title: Leuka ER-1293,SR8278 10 uM

description:
SR21
RNA-Seq (rRNA-depleted stranded (HMR))

value: Leuka ER-1293


title: W_DMSO_A

status: Public on Apr 30 2025

type: SRA

city: Jackson

first: Lavanya

last: Challagundla

state: MS

address: 2500 North State Street

department: Cell and Molecular Biology

country: USA

institute: University of Mississippi Medical Center

library_source: transcriptomic

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

molecule: total RNA

organism: Homo sapiens

source_name: W

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

tag: tissue

value: W

tag: treatment


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_195

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

description: The rows in 'counts.txt' and 'rpkms.txt' are genes and the columns are the cell ids ('Cell_001', 'Cell_002', 'Cell_003', 'Cell_004', 'Cell_005', 'Cell_006', 'Cell_007', 'Cell_008', 'Cell_009', 'Cell_010', 'Cell_011', 'Cell_012', 'Cell_013', 'Cell_014', 'Cell_015', 'Cell_016', 'Cell_017', 'Cell_018', 'Cell_019', 'Cell_020', 'Cell_021', 'Cell_022', 'Cell_023', 'Cell_024', 'Cell_025', 'Cell_026', 'Cell_027', 'Cell_028', 'Cell_029', 'Cell_030', 'Cell_031', 'Cell_032', 'Cell_033', 'Cell_034', 'Cell_035', 'Cell_036', 'Cell_037', 'Cell_038', 'Cell_039', 'Cell_040', 'Cell_041', 'Cell_042', 'Cell_043', 'Cell_044', 'Cell_045', 'Cell_046', 'Cell_047', 'Cell_048', 'Cell_049', 'Cell_050', 'Cell_051', 'Cell_052', 'Cell_053', 'Cell_054', 'Cell_055', 'Cell_056', 'Cell_057', 'Cell_058', 'Cell_059', 'Cell_060', 'Cell_061', 'Cell_062', 'Cell_063', 'Cell_064', 'Cell_065', 'Cell_066', 'Cell_067', 'Cell_068', 'Cell_069', 'Cell_070', 'Cell_071', 'Cell_072', 'Cell_073', 'Cell_074', 'Cell_075', 'Cell_076', 'Cell_077', 'Cell_078', 'Cell_079', 'Cell_080', 'Cell_081', 'Cell_082', 'Cell_083', 'Cell_084', 'Cell_085', 'Cell_086', 'Cell_087', 'Cell_088', 'Cell_089', 'Cell_090', 'Cell_091', 'Cell_092', 'Cell_093', 'Cell_094', 'Cell_095', 'Cell_096', 'Cell_097', 'Cell_098', 'Cell_099', 'Cell_100', 'Cell_101', 'Cell_102', 'Cell_103', 'Cell_104', 'Cell_105', 'Cell_106', 'Cell_107', 'Cell_108', 'Cell_109', 'Cell_110', 'Cell_111', 'Cell_112', 'Cell_113', 'Cell_114', 'Cell_115', 'Cell_116', 'Cell_117', 'Cell_118', 'Cell_119', 'Cell_120', 'Cell_121', 'Cell_122', 'Cell_123', 'Cell_124', 'Cell_125', 'Cell_126', 'Cell_127', 'Cell_128', 'Cell_129', 'Cell_130', 'Cell_131', 'Cell_132', 'Cell_133', 'Cell_134', 'Cell_135', 'Cell_136', 'Cell_137', 'Cell_138', 'Cell_139', 'Cell_140', 'Cell_141', 'Cell_142', 'Cell_143', 'Cell_144', 'Cell_145', 'Cell_146', 'Cell_147', 'Cell_148', 'Cell_149', 'Cell_150', 'Cell_151', 'Cell_152', 'Cell_153', 'Cell_154', 'Cell_155', 'Cell_156', 'Cell_157', 'Cell_158', 'Cell_159', 'Cell_160', 'Cell_161', 'Cell_162', 'Cell_163', 'Cell_164', 'Cell_165', 'Cell_166', 'Cell_167', 'Cell_168', 'Cell_169', 'Cell_170', 'Cell_171', 'Cell_172', 'Cell_173', 'Cell_174', 'Cell_175', 'Cell_176', 'Cell_177', 'Cell_178', 'Cell_179', 'Cell_180', 'Cell_181', 'Cell_182', 'Cell_183', 'Cell_184', 'Cell_185', 'Cell_186', 'Cell_187', 'Cell_188', 'Cell_189', 'Cell_190', 'Cell_191', 'Cell_192', 'Cell_193', 'Cell_194', 'Cell_195', 'Cell_196', 'Cell_197', 'Cell_198', 'Cell_199', 'Cell_200', 'Cell_201', 'Cell_202', 'Cell_203', 'Cell_204', 'Cell_205', 'Cell_206', 'Cell_207', 'Cell_208', 'Cell_209', 'Cell_210', 'Cell_211', 'Cell_212', 'Cell_213', 'Cell_214', 'Cell_215', 'Cell_216', 'Cell_217', 'Cell_218', 'Cell_219', 'Cell_220', 'Cell_221', 'Cell_222', 'Cell_223', 'Cell_224', 'Cell_225', 'Cell_226', 'Cell_227', 'Cell_228', 'Cell_229', 'Cell_230', 'Cell_231', 'Cell_232', 'Cell_233', 'Cell_234', 'Cell_235', 'Cell_236', 