_278', 'Cell_279', 'Cell_280', 'Cell_281', 'Cell_282', 'Cell_283', 'Cell_284', 'Cell_285', 'Cell_286', 'Cell_287', 'Cell_288', 'Cell_289', 'Cell_290', 'Cell_291', 'Cell_292', 'Cell_293', 'Cell_294', 'Cell_295', 'Cell_296', 'Cell_297', 'Cell_298', 'Cell_299', 'Cell_300', 'Cell_301', 'Cell_302', 'Cell_303', 'Cell_304', 'Cell_305', 'Cell_306', 'Cell_307', 'Cell_308', 'Cell_309', 'Cell_310', 'Cell_311', 'Cell_312', 'Cell_313', 'Cell_314', 'Cell_315', 'Cell_316', 'Cell_317', 'Cell_318', 'Cell_319', 'Cell_320', 'Cell_321', 'Cell_322', 'Cell_323', 'Cell_324', 'Cell_325', 'Cell_326', 'Cell_327', 'Cell_328', 'Cell_329', 'Cell_330', 'Cell_331', 'Cell_332', 'Cell_333', 'Cell_334', 'Cell_335', 'Cell_336', 'Cell_337', 'Cell_338', 'Cell_339', 'Cell_340', 'Cell_341', 'Cell_342', 'Cell_343', 'Cell_344', 'Cell_345', 'Cell_346', 'Cell_347', 'Cell_348', 'Cell_349', 'Cell_350', 'Cell_351', 'Cell_352', 'Cell_353', 'Cell_354', 'Cell_355', 'Cell_356', 'Cell_357', 'Cell_358', 'Cell_359', 'Cell_360', 'Cell_361', 'Cell_362', 'Cell_363', 'Cell_364', 'Cell_365', 'Cell_366', 'Cell_367', 'Cell_368', 'Cell_369', 'Cell_370', 'Cell_371', 'Cell_372', 'Cell_373', 'Cell_374', 'Cell_375', 'Cell_376', 'Cell_377', 'Cell_378', 'Cell_379', 'Cell_380', 'Cell_381', 'Cell_382', 'Cell_383', 'Cell_384', 'Cell_385', 'Cell_386', 'Cell_387', 'Cell_388', 'Cell_389', 'Cell_390', 'Cell_391', 'Cell_392', 'Cell_393', 'Cell_394', 'Cell_395', 'Cell_396', 'Cell_397', 'Cell_398', 'Cell_399', 'Cell_400', 'Cell_401', 'Cell_402', 'Cell_403', 'Cell_404', 'Cell_405', 'Cell_406', 'Cell_407', 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'Cell_740', 'Cell_741', 'Cell_742', 'Cell_743', 'Cell_744', 'Cell_745', 'Cell_746', 'Cell_747', 'Cell_748', 'Cell_749', 'Cell_750', 'Cell_751', 'Cell_752', 'Cell_753', 'Cell_754', 'Cell_755', 'Cell_756', 'Cell_757', 'Cell_758', 'Cell_759', 'Cell_760', 'Cell_761', 'Cell_762', 'Cell_763', 'Cell_764', 'Cell_765', 'Cell_766', 'Cell_767', 'Cell_768', 'Cell_769', 'Cell_770', 'Cell_771', 'Cell_772', 'Cell_773', 'Cell_774', 'Cell_775', 'Cell_776', 'Cell_777', 'Cell_778', 'Cell_779', 'Cell_780', 'Cell_781', 'Cell_782', 'Cell_783', 'Cell_784', 'Cell_785', 'Cell_786', 'Cell_787', 'Cell_788', 'Cell_789', 'Cell_790', 'Cell_791', 'Cell_792', 'Cell_793', 'Cell_794', 'Cell_795', 'Cell_796', 'Cell_797', 'Cell_798', 'Cell_799', 'Cell_800', 'Cell_801', 'Cell_802', 'Cell_803', 'Cell_804', 'Cell_805', 'Cell_806', 'Cell_807', 'Cell_808', 'Cell_809', 'Cell_810', 'Cell_811', 'Cell_812', 'Cell_813', 'Cell_814', 'Cell_815', 'Cell_816', 'Cell_817', 'Cell_818', 'Cell_819', 'Cell_820', 'Cell_821', 'Cell_822', 'Cell_823', 'Cell_824', 'Cell_825', 'Cell_826', 'Cell_827', 'Cell_828', 'Cell_829', 'Cell_830', 'Cell_831', 'Cell_832', 'Cell_833', 'Cell_834', 'Cell_835', 'Cell_836', 'Cell_837', 'Cell_838', 'Cell_839', 'Cell_840', 'Cell_841', 'Cell_842', 'Cell_843', 'Cell_844', 'Cell_845', 'Cell_846', 'Cell_847', 'Cell_848', 'Cell_849', 'Cell_850', 'Cell_851', 'Cell_852', 'Cell_853', 'Cell_854', 'Cell_855', 'Cell_856', 'Cell_857', 'Cell_858', 'Cell_859', 'Cell_860', 'Cell_861', 'Cell_862', 'Cell_863', 'Cell_864', 'Cell_865', 'Cell_866', 'Cell_867', 'Cell_868', 'Cell_869', 'Cell_870', 'Cell_871', 'Cell_872', 'Cell_873', 'Cell_874', 'Cell_875', 'Cell_876', 'Cell_877', 'Cell_878', 'Cell_879', 'Cell_880', 'Cell_881', 'Cell_882', 'Cell_883', 'Cell_884', 'Cell_885', 'Cell_886', 'Cell_887', 'Cell_888', 'Cell_889', 'Cell_890', 'Cell_891', 'Cell_892', 'Cell_893', 'Cell_894', 'Cell_895', 'Cell_896', 'Cell_897', 'Cell_898', 'Cell_899', 'Cell_900', 'Cell_901', 'Cell_902', 'Cell_903', 'Cell_904', 'Cell_905', 'Cell_906', 'Cell_907', 'Cell_908', 'Cell_909', 'Cell_910', 'Cell_911', 'Cell_912', 'Cell_913', 'Cell_914', 'Cell_915', 'Cell_916', 'Cell_917', 'Cell_918', 'Cell_919', 'Cell_920', 'Cell_921', 'Cell_922', 'Cell_923', 'Cell_924', 'Cell_925', 'Cell_926', 'Cell_927', 'Cell_928', 'Cell_929', 'Cell_930', 'Cell_931', 'Cell_932', 'Cell_933', 'Cell_934', 'Cell_935', 'Cell_936', 'Cell_937', 'Cell_938', 'Cell_939', 'Cell_940', 'Cell_941', 'Cell_942', 'Cell_943', 'Cell_944', 'Cell_945', 'Cell_946', 'Cell_947', 'Cell_948', 'Cell_949', 'Cell_950', 'Cell_951', 'Cell_952', 'Cell_953', 'Cell_954', 'Cell_955', 'Cell_956', 'Cell_957', 'Cell_958', 'Cell_959', 'Cell_960', 'Cell_961', 'Cell_962', 'Cell_963', 'Cell_964', 'Cell_965', 'Cell_966', 'Cell_967', 'Cell_968', 'Cell_969', 'Cell_970', 'Cell_971', 'Cell_972', 'Cell_973', 'Cell_974', 'Cell_975', 'Cell_976', 'Cell_977', 'Cell_978', 'Cell_979', 'Cell_980', 'Cell_981', 'Cell_982', 'Cell_983', 'Cell_984', 'Cell_985', 'Cell_986', 'Cell_987', 'Cell_988', 'Cell_989', 'Cell_990', 'Cell_991', 'Cell_992', 'Cell_993', 'Cell_994', 'Cell_995', 'Cell_996', 'Cell_997', 'Cell_998', 'Cell_999', 'Cell_1000', 'Cell_1001', 'Cell_1002', 'Cell_1003', 'Cell_1004', 'Cell_1005', 'Cell_1006', 'Cell_1007', 'Cell_1008', 'Cell_1009', 'Cell_1010', 'Cell_1011', 'Cell_1012', 'Cell_1013', 'Cell_1014', 'Cell_1015', 'Cell_1016', 'Cell_1017', 'Cell_1018', 'Cell_1019', 'Cell_1020', 'Cell_1021', 'Cell_1022', 'Cell_1023', 'Cell_1024', 'Cell_1025', 