'Cell_237', 'Cell_238', 'Cell_239', 'Cell_240', 'Cell_241', 'Cell_242', 'Cell_243', 'Cell_244', 'Cell_245', 'Cell_246', 'Cell_247', 'Cell_248', 'Cell_249', 'Cell_250', 'Cell_251', 'Cell_252', 'Cell_253', 'Cell_254', 'Cell_255', 'Cell_256', 'Cell_257', 'Cell_258', 'Cell_259', 'Cell_260', 'Cell_261', 'Cell_262', 'Cell_263', 'Cell_264', 'Cell_265', 'Cell_266', 'Cell_267', 'Cell_268', 'Cell_269', 'Cell_270', 'Cell_271', 'Cell_272', 'Cell_273', 'Cell_274', 'Cell_275', 'Cell_276', 'Cell_277', 'Cell_278', 'Cell_279', 'Cell_280', 'Cell_281', 'Cell_282', 'Cell_283', 'Cell_284', 'Cell_285', 'Cell_286', 'Cell_287', 'Cell_288', 'Cell_289', 'Cell_290', 'Cell_291', 'Cell_292', 'Cell_293', 'Cell_294', 'Cell_295', 'Cell_296', 'Cell_297', 'Cell_298', 'Cell_299', 'Cell_300', 'Cell_301', 'Cell_302', 'Cell_303', 'Cell_304', 'Cell_305', 'Cell_306', 'Cell_307', 'Cell_308', 'Cell_309', 'Cell_310', 'Cell_311', 'Cell_312', 'Cell_313', 'Cell_314', 'Cell_315', 'Cell_316', 'Cell_317', 'Cell_318', 'Cell_319', 'Cell_320', 'Cell_321', 'Cell_322', 'Cell_323', 'Cell_324', 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'Cell_1220', 'Cell_1221', 'Cell_1222', 'Cell_1223', 'Cell_1224', 'Cell_1225', 'Cell_1226', 'Cell_1227', 'Cell_1228', 'Cell_1229', 'Cell_1230', 'Cell_1231', 'Cell_1232', 'Cell_1233', 'Cell_1234', 'Cell_1235', 'Cell_1236', 'Cell_1237', 'Cell_1238', 'Cell_1239', 'Cell_1240', 'Cell_1241', 'Cell_1242', 'Cell_1243', 'Cell_1244', 'Cell_1245', 'Cell_1246', 'Cell_1247', 'Cell_1248', 'Cell_1249', 'Cell_1250', 'Cell_1251', 'Cell_1252', 'Cell_1253', 'Cell_1254', 'Cell_1255', 'Cell_1256', 'Cell_1257', 'Cell_1258', 'Cell_1259', 'Cell_1260', 'Cell_1261', 'Cell_1262', 'Cell_1263', 'Cell_1264', 'Cell_1265', 'Cell_1266', 'Cell_1267', 'Cell_1268', 'Cell_1269', 'Cell_1270', 'Cell_1271', 'Cell_1272', 'Cell_1273', 'Cell_1274', 'Cell_1275', 'Cell_1276', 'Cell_1277', 'Cell_1278', 'Cell_1279', 'Cell_1280', 'Cell_1281', 'Cell_1282', 'Cell_1283', 'Cell_1284', 'Cell_1285', 'Cell_1286', 'Cell_1287', 'Cell_1288', 'Cell_1289', 'Cell_1290', 'Cell_1291', 'Cell_1292', 'Cell_1293', 'Cell_1294', 'Cell_1295', 'Cell_1296', 'Cell_1297', 'Cell_1298', 'Cell_1299', 'Cell_1300', 'Cell_1301', 'Cell_1302', 'Cell_1303', 'Cell_1304', 'Cell_1305', 'Cell_1306', 'Cell_1307', 'Cell_1308', 'Cell_1309', 'Cell_1310', 'Cell_1311', 'Cell_1312', 'Cell_1313', 'Cell_1314', 'Cell_1315', 'Cell_1316', 'Cell_1317', 'Cell_1318', 'Cell_1319', 'Cell_1320', 'Cell_1321', 'Cell_1322', 'Cell_1323', 'Cell_1324', 'Cell_1325', 'Cell_1326', 'Cell_1327', 'Cell_1328', 'Cell_1329', 'Cell_1330', 'Cell_1331', 'Cell_1332', 'Cell_1333', 'Cell_1334', 'Cell_1335', 'Cell_1336', 'Cell_1337', 'Cell_1338', 'Cell_1339', 'Cell_1340', 'Cell_1341', 'Cell_1342', 'Cell_1343', 'Cell_1344', 'Cell_1345', 'Cell_1346', 'Cell_1347', 'Cell_1348', 'Cell_1349', 'Cell_1350', 'Cell_1351', 'Cell_1352', 'Cell_1353', 'Cell_1354', 'Cell_1355', 'Cell_1356', 'Cell_1357', 'Cell_1358', 'Cell_1359', 'Cell_1360', 'Cell_1361', 'Cell_1362', 'Cell_1363', 'Cell_1364', 'Cell_1365', 'Cell_1366', 'Cell_1367', 'Cell_1368', 'Cell_1369', 'Cell_1370', 'Cell_1371', 'Cell_1372', 'Cell_1373', 'Cell_1374', 'Cell_1375', 'Cell_1376', 'Cell_1377', 'Cell_1378', 'Cell_1379', 'Cell_1380', 'Cell_1381', 'Cell_1382', 'Cell_1383', 'Cell_1384', 'Cell_1385', 'Cell_1386', 'Cell_1387', 'Cell_1388', 'Cell_1389', 'Cell_1390', 'Cell_1391', 'Cell_1392', 'Cell_1393', 'Cell_1394', 'Cell_1395', 'Cell_1396', 'Cell_1397', 'Cell_1398', 'Cell_1399', 'Cell_1400', 'Cell_1401', 'Cell_1402', 'Cell_1403', 'Cell_1404', 'Cell_1405', 'Cell_1406', 'Cell_1407', 'Cell_1408', 'Cell_1409', 'Cell_1410', 'Cell_1411', 'Cell_1412', 'Cell_1413', 'Cell_1414', 'Cell_1415').