'Cell_1026', 'Cell_1027', 'Cell_1028', 'Cell_1029', 'Cell_1030', 'Cell_1031', 'Cell_1032', 'Cell_1033', 'Cell_1034', 'Cell_1035', 'Cell_1036', 'Cell_1037', 'Cell_1038', 'Cell_1039', 'Cell_1040', 'Cell_1041', 'Cell_1042', 'Cell_1043', 'Cell_1044', 'Cell_1045', 'Cell_1046', 'Cell_1047', 'Cell_1048', 'Cell_1049', 'Cell_1050', 'Cell_1051', 'Cell_1052', 'Cell_1053', 'Cell_1054', 'Cell_1055', 'Cell_1056', 'Cell_1057', 'Cell_1058', 'Cell_1059', 'Cell_1060', 'Cell_1061', 'Cell_1062', 'Cell_1063', 'Cell_1064', 'Cell_1065', 'Cell_1066', 'Cell_1067', 'Cell_1068', 'Cell_1069', 'Cell_1070', 'Cell_1071', 'Cell_1072', 'Cell_1073', 'Cell_1074', 'Cell_1075', 'Cell_1076', 'Cell_1077', 'Cell_1078', 'Cell_1079', 'Cell_1080', 'Cell_1081', 'Cell_1082', 'Cell_1083', 'Cell_1084', 'Cell_1085', 'Cell_1086', 'Cell_1087', 'Cell_1088', 'Cell_1089', 'Cell_1090', 'Cell_1091', 'Cell_1092', 'Cell_1093', 'Cell_1094', 'Cell_1095', 'Cell_1096', 'Cell_1097', 'Cell_1098', 'Cell_1099', 'Cell_1100', 'Cell_1101', 'Cell_1102', 'Cell_1103', 'Cell_1104', 'Cell_1105', 'Cell_1106', 'Cell_1107', 'Cell_1108', 'Cell_1109', 'Cell_1110', 'Cell_1111', 'Cell_1112', 'Cell_1113', 'Cell_1114', 'Cell_1115', 'Cell_1116', 'Cell_1117', 'Cell_1118', 'Cell_1119', 'Cell_1120', 'Cell_1121', 'Cell_1122', 'Cell_1123', 'Cell_1124', 'Cell_1125', 'Cell_1126', 'Cell_1127', 'Cell_1128', 'Cell_1129', 'Cell_1130', 'Cell_1131', 'Cell_1132', 'Cell_1133', 'Cell_1134', 'Cell_1135', 'Cell_1136', 'Cell_1137', 'Cell_1138', 'Cell_1139', 'Cell_1140', 'Cell_1141', 'Cell_1142', 'Cell_1143', 'Cell_1144', 'Cell_1145', 'Cell_1146', 'Cell_1147', 'Cell_1148', 'Cell_1149', 'Cell_1150', 'Cell_1151', 'Cell_1152', 'Cell_1153', 'Cell_1154', 'Cell_1155', 'Cell_1156', 'Cell_1157', 'Cell_1158', 'Cell_1159', 'Cell_1160', 'Cell_1161', 'Cell_1162', 'Cell_1163', 'Cell_1164', 'Cell_1165', 'Cell_1166', 'Cell_1167', 'Cell_1168', 'Cell_1169', 'Cell_1170', 'Cell_1171', 'Cell_1172', 'Cell_1173', 'Cell_1174', 'Cell_1175', 'Cell_1176', 'Cell_1177', 'Cell_1178', 'Cell_1179', 'Cell_1180', 'Cell_1181', 'Cell_1182', 'Cell_1183', 'Cell_1184', 'Cell_1185', 'Cell_1186', 'Cell_1187', 'Cell_1188', 'Cell_1189', 'Cell_1190', 'Cell_1191', 'Cell_1192', 'Cell_1193', 'Cell_1194', 'Cell_1195', 'Cell_1196', 'Cell_1197', 'Cell_1198', 'Cell_1199', 'Cell_1200', 'Cell_1201', 'Cell_1202', 'Cell_1203', 'Cell_1204', 'Cell_1205', 'Cell_1206', 'Cell_1207', 'Cell_1208', 'Cell_1209', 'Cell_1210', 'Cell_1211', 'Cell_1212', 'Cell_1213', 'Cell_1214', 'Cell_1215', 'Cell_1216', 'Cell_1217', 'Cell_1218', 'Cell_1219', 'Cell_1220', 'Cell_1221', 'Cell_1222', 'Cell_1223', 'Cell_1224', 'Cell_1225', 'Cell_1226', 'Cell_1227', 'Cell_1228', 'Cell_1229', 'Cell_1230', 'Cell_1231', 'Cell_1232', 'Cell_1233', 'Cell_1234', 'Cell_1235', 'Cell_1236', 'Cell_1237', 'Cell_1238', 'Cell_1239', 'Cell_1240', 'Cell_1241', 'Cell_1242', 'Cell_1243', 'Cell_1244', 'Cell_1245', 'Cell_1246', 'Cell_1247', 'Cell_1248', 'Cell_1249', 'Cell_1250', 'Cell_1251', 'Cell_1252', 'Cell_1253', 'Cell_1254', 'Cell_1255', 'Cell_1256', 'Cell_1257', 'Cell_1258', 'Cell_1259', 'Cell_1260', 'Cell_1261', 'Cell_1262', 'Cell_1263', 'Cell_1264', 'Cell_1265', 'Cell_1266', 'Cell_1267', 'Cell_1268', 'Cell_1269', 'Cell_1270', 'Cell_1271', 'Cell_1272', 'Cell_1273', 'Cell_1274', 'Cell_1275', 'Cell_1276', 'Cell_1277', 'Cell_1278', 'Cell_1279', 'Cell_1280', 'Cell_1281', 'Cell_1282', 'Cell_1283', 'Cell_1284', 'Cell_1285', 'Cell_1286', 'Cell_1287', 'Cell_1288', 'Cell_1289', 'Cell_1290', 'Cell_1291', 'Cell_1292', 'Cell_1293', 'Cell_1294', 'Cell_1295', 'Cell_1296', 'Cell_1297', 'Cell_1298', 'Cell_1299', 'Cell_1300', 'Cell_1301', 'Cell_1302', 'Cell_1303', 'Cell_1304', 'Cell_1305', 'Cell_1306', 'Cell_1307', 'Cell_1308', 'Cell_1309', 'Cell_1310', 'Cell_1311', 'Cell_1312', 'Cell_1313', 'Cell_1314', 'Cell_1315', 'Cell_1316', 'Cell_1317', 'Cell_1318', 'Cell_1319', 'Cell_1320', 'Cell_1321', 'Cell_1322', 'Cell_1323', 'Cell_1324', 'Cell_1325', 'Cell_1326', 'Cell_1327', 'Cell_1328', 'Cell_1329', 'Cell_1330', 'Cell_1331', 'Cell_1332', 'Cell_1333', 'Cell_1334', 'Cell_1335', 'Cell_1336', 'Cell_1337', 'Cell_1338', 'Cell_1339', 'Cell_1340', 'Cell_1341', 'Cell_1342', 'Cell_1343', 'Cell_1344', 'Cell_1345', 'Cell_1346', 'Cell_1347', 'Cell_1348', 'Cell_1349', 'Cell_1350', 'Cell_1351', 'Cell_1352', 'Cell_1353', 'Cell_1354', 'Cell_1355', 'Cell_1356', 'Cell_1357', 'Cell_1358', 'Cell_1359', 'Cell_1360', 'Cell_1361', 'Cell_1362', 'Cell_1363', 'Cell_1364', 'Cell_1365', 'Cell_1366', 'Cell_1367', 'Cell_1368', 'Cell_1369', 'Cell_1370', 'Cell_1371', 'Cell_1372', 'Cell_1373', 'Cell_1374', 'Cell_1375', 'Cell_1376', 'Cell_1377', 'Cell_1378', 'Cell_1379', 'Cell_1380', 'Cell_1381', 'Cell_1382', 'Cell_1383', 'Cell_1384', 'Cell_1385', 'Cell_1386', 'Cell_1387', 'Cell_1388', 'Cell_1389', 'Cell_1390', 'Cell_1391', 'Cell_1392', 'Cell_1393', 'Cell_1394', 'Cell_1395', 'Cell_1396', 'Cell_1397', 'Cell_1398', 'Cell_1399', 'Cell_1400', 'Cell_1401', 'Cell_1402', 'Cell_1403', 'Cell_1404', 'Cell_1405', 'Cell_1406', 'Cell_1407', 'Cell_1408', 'Cell_1409', 'Cell_1410', 'Cell_1411', 'Cell_1412', 'Cell_1413', 'Cell_1414', 'Cell_1415').


title: Lung Influenza rep 9

status: Public on Apr 30 2025

type: SRA

city: Groningen

first: Barbro

middle: N

last: Melgert

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

description: Library name: 104532-001-066

library_source: transcriptomic

data_processing:
Preprocessing of the raw data was performed by GenomeScan and included FastQC, trimming of the adaptors using Cutadapt v.2.10
Assembly: mapping to GRCm38.p6 murine genome and H3N2 viral genome using STAR v2.5.4
Supplementary files format and content: CVS file includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
Total RNA was extracted from lung tissue using a Maxwell® 16 LEV simplyRNA Tissue Kit (Promega, catalog #AS1280, The Netherlands) following the manufacturer’s protocol.
rRNA reduction and first strand synthesis was performed, after which cDNA was prepared for Illumina short read sequencing, using 4 lanes 150bp paired-end.

tag: tissue

value: Lung

tag: cell type

value: Mixed cells from whole lung

tag: genotype

value: Wildtype C57Bl6

tag: Sex

value: female

tag: treatment

value: Influenza

tag: batch


title: T8P7_P3_d11_NORM_4_S36 [Sample 33]

city: Clayton

first: Nitika

last: Kandhari

state: VIC

address: Wellington Road

country: Australia

institute: Monash University

description: Triple hypoxic experiment: Day 11_Passage 3_Normoxic control _replicate 1

data_processing:
samples 1-23 were processed as follows: Raw fastq files have been analysed with nfcore/RNAseq pipeline version 3.10 using STAR aligner option (Dobin et al., 2013), with -umi flag, mapping raw reads to  Ensembl/GRCh38.release-109 reference genome, reads were quantified with salmon.
samples 24-71 were processed as follows: Raw fastq files were aligned using STAR aligner option (Dobin et al., 2013) mapping raw reads to Ensembl/GRCh38 v106. The BAM files were sorted and indexed using “samtools” software v.1.15.1.  “umi_tools” software v.1.1.2  was sued to remove duplicated reads based on Unique Molecular Identifiers (UMIs). Count data was generated using “featureCounts” tool v.2.0.1 on sorted deduplicated BAM files (7). The resulting count data were imported into R programming language to assemble the gene expression matrix. “biomaRt” R package v.2.46.3 was used to map Ensembl gene Ids to gene symbols.
For all analysis - raw counts were then analysed with Degust (Powell 2015) web tool to do differential expression analysis to produce list of differentially expressed genes and several quality plots including classical multidimensional scaling (MDS) and MA plots
In this analysis limma voom (Law et al. 2014) was used for differential expression analysis. Degust (Powell 2015) largely follows limma voom workflow with typical counts per million (CPM) library size normalisation and trimmed mean of M values (TMM) normalisation (Robinson and Oshlack 2010) for RNA composition normalisation.
Assembly: GRCh38 release 109 (samples 1-23) GRCh38 release 106 (samples 24-71)
Supplementary files format and content: raw gene counts, text file, tab separated, includes all samples

organism: Homo sapiens

source_name: 522.3 iPSCs – female (16 year old)

extract_protocol:
RNA Extraction (ISOLATE II RNA Mini Kit 50): BIO-52072. Following manufacturer's instruction
RNA libraries for RNA-seq were prepared at Monash Health Translational Precinct (MHTP), Medical Genomics Facility using Novel RNA-Seq pipeline (Version 01/09/2021). Briefly index is added during initial pA priming and pooled samples amplified using template switching oligo.