library_source: transcriptomic single cell

data_processing:
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

tag: cell type

value: spinal neuron differentiation

tag: genotype

value: heterogenous protocol

tag: sequencing batch


title: N_LPS_C

source_name: N

value: N


title: Leuka ER-1293,SR9011 5 uM

city: Montréal

first: Jean-Philippe

last: Goulet

state: Québec

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

country: Canada

institute: Université de Montréal

description:
SR20
RNA-Seq (rRNA-depleted stranded (HMR))

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

source_name: Memory CD4+ T cells

growth_protocol: N/Ap

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

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

tag: subject

tag: hiv status

value: Uninfected

value: Memory CD4+ T cells


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_193


title: N_LPS_A


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_194


title: ALET-HIV2,SR9011 5 uM

description:
SR2
RNA-Seq (rRNA-depleted stranded (HMR))


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_192


title: PCL implant, Control replicate 4

city: Baltimore

first: Jennifer

last: Elisseeff

state: MD

address: 1800 Orleans St

institute: Johns Hopkins

description: Library name: NEG-ETBF-4

data_processing:
STAR aligner with default parameters used to align sequences to GRCm39 reference then perform quantification using GeneCounts mode.
Assembly: GRCm39 primary assembly
Supplementary files format and content: tab delimited file with raw counts for each individual sample

organism: Mus musculus

source_name: Quadricep

extract_protocol:
RNA was extracted with the RNeasy Kit (Qiagen)
Library preparation with unique dual indexes was performed using the Illumina Standard Total RNA Ligation Kit.

treatment_protocol: On Day -11, both groups were treated with antibiotics for 4 days. On Day -7, antibiotics were removed; the control group was inoculated with DPBS and the experimental group was inoculated with ETBF.On Day 0, both groups underwent volumetric muscle loss surgery with PCL implantation in the defect space. At Week 6, quadricep muscles were harvested, processed into a single cell suspension, and stained for fluorescence activated cell sorting (FACS). The CD45-CD31-CD29+ fraction was isolated as the stromal cell population. Stromal cells were sorted directly into Buffer RLT (Qiagen) with 1X beta-mercaptoethanol, flash frozen on dry ice, and transferred to -80°C for storage until RNA extraction.

value: Quadricep

value: Stromal

value: +ABX -ETBF +PCL


title: PCL implant, Control replicate 1

description: Library name: NEG-ETBF-1


title: PCL implant, Control replicate 3

description: Library name: NEG-ETBF-3


title: N_DMSO_C


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_197


title: Leuka CLOCK6,SR8278 10 uM

description:
SR18
RNA-Seq (rRNA-depleted stranded (HMR))

value: Leuka CLOCK6


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_190


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_191


title: PCL implant, Control replicate 2

description: Library name: NEG-ETBF-2


title: PCL implant, ETBF replicate 3

description: Library name: POS-ETBF-3

value: +ABX +ETBF +PCL


title: Leuka CLOCK6,DMSO

description:
SR16
RNA-Seq (rRNA-depleted stranded (HMR))

value: DMSO


title: N_DMSO_A


title: Leuka CLOCK6,SR9011 5 uM

description:
SR17
RNA-Seq (rRNA-depleted stranded (HMR))


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_189


title: PCL implant, ETBF replicate 2

description: Library name: POS-ETBF-2


title: IA_LPS_C

source_name: IA

value: IA


title: N_LPS_B


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_188


title: IA_LPS_B


title: PCL implant, ETBF replicate 1

description: Library name: POS-ETBF-1


title: ALET-HIV7,SR8278 10 uM

description:
SR15
RNA-Seq (rRNA-depleted stranded (HMR))


title: Leuka ER-1293,DMSO

description:
SR19
RNA-Seq (rRNA-depleted stranded (HMR))


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_187


title: IA_LPS_A


title: ALET-HIV7,DMSO

description:
SR13
RNA-Seq (rRNA-depleted stranded (HMR))


title: ALET-HIV7,SR9011 5 uM

description:
SR14
RNA-Seq (rRNA-depleted stranded (HMR))


title: N_DMSO_B


title: PCL implant, ETBF replicate 4

description: Library name: POS-ETBF-4


title: Brain, BCAS+WD-Exos1, 28d, rep6

city: Wuhan

first: Hang

last: Zhang

address: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology 1095 Jiefang Avenue 430030 Wuhan China

country: China

institute: Tongji hospital

description: Library name: BCAS+WD-Exos6

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: GRCcm39
Supplementary files format and content: text file includes raw counts for each Sample

source_name: Brain

extract_protocol:
Microglia cells were isolated into lysate by FACS to extract total RNA. Double-stranded cDNA was synthesized using Smart-seq2 amplification technology, and the amplified product fragments were detected using Agilent 2100 chips.
Libraries were constructed using V6 RNA-Seq preparation tool.

treatment_protocol: BCAS mice were given 100 μg exosomes each time via the tail vein every 3 days for 28 days

value: Brain

value: microglia

value: WT


title: ALET-HIV6,SR8278 10 uM

description:
SR12
RNA-Seq (rRNA-depleted stranded (HMR))


title: Brain, BCAS+WD-Exos1, 28d, rep5

description: Library name: BCAS+WD-Exos5


title: Brain, BCAS+WD-Exos1, 28d, rep4

description: Library name: BCAS+WD-Exos4


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_185


title: IA_DMSO_C


title: IA_DMSO_B


title: ALET-HIV6,SR9011 5 uM

description:
SR11
RNA-Seq (rRNA-depleted stranded (HMR))


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_184


title: Brain, BCAS+WD-Exos1, 28d, rep3

description: Library name: BCAS+WD-Exos3


title: IA_DMSO_A


title: ALET-HIV6,DMSO

description:
SR10
RNA-Seq (rRNA-depleted stranded (HMR))


title: Brain, BCAS+WD-Exos1, 28d, rep2

description: Library name: BCAS+WD-Exos2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_183


title: ALET-HIV2,DMSO

description:
SR1
RNA-Seq (rRNA-depleted stranded (HMR))


title: I2_LPS_C


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_182


title: Brain, BCAS+WD-Exos1, 28d, rep1

description: Library name: BCAS+WD-Exos1


title: I2_LPS_B


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_181


title: SAS cell, shKDM4C

city: Hsinchu

first: Wen-Ching

last: Wang

address: NO.101, Sec. 2, Kuang-Fu Road, Hsinchu 300044, Taiwan (R.O.C)

department: Insitute of Molecular & Cellular Biology

country: Taiwan

institute: National Tsing Hua University

data_processing:
The original data obtained by high-throughput sequencing (Illumina NovaSeq 6000 platform) were transformed into raw sequenced reads by CASAVA base calling and stored in FASTQ format. FastQC and MultiQC were used to check fastq files for quality.
The obtained raw paired-end reads were filtered by Trimmomatic to discard low-quality reads, trim adaptor sequences, and eliminate poor-quality bases with the following parameters: LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15MINLEN:30.
The obtained high-quality data (clean reads) was used for subsequent analysis. Read pairs from each sample were aligned to the reference genome (e.g., H. sapiens, GRCh38) by the HISAT2 software.
Feature Counts was used to count the reads numbers mapped to individual genes. For gene expression, the “Trimmed Mean of M-values” normalization (TMM) was performed DEGseq without biological duplicate and the “Relative Log Expression” normalization (RLE) was performed using DESeq2 with biological duplicate.
Differentially expressed genes (DEGs) analysis of two conditions was performed in R using DEGseq (without biological replicate) and DESeq2 (with biological replicate), which based on negative binomial distribution and Poisson distribution model, respectively. The resulting p-values were adjusted using the Benjamini and Hochberg’s approach for controlling the FDR.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: excel file includes log2FoldChange values

source_name: Oral cavity, tongue

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

extract_protocol:
Control (LKO) and shKDM4C SAS cells (1 x 10^6 cells) were seede in a 10-cm dish and incubated at 37℃ overnight. Total RNA was extracted using TRIzol reagent (Thermo).
A total amount of 1 µg total RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel, Switzerland) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using magnetic oligo-dT beads.  Captured mRNA was fragmented by incubating at a high temperature in the presence of magnesium in KAPA Fragment, Prime and Elute Buffer (1x). First strand cDNA was synthesized using random hexamer priming. Combined 2nd strand synthesis and A-tailing, which converts the cDNA:RNA hybrid to double-stranded cDNA (dscDNA), incorporated dUTP into the second cDNA strand, and added dAMP to the 3’ ends of the resulting dscDNA. dsDNA adapter with 3’dTMP overhangs were ligated to library insert fragments to generate the library fragments carrying the adapters. In order to select cDNA fragments of preferentially 300~400bp in length, the library fragments were purified with KAPA Pure Beads system (KAPA Biosystems, Roche, Basel, Switzerland). The library carrying appropriate adapter sequences at both ends was amplified using KAPA HiFi HotStart ReadyMix (KAPA Biosystems, Roche, Basel, Switzerland) along with library amplification primers. The strand marked with dUTP in not amplified, allowing strand-specific sequencing. At last, PCR products were purified using KAPA Pure Beads system and the library quality was assessed on the Qsep 100 DNA/RNA Analyzer (BiOptic Inc., Taiwan).