value: Adult kidney organoid

tag: gender

value: Tubuloids derived from d20 kidney organoids

value: Derived from GM04522 fibroblasts (Coriell Inst)

value: Day 11_Passage 3_Normoxic control


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_144

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

library_source: transcriptomic single cell

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

molecule: polyA RNA

extract_protocol:
Neuronal cultures were treated for 1 hour with 5 µM Y-27632 before dissociation with trypsin or accutase. The cells were resuspended in FACS buffer (HBSS with magnesium and calcium, 2% w/v bovine serum albumine, 2% v/v knockout serum replacement, 2% v/v B-27 supplement, 25 mM D-glucose, 5 µM Y-27632). Single live cells were isolated by fluorescence activated cell sorting (FACS) using Topro-3 iodide and were directly lysed in ice-cold single-cell lysis buffer (0.2% w/v Triton X-100, 0.5% v/v recombinant RNase inhibitor, 10 µM Smarter_oligo-dTVN, 25 mM dNTP, 100 mM DL-dithiothreitol, 4e-5 diluted ERCC spike-in RNAs, in ultrapure water). Protocol according to Schweingruber C, et al. 2023. Methods Mol Biol (PMID: 36264494).
Individual single cell libraries were prepared using the Smart-Seq2 protocol followed by tagmentation using components form the Nextera XT DNA library preparation kit (Illumina). Protocols with adaptations according to Schweingruber C, et al. 2023. Methods Mol Biol (PMID: 36264494).

treatment_protocol:
Heterogenous protocol: Differentiation of adherent cells for two days in medium 1 (200 nM LDN193189, 10 µM SB431542, 25 ng/mL SHH-C25II, 250 nM Purmorphamine, 1 µM retinoic acid), followed by seven days medium 2 (medium 1 with 3 µM CHIR99021), one day of medium d3 (Medium 2 with 200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT-3, and CNTF), and three days of medium 4 (3 µM CHIR99021, 25 ng/mL SHH-C25II, 250 nM Purmorphamine, 1 µM retinoic acid, with 200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT-3, and CNTF). From day 14 onwards, culture was kept in medium 5 (200 µM ascorbic acid, 125 µM db-cAMP, 2.5 µM DAPT, 10 ng/mL each of BDNF, GDNF, NT3, and CNTF).
Homogenous protocol according to Nijssen J, et al. 2019. Bioprotocol (PMID: 33654821). The neurons were cultured until day 28.

tag: cell line

value: spinal neuron differentiation

value: heterogenous protocol

tag: sequencing batch


title: Lung Influenza rep 3

description: Library name: 104532-001-011


title: Healthy4_PBMC_BCR

city: Bethesda

first: Shouguo

last: Gao

state: MD

address: 9000 Rockville Pike

department: NHLBI

country: USA

institute: National Institutes of Health

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Paired-end reads were mapped to the hg38 genome with cellranger for gene-level read counts
Sample demultiplexing, barcode processing, alignment, filtering, UMI counting,and csv files of TCR clonality were performed using the cellranger analysis pipeline.
Data normalization, dimension reduction, and differential expression analysis were performed using R and the Seurat R package.
T cell receptor and B cell receptor VDJ analysis: Cellranger
VDJ of T cells and B cells were infered with cellranger vdj pipeline to get TCR and BCR contig annotations.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Human peripheral blood

extract_protocol: Libraries of gene expression (PBMCs) and TCR/BCR sequencing for patients and healthy donors were generated using Genomics Chromium Single Cell 5' Solution Kit from 10XGenomics v2 (Dual index).

tag: disease state

value: Healthy

value: Human peripheral blood

value: PBMCs

value: Male

tag: age

tag: response at primary end point

tag: library type

value: VDJ (BCR)


title: T8P7_P3_d11_NORM_3_S35 [Sample 34]

description: Triple hypoxic experiment: Day 11_Passage 3_Normoxic control _replicate 2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_139


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_143


title: T8P7_P3_d6_HYPx1_1_S37 [Sample 32]

description: Triple hypoxic experiment: Day 6_Passage 3_Tubuloid injured 1 time with hypoxia _replicate 3


title: Lung Influenza rep 2

description: Library name: 104532-001-010


title: Healthy3_PBMC_BCR

description: 10x Genomics


title: T8P7_P3_d11_HYPx3_3_S48 [Sample 36]

description: Triple hypoxic experiment: Day 11_Passage 3_Tubuloid injured 3 times with hypoxia _replicate 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_138


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_137


title: Lung Influenza rep 7

description: Library name: 104532-001-015


title: Lung Influenza rep 1

description: Library name: 104532-001-009


title: Lung Influenza rep 6

description: Library name: 104532-001-014


title: T8P7_P3_d6_HYPx1_2_S38 [Sample 31]

description: Triple hypoxic experiment: Day 6_Passage 3_Tubuloid injured 1 time with hypoxia _replicate 2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_136


title: Healthy1_PBMC_BCR

description: 10x Genomics


title: Lung Saline rep 9

description: Library name: 104532-001-065

value: Saline


title: T8P7_P3_d6_HYPx1_3_S39 [Sample 30]

description: Triple hypoxic experiment: Day 6_Passage 3_Tubuloid injured 1 time with hypoxia _replicate 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_135


title: VEXAS17_PBMC2_GEX

description: 10x Genomics

value: VEXAS

value: GEX


title: Lung Saline rep 8

description: Library name: 104532-001-008

value: Lung

value: Mixed cells from whole lung

value: Wildtype C57Bl6


title: VEXAS17_PBMC1_GEX

description: 10x Genomics


title: T8P7_P3_d6_HYPx3_2_S44 [Sample 28]

description: Triple hypoxic experiment: Day 6_Passage 3_Tubuloid injured 3 times with hypoxia _replicate 2

value: Adult kidney organoid

value: female


title: Lung Saline rep 7

description: Library name: 104532-001-007


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_134


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_133


title: VEXAS16_PBMC1_GEX

description: 10x Genomics


title: VEXAS16_PBMC2_GEX

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_132


title: Lung Saline rep 5

description: Library name: 104532-001-005


title: Lung Saline rep 6

description: Library name: 104532-001-006


title: T8P7_P3_d6_HYPx3_3_S45 [Sample 27]

description: Triple hypoxic experiment: Day 6_Passage 3_Tubuloid injured 3 times with hypoxia _replicate 1

value: Tubuloids derived from d20 kidney organoids

value: Derived from GM04522 fibroblasts (Coriell Inst)


title: Healthy2_PBMC_BCR

description: 10x Genomics


title: T8P7_P3_d6_NORM_3_S32 [Sample 25]

description: Triple hypoxic experiment: Day 6_Passage 3_Normoxic control _replicate 2

value: Day 6_Passage 3_Normoxic control


title: Lung Saline rep 4

description: Library name: 104532-001-004


title: VEXAS15_PBMC2_GEX

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_130

value: spinal neuron differentiation

value: heterogenous protocol


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_131


title: T8P7_P3_d6_NORM_4_S33 [Sample 24]

description: Triple hypoxic experiment: Day 6_Passage 3_Normoxic control _replicate 1


title: Lung Saline rep 2

description: Library name: 104532-001-002


title: T8P7_P3_d6_NORM_2_S31 [Sample 26]

description: Triple hypoxic experiment: Day 6_Passage 3_Normoxic control _replicate 3