value: Oral cavity, tongue

value: SAS

value: squamous cell

value: KDM4C knockdown


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_KO_Cell_186

value: spinal neuron differentiation

value: heterogenous protocol


title: Brain, BCAS+ND-Exos1, 28d, rep6

description: Library name: BCAS+ND-Exos6


title: I2_LPS_A


title: SAS cell, shLKO


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_180


title: Brain, BCAS+ND-Exos1, 28d, rep5

description: Library name: BCAS+ND-Exos5


title: I2_DMSO_C


title: VEXAS17_PBMC2_TCR

city: Bethesda

first: Shouguo

last: Gao

address: 9000 Rockville Pike

department: NHLBI

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: VEXAS

value: Human peripheral blood

value: PBMCs

tag: Sex

value: Male

tag: age

tag: response at primary end point

tag: library type

value: VDJ (TCR)


title: I2_DMSO_B


title: Brain, BCAS+ND-Exos1, 28d, rep3

description: Library name: BCAS+ND-Exos3


title: VEXAS17_PBMC1_TCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_178


title: I2_DMSO_A


title: VEXAS16_PBMC2_TCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_177


title: T8P7_P1_d11_HYP_1_S10 [Sample 71]

city: Clayton

first: Nitika

last: Kandhari

state: VIC

address: Wellington Road

country: Australia

institute: Monash University

description: Triple hypoxic experiment: Day 11_Passage 1_Hypoxic injured Tubuloid _replicate 3

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

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: female

value: Tubuloids derived from d20 kidney organoids

value: Derived from GM04522 fibroblasts (Coriell Inst)


title: VEXAS16_PBMC1_TCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_176


title: Brain, BCAS+ND-Exos1, 28d, rep1

description: Library name: BCAS+ND-Exos1

value: Brain

value: microglia


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_179


title: T8P7_P1_d11_HYP_2_S11 [Sample 70]

description: Triple hypoxic experiment: Day 11_Passage 1_Hypoxic injured Tubuloid _replicate 2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_175


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_174


title: VEXAS15_PBMC1_TCR

description: 10x Genomics


title: T8P7_P1_d11_HYP_4_S12 [Sample 69]

description: Triple hypoxic experiment: Day 11_Passage 1_Hypoxic injured Tubuloid _replicate 1