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_129


title: VEXAS14_PBMC2_GEX

description: 10x Genomics

value: Human peripheral blood


title: VEXAS14_PBMC1_GEX

description: 10x Genomics

value: PBMCs


title: T8P7_P3_d6_HYPx3_1_S43 [Sample 29]

description: Triple hypoxic experiment: Day 6_Passage 3_Tubuloid injured 3 times with hypoxia _replicate 3


title: Adult tubuloid donor 3_P2_1_S43 [Sample 23]

description: Adult tubuloid_line 3_passage 2

source_name: Nephrectomy - male

value: male

value: Adult tubuloids derived from nephrectomies

value: Nephrectomy - male

value: Adult tubuloid_line 3_passage 2


title: Lung Saline rep 1

description: Library name: 104532-001-001

value: Saline


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_128


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_127


title: VEXAS13_PBMC1_GEX

description: 10x Genomics

value: VEXAS

value: Male

value: GEX


title: FLOX

city: WuHan

first: ZHUO

last: WENFENG

address: 湖北省武汉市硚口区航空路13号

country: China

institute: The Huazhong University of Science and Technology

description: Library name: Sample 1

data_processing:
The raw sequencing data was precessed by Fastp firstly (Chen, Zhou et al. 2018) to trim primer sequence and low quality bases. And then we used SeekOne®Tools to precess sequence data and aligned to human GRCh38 in order to obtain gene expression matrix. We used Seurat (version 4.0.0) to filter low quality cells, cells with number of detected genes <200 or >5000 were omitted, and use MAD variance normal (Pijuan et al., 2019) to remove cells affected by mitochondrial genes. And the remaining cells were used for the following analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: tumor

extract_protocol:
After tumor harvested, tissues were washed in ice-cold RPMI1640 and dissociated using Multi-tissue dissociation kit 2 (Miltenyi) from Miltenyi Biotec as instructions. Cell count and viability was estimated using fluorescence Cell Analyzer (Countstar® Rigel S2) with AO/PI reagent after removal erythrocytes (Miltenyi 130-094-183) and then debris and dead cells removal was decided to be performed or not (Miltenyi 130-109-398/130-090-101). Finally, fresh cells were washed twice in the RPMI1640 and then resuspended at 1×106 cells per ml in 1×PBS and 0.04% bovine serum albuminat.
Single-cell RNA-Seq libraries were prepared using SeekOne® MM Single Cell 3’ library preparation kit (SeekGene Catalog No.). Briefly, appropriate number of cells were loaded into the flow channel of SeekOne® MM chip which had 170,000 microwells and allowed to settle in microwells by gravity. After removing the unsettled cells, sufficient Cell Barcoded Magnetic Beads (CBBs) were pipetted into flow channel and also allowed to settle in microwells with the help of a magnetic field. Next excess CBBs were rinsed out and cells in MM chip were lysed to release RNA which was captured by the CBB in the same microwell. Then all CBBs were collected and reverse transcription were performed at 37℃for 30 minutes to lable cDNA with cell barcode on the beads. Further Exonuclease I treatment were performed to remove unused primer on CBBs. Subsequently, barcoded cDNA on the CBBs was hybridized with random primer which had reads 2 SeqPrimer sequence on the 5’ end and could extend to form the second strand DNA with cell barcode on the 3’ end. The resulting second strand DNA were denatured off the CBBs, purified and amplified in PCR reaction. The amplified cDNA product was then cleaned to remove unwanted fragment and added to full length sequencing adapter and sample index by indexed PCR. The indexed sequencing libraries were cleanup with SPRI beads, quantified by quantitative PCR (KAPA Biosystems KK4824) and then sequenced on illumina NovaSeq 6000 with PE150 read length or DNBSEQ-T7 platform with PE100 read length.

value: tumor

value: FLOX


title: Adult tubuloid donor 1_P1_2_S41 [Sample 20]

description: Adult tubuloid_line 1_passage 1_technical replicate 2

source_name: Nephrectomy - female

value: Adult kidney organoid

value: female

value: Nephrectomy - female

value: Adult tubuloid_line 1_passage 1


title: VEXAS12_PBMC2_GEX

description: 10x Genomics


title: Lung Saline rep 3

description: Library name: 104532-001-003

value: Lung

value: Mixed cells from whole lung

value: Wildtype C57Bl6


title: Adult tubuloid donor 1_P1_3_S42 [Sample 21]

description: Adult tubuloid_line 1_passage 1_technical replicate 3


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_125

value: spinal neuron differentiation

value: heterogenous protocol


title: VEXAS12_PBMC1_GEX

description: 10x Genomics

value: Human peripheral blood

value: PBMCs


title: VEXAS15_PBMC1_GEX

description: 10x Genomics


title: VEXAS11_PBMC1_GEX

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_123


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_124


title: T7P5_d11_NORM_1_S19 [Sample 16]

description: iTubuloid_line 3_Passage 5 day 11_ technical replicate 1

value: Tubuloids derived from d20 kidney organoids

value: Derived from GM04522 fibroblasts (Coriell Inst)

value: iTubuloid_line 3_Passage 5 day 11


title: VEXAS11_PBMC2_GEX

description: 10x Genomics

value: VEXAS

value: Male

value: GEX


title: T7P5_d11_NORM_3_S21 [Sample 18]

value: Adult kidney organoid


title: T7P5_d6_NORM_3_S3 [Sample 15]

description: iTubuloid_line 3_Passage 5 day 6_ technical replicate 3

value: female

value: iTubuloid_line 3_Passage 5 day 6


title: VEXAS10_PBMC1_GEX

description: 10x Genomics


title: VEXAS10_PBMC2_GEX

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_120

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', 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'Cell_1374', 'Cell_1375', 'Cell_1376', 'Cell_1377', 'Cell_1378', 'Cell_1379', 'Cell_1380', 'Cell_1381', 'Cell_1382', 'Cell_1383', 'Cell_1384', 'Cell_1385', 'Cell_1386', 'Cell_1387', 'Cell_1388', 'Cell_1389', 'Cell_1390', 'Cell_1391', 'Cell_1392', 'Cell_1393', 'Cell_1394', 'Cell_1395', 'Cell_1396', 'Cell_1397', 'Cell_1398', 'Cell_1399', 'Cell_1400', 'Cell_1401', 'Cell_1402', 'Cell_1403', 'Cell_1404', 'Cell_1405', 'Cell_1406', 'Cell_1407', 'Cell_1408', 'Cell_1409', 'Cell_1410', 'Cell_1411', 'Cell_1412', 'Cell_1413', 'Cell_1414', 'Cell_1415').


title: T7P5_d6_NORM_2_S2 [Sample 14]

description: iTubuloid_line 3_Passage 5 day 6_ technical replicate 2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_122


title: VEXAS9_PBMC_GEX

description: 10x Genomics


title: VEXAS13_PBMC2_GEX

description: 10x Genomics


title: MCT1-KO

address: 湖北省武汉市硚口区航空路13号

description: Library name: Sample 2

value: tumor


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_126


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_119


title: Adult tubuloid donor 1_P1_1_S40 [Sample 19]

description: Adult tubuloid_line 1_passage 1_technical replicate 1

value: Adult tubuloids derived from nephrectomies

value: Nephrectomy - female

value: Adult tubuloid_line 1_passage 1


title: T7P5_d6_NORM_1_S1 [Sample 13]

description: iTubuloid_line 3_Passage 5 day 6_ technical replicate 1


title: Healthy4_PBMC_GEX

description: 10x Genomics

value: Healthy


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_118

value: spinal neuron differentiation

value: heterogenous protocol


title: T6P5_d11_NORM_2_S26 [Sample 11]

description: iTubuloid_line 2_Passage 5 day 11_ technical replicate 1

source_name: D4C4 iPSC -female

value: 32-year-old female derived from human gingival tissue

value: iTubuloid_line 2_Passage 5 day 11


title: T7P5_d11_NORM_2_S20 [Sample 17]

value: Tubuloids derived from d20 kidney organoids

value: Derived from GM04522 fibroblasts (Coriell Inst)


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_117


title: T6P5_d11_NORM_3_S27 [Sample 12]


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_121


title: Healthy3_PBMC_GEX

description: 10x Genomics

value: Human peripheral blood

value: PBMCs


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_116


title: Healthy2_PBMC_GEX

description: 10x Genomics

value: Male

value: GEX


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_115


title: T6P5_d11_NORM_1_S25 [Sample 10]

value: Adult kidney organoid

value: female


title: Healthy1_PBMC_GEX

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_114


title: T6P5_d6_NORM_3_S9 [Sample 9]

description: iTubuloid_line 2_Passage 5 day 6_ technical replicate 3

value: iTubuloid_line 2_Passage 5 day 6


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_113


title: RBE_shJOSD2_rep3

city: Hang Zhou

first: Meijia

last: Qian

state: Zhejiang

address: No.866 Yuhangtang Road, Xihu District

department: Zhejiang University

institute: College of Pharmaceutical Sciences

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: RBE

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: RBE


title: RBE_shJOSD2_rep2


title: T5P5_d11_NORM_3_S33 [Sample 6]

description: iTubuloid_line 1_Passage 5 day 11_ technical replicate 1

source_name: 808 iPSC - male

value: male

value: Derived from GM21808 fibroblasts (Coriell Inst)

value: iTubuloid_line 1_Passage 5 day 11


title: T6P5_d6_NORM_1_S7 [Sample 7]

description: iTubuloid_line 2_Passage 5 day 6_ technical replicate 1


title: Adult tubuloid donor 2_P1_1_S44 [Sample 22]

description: Adult tubuloid_line 2_passage 1

value: Adult tubuloids derived from nephrectomies

value: Nephrectomy - male

value: Adult tubuloid_line 2_passage 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_111

value: spinal neuron differentiation

value: heterogenous protocol


title: T5P5_d11_NORM_2_S32 [Sample 5]

value: Tubuloids derived from d20 kidney organoids


title: RBE_shIDH1_rep3


title: Healthy7_PBMC_GEX

description: 10x Genomics

value: Healthy

value: Human peripheral blood


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_110


title: T5P5_d11_NORM_1_S31 [Sample 4]


title: RBE_shJOSD2_rep1


title: T5P5_d6_NORM_3_S15 [Sample 3]

description: iTubuloid_line 1_Passage 5 day 6_ technical replicate 3

value: iTubuloid_line 1_Passage 5 day 6


title: RBE_shIDH1_rep1


title: RBE_shIDH1_rep2


title: T5P5_d6_NORM_2_S14 [Sample 2]

description: iTubuloid_line 1_Passage 5 day 6_ technical replicate 2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_108


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_107


title: T6P5_d6_NORM_2_S8 [Sample 8]

description: iTubuloid_line 2_Passage 5 day 6_ technical replicate 2

value: 32-year-old female derived from human gingival tissue


title: RBE_Ctrl_rep3

value: Ctrl


title: RBE_Ctrl_rep2


title: T5P5_d6_NORM_1_S13 [Sample 1]

description: iTubuloid_line 1_Passage 5 day 6_ technical replicate 1

value: Adult kidney organoid


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_112


title: RNA-seq, AMLE400ug/ml, rep2

city: Daejeon

first: Suyoung

last: Choi

address: 266, Munhwa-ro, Jung-gu

department: Department of Medical Science

country: South Korea

institute: Chungnam National University

description:
Library name: Sample 5
Colum name in DMSO_APP_Readcount.csv: APP2
DMSO_APP_Readcount.csv

data_processing:
RNA-seq, Quality control (QC) and read count matrix generation were performed using Python (v3.8.10) and R in a Linux environment. Trim Galore (v0.6.7) was used for low-quality read filtering. Reads were aligned to the mm10 reference genome using STAR aligner (v2.7.11b). SAMtools (v1.7) was used to convert SAM files into BAM files. Gene count matrices were generated for downstream analysis. ATAC-seq data quality was assessed with FastQC, and reads were trimmed for adapters and low-quality bases using Trim Galore (v0.6.7). Clean reads were aligned to the mm10 genome with Bowtie2 (v2.4.4); only properly mapped reads (MAPQ >30) were retained. PCR duplicates were removed using Picard MarkDuplicates (v2.26.3). Peaks were called using MACS3 (v3.0.0a7) and visualized with Deeptools (v3.5.1). Differential peak analysis was conducted with csaw (v1.28.0), and peak annotation and visualization were performed using ChIPseeker (v1.30.0). Motif enrichment was analyzed with HOMER (findMotifsGenome.pl), and motifs with p < 0.01 were considered significant.
Assembly: mm10
Supplementary files format and content: RNA-seq csv files include raw read count metrix for each sample
Supplementary files format and content: ATAC-seq BigWig, bed, and narrowPeak for DMSO and AMLE treated sample

source_name: BMDCs

extract_protocol:
Total RNA was extracted using the Trizol method (Invitrogen, AM9738) from BMDCs.
For RNA-seq libraries, the manufacturer's protocol for the TruSeq Stranded mRNA Library Prep Kit was followed (Guide #1000000040498). RNA sequencing was performed on the Illumina HiSeq 2500, generating raw fastq.gz files of 1.7-2.2 G per sample, with 67-81 million reads after merging. ATAC-seq libraries were prepared using the ATAC-seq kit (AT53150, Active Motif) and the Omni-ATAC protocol (Corces et al., 2017, Nature Methods 14, 959-962. 10.1038/nmeth.4396). Briefly, nuclear suspensions obtained from 100,000 BMDC samples treated with AMLE or control vehicle were incubated with assembled Tn5 transposase for 30 min at 37°C. The tagged DNA was purified using a MinElute PCR Purification Kit, amplified using Nextera PCR primers, purified using SPRI beads and sequenced using a NovaSeq 6000 sequencer (Illumina).