title: Brain, BCAS+ND-Exos1, 28d, rep2

description: Library name: BCAS+ND-Exos2

value: WT


title: VEXAS15_PBMC2_TCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_173

description: The rows in 'counts.txt' and 'rpkms.txt' are genes and the columns are the cell ids ('Cell_001', 'Cell_002', 'Cell_003', 'Cell_004', 'Cell_005', 'Cell_006', 'Cell_007', 'Cell_008', 'Cell_009', 'Cell_010', 'Cell_011', 'Cell_012', 'Cell_013', 'Cell_014', 'Cell_015', 'Cell_016', 'Cell_017', 'Cell_018', 'Cell_019', 'Cell_020', 'Cell_021', 'Cell_022', 'Cell_023', 'Cell_024', 'Cell_025', 'Cell_026', 'Cell_027', 'Cell_028', 'Cell_029', 'Cell_030', 'Cell_031', 'Cell_032', 'Cell_033', 'Cell_034', 'Cell_035', 'Cell_036', 'Cell_037', 'Cell_038', 'Cell_039', 'Cell_040', 'Cell_041', 'Cell_042', 'Cell_043', 'Cell_044', 'Cell_045', 'Cell_046', 'Cell_047', 'Cell_048', 'Cell_049', 'Cell_050', 'Cell_051', 'Cell_052', 'Cell_053', 'Cell_054', 'Cell_055', 'Cell_056', 'Cell_057', 'Cell_058', 'Cell_059', 'Cell_060', 'Cell_061', 'Cell_062', 'Cell_063', 'Cell_064', 'Cell_065', 'Cell_066', 'Cell_067', 'Cell_068', 'Cell_069', 'Cell_070', 'Cell_071', 'Cell_072', 'Cell_073', 'Cell_074', 'Cell_075', 'Cell_076', 'Cell_077', 'Cell_078', 'Cell_079', 'Cell_080', 'Cell_081', 'Cell_082', 'Cell_083', 'Cell_084', 'Cell_085', 'Cell_086', 'Cell_087', 'Cell_088', 'Cell_089', 'Cell_090', 'Cell_091', 'Cell_092', 'Cell_093', 'Cell_094', 'Cell_095', 'Cell_096', 'Cell_097', 'Cell_098', 'Cell_099', 'Cell_100', 'Cell_101', 'Cell_102', 'Cell_103', 'Cell_104', 'Cell_105', 'Cell_106', 'Cell_107', 'Cell_108', 'Cell_109', 'Cell_110', 'Cell_111', 'Cell_112', 'Cell_113', 'Cell_114', 'Cell_115', 'Cell_116', 'Cell_117', 'Cell_118', 'Cell_119', 'Cell_120', 'Cell_121', 'Cell_122', 'Cell_123', 'Cell_124', 'Cell_125', 'Cell_126', 'Cell_127', 'Cell_128', 'Cell_129', 'Cell_130', 'Cell_131', 'Cell_132', 'Cell_133', 'Cell_134', 'Cell_135', 'Cell_136', 'Cell_137', 'Cell_138', 'Cell_139', 'Cell_140', 'Cell_141', 'Cell_142', 'Cell_143', 'Cell_144', 'Cell_145', 'Cell_146', 'Cell_147', 'Cell_148', 'Cell_149', 'Cell_150', 'Cell_151', 'Cell_152', 'Cell_153', 'Cell_154', 'Cell_155', 'Cell_156', 'Cell_157', 'Cell_158', 'Cell_159', 'Cell_160', 'Cell_161', 'Cell_162', 'Cell_163', 'Cell_164', 'Cell_165', 'Cell_166', 'Cell_167', 'Cell_168', 'Cell_169', 'Cell_170', 'Cell_171', 'Cell_172', 'Cell_173', 'Cell_174', 'Cell_175', 'Cell_176', 'Cell_177', 'Cell_178', 'Cell_179', 'Cell_180', 'Cell_181', 'Cell_182', 'Cell_183', 'Cell_184', 'Cell_185', 'Cell_186', 'Cell_187', 'Cell_188', 'Cell_189', 'Cell_190', 'Cell_191', 'Cell_192', 'Cell_193', 'Cell_194', 'Cell_195', 'Cell_196', 'Cell_197', 'Cell_198', 'Cell_199', 'Cell_200', 'Cell_201', 'Cell_202', 'Cell_203', 'Cell_204', 'Cell_205', 'Cell_206', 'Cell_207', 'Cell_208', 'Cell_209', 'Cell_210', 'Cell_211', 'Cell_212', 'Cell_213', 'Cell_214', 'Cell_215', 'Cell_216', 'Cell_217', 'Cell_218', 'Cell_219', 'Cell_220', 'Cell_221', 'Cell_222', 'Cell_223', 'Cell_224', 'Cell_225', 'Cell_226', 'Cell_227', 'Cell_228', 'Cell_229', 'Cell_230', 'Cell_231', 'Cell_232', 'Cell_233', 'Cell_234', 'Cell_235', 'Cell_236', 'Cell_237', 'Cell_238', 'Cell_239', 'Cell_240', 'Cell_241', 'Cell_242', 'Cell_243', 'Cell_244', 'Cell_245', 'Cell_246', 'Cell_247', 'Cell_248', 'Cell_249', 'Cell_250', 'Cell_251', 'Cell_252', 'Cell_253', 'Cell_254', 'Cell_255', 'Cell_256', 'Cell_257', 'Cell_258', 'Cell_259', 'Cell_260', 'Cell_261', 'Cell_262', 'Cell_263', 'Cell_264', 'Cell_265', 'Cell_266', 'Cell_267', 'Cell_268', 'Cell_269', 'Cell_270', 'Cell_271', 'Cell_272', 'Cell_273', 'Cell_274', 'Cell_275', 'Cell_276', 'Cell_277', 'Cell_278', 'Cell_279', 'Cell_280', 'Cell_281', 'Cell_282', 'Cell_283', 'Cell_284', 'Cell_285', 'Cell_286', 'Cell_287', 'Cell_288', 'Cell_289', 'Cell_290', 'Cell_291', 'Cell_292', 'Cell_293', 'Cell_294', 'Cell_295', 'Cell_296', 'Cell_297', 'Cell_298', 'Cell_299', 'Cell_300', 'Cell_301', 'Cell_302', 'Cell_303', 'Cell_304', 'Cell_305', 'Cell_306', 'Cell_307', 