value: BMDCs

value: 8-10 weeks old

tag: time

value: 24h, After treatment

value: AMLE (400ug/ml)

tag: strain

value: C57BL/6, WT


title: RNA-seq, AMLE400ug/ml, rep3

description:
Library name: Sample 6
Colum name in DMSO_APP_Readcount.csv: APP3
DMSO_APP_Readcount.csv


title: RNA-seq, AMLE400ug/ml, rep1

description:
Library name: Sample 4
Colum name in DMSO_APP_Readcount.csv: APP1
DMSO_APP_Readcount.csv


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_105


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_103


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_104


title: H_NP,  rep2

city: Changchun

first: Yinghua

last: Zhao

address: Dongminzhu street 519

institute: 1st hosptal of Jinli University

data_processing:
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp)with parameters -q 20 --length_required 30 -5 20 -3 20 -W 4 -M 20 -n 0.
Then clean reads were separately aligned to reference genome with orientation mode using hisat software.
The expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: mm9
Supplementary files format and content: tab-delimited text file includes TPM values for all Samples

growth_protocol: HEK293T cell lines were grown and maintained in DMEM, high glucose (Hyclone) containing 10% heat-inactivated FBS (BBI), 100 U/ml of ampicillin, and 100 μg/ml of streptomycin (Sangon).

extract_protocol:
Total RNA was extracted from the sample using TRIzol® Reagent according the manufacturer’s instructions (Invitrogen) and genomic DNA was removed using DNase I (TaKara). Then RNA quality was determined by 2100 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA sample (OD260/280=1.8~2.2, OD260/230≥2.0, RIN≥6.5, 28S:18S≥1.0, >10μg) was used to construct sequencing library.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: HEK293T cells were transfected with GFP-tagged HTNV Gc or NP proteins expressing plasmids using Lipofectamine 3000 according to the manufacturer's instructions. The GFP empty vector was used as a control. At 24 h post transfection, the GFP-positive cells were sorted by FACSAria III cell sorter (BD, New York, USA) for RNA sequencing (n=3) at Majorbio Bio-pharm Biotechnology Co., Ltd. (Shanghai, China) (http://www.majorbio.com/).

value: human embryonic kidney cells

value: transiently-expressing HTNV NP protein

value: transfected with HTNV NP protein plasmid for 24 h.


title: RNA-seq, DMSO0.04%, rep3

description:
Library name: Sample 3
Colum name in DMSO_APP_Readcount.csv: DMSO3
DMSO_APP_Readcount.csv


title: H_NP,  rep1


title: RNA-seq, DMSO0.04%, rep2

description:
Library name: Sample 2
Colum name in DMSO_APP_Readcount.csv: DMSO2
DMSO_APP_Readcount.csv


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_102

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', 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'Cell_906', 'Cell_907', 'Cell_908', 'Cell_909', 'Cell_910', 'Cell_911', 'Cell_912', 'Cell_913', 'Cell_914', 'Cell_915', 'Cell_916', 'Cell_917', 'Cell_918', 'Cell_919', 'Cell_920', 'Cell_921', 'Cell_922', 'Cell_923', 'Cell_924', 'Cell_925', 'Cell_926', 'Cell_927', 'Cell_928', 'Cell_929', 'Cell_930', 'Cell_931', 'Cell_932', 'Cell_933', 'Cell_934', 'Cell_935', 'Cell_936', 'Cell_937', 'Cell_938', 'Cell_939', 'Cell_940', 'Cell_941', 'Cell_942', 'Cell_943', 'Cell_944', 'Cell_945', 'Cell_946', 'Cell_947', 'Cell_948', 'Cell_949', 'Cell_950', 'Cell_951', 'Cell_952', 'Cell_953', 'Cell_954', 'Cell_955', 'Cell_956', 'Cell_957', 'Cell_958', 'Cell_959', 'Cell_960', 'Cell_961', 'Cell_962', 'Cell_963', 'Cell_964', 'Cell_965', 'Cell_966', 'Cell_967', 'Cell_968', 'Cell_969', 'Cell_970', 'Cell_971', 'Cell_972', 'Cell_973', 'Cell_974', 'Cell_975', 'Cell_976', 'Cell_977', 'Cell_978', 'Cell_979', 'Cell_980', 'Cell_981', 'Cell_982', 'Cell_983', 'Cell_984', 'Cell_985', 'Cell_986', 'Cell_987', 'Cell_988', '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


title: H_GC, rep3

value: transiently-expressing HTNV Gc protein

value: transfected with HTNV Gc protein plasmid for 24 h.


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_109

value: heterogenous protocol


title: RNA-seq, DMSO0.04%, rep1

description:
Library name: Sample 1
Colum name in DMSO_APP_Readcount.csv: DMSO1
DMSO_APP_Readcount.csv


title: H_GC, rep1


title: H_GC, rep2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_101


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_106


title: 290 NTKO fast

city: Lexington

first: Moumita

last: Banerjee

state: Kentucky

address: 760 Press Avenue

department: Markey Cancer Center

institute: University of Kentucky

description:
Library name: Sample 11
s11

data_processing:
Sequencing reads were trimmed and filtered using Trimmomatic to remove adapters and low quality bases. Trimmed reads were mapped to the mouse reference genome assembly GRCm38 transcripts annotation using RSEM.
Assembly: GRCm38
Supplementary files format and content: Gene raw count reported by RSEM

source_name: liver

growth_protocol: Four month old NTS WT and KO female mice (sex and age matched littermates) on normal chow

extract_protocol:
total RNA was extracted using Qiagen Rneasy kit.
Total 2000ng of RNA were used for cDNA synthesis and library preparation using High Capacity cDNA Reverse Transcription Kit (Thermofisher).

treatment_protocol: fed (ad libitum) or fasted for 22h

value: liver

value: female

tag: pathology

value: normal

value: NTS KO

value: fasted


title: 295 NTKO fast

description:
Library name: Sample 12
s12


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_099


title: H_NP,  rep3


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_098


title: 284 NTKO fast

description:
Library name: Sample 10
s10


title: H_GFP, rep2

value: transiently-expressing GFP

value: transfected with GFP control vcetor for 24 h.


title: RBE_Ctrl_rep1

value: RBE

value: Ctrl


title: H_GFP, rep3


title: 319 NTKO fed

description:
Library name: Sample 9
s9

value: fed


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_097


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_096


title: 303 NTKO fed

description:
Library name: Sample 8
s8


title: 277 NTKO fed

description:
Library name: Sample 7
s7


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_094


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_095


title: H_GFP, rep1

value: human embryonic kidney cells


title: huIgG treatment 3

city: omaha

first: Prakash

last: Radhakrishnan

state: NE

address: 986805 Nebraska Medical Center

department: Eppley Institute for Research in Cancer

institute: University of Nebraska Medical Center

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp
Sequence reads were trimmed for adaptor sequence/low-quality sequences. These included bases that could not be determined and low quality reads (when a Qscore of more than 50% of bases of the read is <=5).
Trimmed sequence reads were mapped to GRCh38/Hg38 using HISAT2.
Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software
Assembly: GRCh38/hg38
Supplementary files format and content: gene counts, log2FoldChange