'Cell_308', 'Cell_309', 'Cell_310', 'Cell_311', 'Cell_312', 'Cell_313', 'Cell_314', 'Cell_315', 'Cell_316', 'Cell_317', 'Cell_318', 'Cell_319', 'Cell_320', 'Cell_321', 'Cell_322', 'Cell_323', 'Cell_324', 'Cell_325', 'Cell_326', 'Cell_327', 'Cell_328', 'Cell_329', 'Cell_330', 'Cell_331', 'Cell_332', 'Cell_333', 'Cell_334', 'Cell_335', 'Cell_336', 'Cell_337', 'Cell_338', 'Cell_339', 'Cell_340', 'Cell_341', 'Cell_342', 'Cell_343', 'Cell_344', 'Cell_345', 'Cell_346', 'Cell_347', 'Cell_348', 'Cell_349', 'Cell_350', 'Cell_351', 'Cell_352', 'Cell_353', 'Cell_354', 'Cell_355', 'Cell_356', 'Cell_357', 'Cell_358', 'Cell_359', 'Cell_360', 'Cell_361', 'Cell_362', 'Cell_363', 'Cell_364', 'Cell_365', 'Cell_366', 'Cell_367', 'Cell_368', 'Cell_369', 'Cell_370', 'Cell_371', 'Cell_372', 'Cell_373', 'Cell_374', 'Cell_375', 'Cell_376', 'Cell_377', 'Cell_378', 'Cell_379', 'Cell_380', 'Cell_381', 'Cell_382', 'Cell_383', 'Cell_384', 'Cell_385', 'Cell_386', 'Cell_387', 'Cell_388', 'Cell_389', 'Cell_390', 'Cell_391', 'Cell_392', 'Cell_393', 'Cell_394', 'Cell_395', 'Cell_396', 'Cell_397', 'Cell_398', 'Cell_399', 'Cell_400', 'Cell_401', 'Cell_402', 'Cell_403', 'Cell_404', 'Cell_405', 'Cell_406', 'Cell_407', 'Cell_408', 'Cell_409', 'Cell_410', 'Cell_411', 'Cell_412', 'Cell_413', 'Cell_414', 'Cell_415', 'Cell_416', 'Cell_417', 'Cell_418', 'Cell_419', 'Cell_420', 'Cell_421', 'Cell_422', 'Cell_423', 'Cell_424', 'Cell_425', 'Cell_426', 'Cell_427', 'Cell_428', 'Cell_429', 'Cell_430', 'Cell_431', 'Cell_432', 'Cell_433', 'Cell_434', 'Cell_435', 'Cell_436', 'Cell_437', 'Cell_438', 'Cell_439', 'Cell_440', 'Cell_441', 'Cell_442', 'Cell_443', 'Cell_444', 'Cell_445', 'Cell_446', 'Cell_447', 'Cell_448', 'Cell_449', 'Cell_450', 'Cell_451', 'Cell_452', 'Cell_453', 'Cell_454', 'Cell_455', 'Cell_456', 'Cell_457', 'Cell_458', 'Cell_459', 'Cell_460', 'Cell_461', 'Cell_462', 'Cell_463', 'Cell_464', 'Cell_465', 'Cell_466', 'Cell_467', 'Cell_468', 'Cell_469', 'Cell_470', 'Cell_471', 'Cell_472', 'Cell_473', 'Cell_474', 'Cell_475', 'Cell_476', 'Cell_477', 'Cell_478', 'Cell_479', 'Cell_480', 'Cell_481', 'Cell_482', 'Cell_483', 'Cell_484', 'Cell_485', 'Cell_486', 'Cell_487', 'Cell_488', 'Cell_489', 'Cell_490', 'Cell_491', 'Cell_492', 'Cell_493', 'Cell_494', 'Cell_495', 'Cell_496', 'Cell_497', 'Cell_498', 'Cell_499', 'Cell_500', 'Cell_501', 'Cell_502', 'Cell_503', 'Cell_504', 'Cell_505', 'Cell_506', 'Cell_507', 'Cell_508', 'Cell_509', 'Cell_510', 'Cell_511', 'Cell_512', 'Cell_513', 'Cell_514', 'Cell_515', 'Cell_516', 'Cell_517', 'Cell_518', 'Cell_519', 'Cell_520', 'Cell_521', 'Cell_522', 'Cell_523', 'Cell_524', 'Cell_525', 'Cell_526', 'Cell_527', 'Cell_528', 'Cell_529', 'Cell_530', 'Cell_531', 'Cell_532', 'Cell_533', 'Cell_534', 'Cell_535', 'Cell_536', 'Cell_537', 'Cell_538', 'Cell_539', 'Cell_540', 'Cell_541', 'Cell_542', 'Cell_543', 'Cell_544', 'Cell_545', 'Cell_546', 'Cell_547', 'Cell_548', 'Cell_549', 'Cell_550', 'Cell_551', 'Cell_552', 'Cell_553', 'Cell_554', 'Cell_555', 'Cell_556', 'Cell_557', 'Cell_558', 'Cell_559', 'Cell_560', 'Cell_561', 'Cell_562', 'Cell_563', 'Cell_564', 'Cell_565', 'Cell_566', 'Cell_567', 'Cell_568', 'Cell_569', 'Cell_570', 'Cell_571', 'Cell_572', 'Cell_573', 'Cell_574', 'Cell_575', 'Cell_576', 'Cell_577', 'Cell_578', 'Cell_579', 'Cell_580', 'Cell_581', 'Cell_582', 'Cell_583', 'Cell_584', 'Cell_585', 'Cell_586', 'Cell_587', 'Cell_588', 'Cell_589', 'Cell_590', 'Cell_591', 'Cell_592', 'Cell_593', 'Cell_594', 'Cell_595', 'Cell_596', 'Cell_597', 'Cell_598', 'Cell_599', 'Cell_600', 'Cell_601', 'Cell_602', 'Cell_603', 'Cell_604', 'Cell_605', 'Cell_606', 'Cell_607', 'Cell_608', 'Cell_609', 'Cell_610', 'Cell_611', 'Cell_612', 'Cell_613', 'Cell_614', 'Cell_615', 'Cell_616', 'Cell_617', 'Cell_618', 'Cell_619', 'Cell_620', 'Cell_621', 'Cell_622', 'Cell_623', 'Cell_624', 'Cell_625', 'Cell_626', 'Cell_627', 'Cell_628', 'Cell_629', 'Cell_630', 'Cell_631', 'Cell_632', 'Cell_633', 'Cell_634', 'Cell_635', 'Cell_636', 'Cell_637', 