source_name: Patient-derived Organoids

growth_protocol: PDAC tumor tissue was obtained from the Rapid Autopsy Program (RAP) at UNMC. After checking for the expression of MUC16, RAP#142 tumor tissue was minced and washed with 10ml ice cold wash medium (DMEM (high glucose) with 1% FBS and 1% pen/strep) into a centrifuge tube, allowed to settle, and then the supernatant was removed, and the step repeated 2X. The sample was digested in pre-warmed digestion solution (2.5 mg/ml Collagenase ll, 2.5 mg/ml Dispase ll, 0.1mg/ml DNase l, 10uM Y-27632, 1mg/ml Trypsin inhibitor) on a shaker at 37 degrees for 45 min. The solution was pipetted up and down with a 10 ml pipette and checked for the presence of cells. The material was centrifuged at 300g for 5 min. The wash step was repeated 2X, and the pellet was plated in Cultrex RGF-BME, Type 2 (R&D 3533-005-02) in 12 well-pre-warmed plates and incubated at 37 degrees upside down for 20 minutes. Human Pancreas medium (Ad DMEM/F12 supplemented w 1x hepes, glutamax, pen/strep, B27-vitamin A 1X, wnt CM 50%, RSPO-1 CM 10%, noggin CM 10%, N2 1X, Nicotinamide 10mM, N-acetylcysteine 1.25mM, Primocin 100ug/ml, EGF 50ng/ml, FGF-10 100ng/ml, Gastrin l 10nM, A83-01 500nM, PGE2 3uM) was added and cells grown for 1-2 weeks.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
Sequencing libraries were generated using NEBNext® Ultra TM RNA Library Prep Kit

treatment_protocol: After reaching 60-70% confluency, the organoid was treated with 40 µg/mL huAR9.6 and isotype control huIgG for 24 hr.

value: Patient-derived Organoids

value: Pancreatic Cancer

value: MUC16 expressing

value: Isotype control antibody


title: huIgG treatment 2


title: 322 NTWT fast

description:
Library name: Sample 6
s6

value: NTS WT


title: huIgG treatment 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_093

value: spinal neuron differentiation

value: heterogenous protocol


title: 282 NTWT fast

description:
Library name: Sample 5
s5

value: liver

value: female


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_100


title: huAR9.6 treatment 3

value: anti-MUC16 antibody


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_092

value: Control


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_091


title: 265 NTWT fast

description:
Library name: Sample 4
s4

value: normal

value: fasted


title: 323 NTWT fed

description:
Library name: Sample 3
s3


title: huAR9.6 treatment 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_090


title: huAR9.6 treatment 2


title: 257 NTWT fed

description:
Library name: Sample 2
s2


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_967

data_processing:
Samples were sequenced on NovaSeq6000 (NovaSeq Control Software 1.7.0/RTA v3.4.4) with a 51nt(Read1)-8nt(Index1)-8nt(Index2)-51nt(Read2) setup using 'NovaSeqXp' workflow in 'S1' mode flowcell. The Bcl to FastQ conversion was performed using bcl2fastq_v2.20.0.422 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina 1.8+.
Demultiplexing and quality control was performed at NGI Sweden (Stockholm node) as described for each fastq file. Each fastq file corresponds to a single cell.
Reads were mapped to the human reference genome hg38 using STAR version 2.7.0e (with parameter “-outSAMstrandField=intronMotif”) (Dobin A, et al. 2013. Bioinformatics, PMID: 23104886).
Aligned reads were assigned to genomic locations with the ‘rpkmforgenes.py’ script (Ramsköld  D, et al. 2009. PLoS Comput Biol, PMID: 20011106), using an annotation GTF file from Ensembl version 95 (GRCh38.95) (with parameters “-fulltranscript” and “-rmnameoverlap”).
Cells with less than 100,000 uniquely mapped reads and/or less than 5,000 detected genes were excluded.
Assembly: hg38
Supplementary files format and content: A counts table for all single cells named 'counts.txt'.
Supplementary files format and content: A data table with normalized abundance in reads per kilobase million (rpkm) for all single cells called 'rpkms.txt'.

value: homogenous protocol


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_089


title: 254 NTWT fed

description:
Library name: Sample 1
s1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_966


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_965


title: RAW264.7, IL-4+ISO+ICI

city: Shijiazhuang

first: Shuxian

last: Yin

state: Hebei province

address: zhongshan road

institute: Hebei Medical University

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

growth_protocol: RAW264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

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

treatment_protocol: RAW264.7  cells were induced by treatment of IL-4 (20 ng/mL), ISO (250 μM）, and ICI118,551(10 μM).

value: macrophage

value: WT


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_087


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_088


title: RAW264.7, IL-4


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_086


title: RAW264.7, IL-4+ISO


title: Neuro-2a cells, shArf1-2-3

city: 上海

first: Xv

last: Li

address: 复旦大学

institute: fudan university

data_processing:
Firstly, the raw downstream data (Raw Data) is filtered, and the high quality sequence (Clean Data) obtained after filtering is compared to the reference genome of the species. Based on the comparison results, the expression amount of each gene is calculated. On this basis, the samples were further subjected to expression difference analysis, enrichment analysis and cluster analysis. The Reads on the comparison were spliced and the transcript sequences were reduced.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes read counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: brain

extract_protocol:
RNA was hanvested using Trizol. Total RNA was used for the construction of sequencing libraries.
In this project, mRNA with polyA structure in total RNA was enriched by Oligo(dT) magnetic beads, and ion interruption was used to break the RNA into fragments of about 300bp in length. The length of 300bp was chosen because the length of the junction is fixed, if the length of the interrupted fragment is shorter, it will lead to a high proportion of the junction sequence, which will reduce the proportion of valid data; if the length of the interrupted fragment is longer, it is not conducive to the generation of clusters in the process of on-line sequencing. The first strand of cDNA was synthesised using RNA as a template with 6-base random primers and reverse transcriptase, and the first strand cDNA was used as a template for the second strand cDNA synthesis.

value: brain

value: neuroblast

value: Arf1 knockdown

value: no


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_964


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_963


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_962


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_083


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_960


title: Neuro-2a cells, shArf1-2-1


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_961


title: Neuro-2a cells, shArf1-2-2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_082


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_959


title: Neuro-2a cells, shArf1-1-3


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_081


title: Neuro-2a cells, shArf1-1-2


title: Neuro-2a cells, shArf1-1-1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_080


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_079


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_958


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_957


title: Neuro-2a cells, shlucif-3

value: luciferase knockdown


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_085


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_956


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_078


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_955


title: Neuro-2a cells, shlucif-1


title: Neuro-2a cells, shlucif-2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_077


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_954


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_076


title: PT id10 normal tissue

city: Tsukiji

first: Rei

last: Noguchi

state: Tokyo

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

department: Division of Rare Cancer Research

country: Japan

institute: National Cancer Center Research Institute

description:
CRC15019N
Ion AmpliSeq Transcriptome

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

source_name: normal colon

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

value: normal colon


title: Diff_D4_Protocol_P2_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_953

value: spinal neuron differentiation