'Cell_638', 'Cell_639', 'Cell_640', 'Cell_641', 'Cell_642', 'Cell_643', 'Cell_644', 'Cell_645', 'Cell_646', 'Cell_647', 'Cell_648', 'Cell_649', 'Cell_650', 'Cell_651', 'Cell_652', 'Cell_653', 'Cell_654', 'Cell_655', 'Cell_656', 'Cell_657', 'Cell_658', 'Cell_659', 'Cell_660', 'Cell_661', 'Cell_662', 'Cell_663', 'Cell_664', 'Cell_665', 'Cell_666', 'Cell_667', 'Cell_668', 'Cell_669', 'Cell_670', 'Cell_671', 'Cell_672', 'Cell_673', 'Cell_674', 'Cell_675', 'Cell_676', 'Cell_677', 'Cell_678', 'Cell_679', 'Cell_680', 'Cell_681', 'Cell_682', 'Cell_683', 'Cell_684', 'Cell_685', 'Cell_686', 'Cell_687', 'Cell_688', 'Cell_689', 'Cell_690', 'Cell_691', 'Cell_692', 'Cell_693', 'Cell_694', 'Cell_695', 'Cell_696', 'Cell_697', 'Cell_698', 'Cell_699', 'Cell_700', 'Cell_701', 'Cell_702', 'Cell_703', 'Cell_704', 'Cell_705', 'Cell_706', 'Cell_707', 'Cell_708', 'Cell_709', 'Cell_710', 'Cell_711', 'Cell_712', 'Cell_713', 'Cell_714', 'Cell_715', 'Cell_716', 'Cell_717', 'Cell_718', 'Cell_719', 'Cell_720', 'Cell_721', 'Cell_722', 'Cell_723', 'Cell_724', 'Cell_725', 'Cell_726', 'Cell_727', 'Cell_728', 'Cell_729', 'Cell_730', 'Cell_731', 'Cell_732', 'Cell_733', 'Cell_734', 'Cell_735', 'Cell_736', 'Cell_737', 'Cell_738', 'Cell_739', 'Cell_740', 'Cell_741', 'Cell_742', 'Cell_743', 'Cell_744', 'Cell_745', 'Cell_746', 'Cell_747', 'Cell_748', 'Cell_749', 'Cell_750', 'Cell_751', 'Cell_752', 'Cell_753', 'Cell_754', 'Cell_755', 'Cell_756', 'Cell_757', 'Cell_758', 'Cell_759', 'Cell_760', 'Cell_761', 'Cell_762', 'Cell_763', 'Cell_764', 'Cell_765', 'Cell_766', 'Cell_767', 'Cell_768', 'Cell_769', 'Cell_770', 'Cell_771', 'Cell_772', 'Cell_773', 'Cell_774', 'Cell_775', 'Cell_776', 'Cell_777', 'Cell_778', 'Cell_779', 'Cell_780', 'Cell_781', 'Cell_782', 'Cell_783', 'Cell_784', 'Cell_785', 'Cell_786', 'Cell_787', 'Cell_788', 'Cell_789', 'Cell_790', 'Cell_791', 'Cell_792', 'Cell_793', 'Cell_794', 'Cell_795', 'Cell_796', 'Cell_797', 'Cell_798', 'Cell_799', 'Cell_800', 'Cell_801', 'Cell_802', 'Cell_803', 'Cell_804', 'Cell_805', 'Cell_806', 'Cell_807', 'Cell_808', 'Cell_809', 'Cell_810', 'Cell_811', 'Cell_812', 'Cell_813', 'Cell_814', 'Cell_815', 'Cell_816', 'Cell_817', 'Cell_818', 'Cell_819', 'Cell_820', 'Cell_821', 'Cell_822', 'Cell_823', 'Cell_824', 'Cell_825', 'Cell_826', 'Cell_827', 'Cell_828', 'Cell_829', 'Cell_830', 'Cell_831', 'Cell_832', 'Cell_833', 'Cell_834', 'Cell_835', 'Cell_836', 'Cell_837', 'Cell_838', 'Cell_839', 'Cell_840', 'Cell_841', 'Cell_842', 'Cell_843', 'Cell_844', 'Cell_845', 'Cell_846', 'Cell_847', 'Cell_848', 'Cell_849', 'Cell_850', 'Cell_851', 'Cell_852', 'Cell_853', 'Cell_854', 'Cell_855', 'Cell_856', 'Cell_857', 'Cell_858', 'Cell_859', 'Cell_860', 'Cell_861', 'Cell_862', 'Cell_863', 'Cell_864', 'Cell_865', 'Cell_866', 'Cell_867', 'Cell_868', 'Cell_869', 'Cell_870', 'Cell_871', 'Cell_872', 'Cell_873', 'Cell_874', 'Cell_875', 'Cell_876', 'Cell_877', 'Cell_878', 'Cell_879', 'Cell_880', 'Cell_881', 'Cell_882', 'Cell_883', 'Cell_884', 'Cell_885', 'Cell_886', 'Cell_887', 'Cell_888', 'Cell_889', 'Cell_890', 'Cell_891', 'Cell_892', 'Cell_893', 'Cell_894', 'Cell_895', 'Cell_896', 'Cell_897', 'Cell_898', 'Cell_899', 'Cell_900', 'Cell_901', 'Cell_902', 'Cell_903', 'Cell_904', 'Cell_905', 'Cell_906', 'Cell_907', 'Cell_908', 'Cell_909', 'Cell_910', 'Cell_911', 'Cell_912', 'Cell_913', 'Cell_914', 'Cell_915', 'Cell_916', 'Cell_917', 'Cell_918', 'Cell_919', 'Cell_920', 'Cell_921', 'Cell_922', 'Cell_923', 'Cell_924', 'Cell_925', 'Cell_926', 'Cell_927', 'Cell_928', 'Cell_929', 'Cell_930', 'Cell_931', 'Cell_932', 'Cell_933', 'Cell_934', 'Cell_935', 'Cell_936', 'Cell_937', 'Cell_938', 'Cell_939', 'Cell_940', 'Cell_941', 'Cell_942', 'Cell_943', 'Cell_944', 'Cell_945', 'Cell_946', 'Cell_947', 'Cell_948', 'Cell_949', 'Cell_950', 'Cell_951', 'Cell_952', 'Cell_953', 'Cell_954', 'Cell_955', 'Cell_956', 'Cell_957', 'Cell_958', 'Cell_959', 'Cell_960', 'Cell_961', 'Cell_962', 'Cell_963', 'Cell_964', 'Cell_965', 'Cell_966', 'Cell_967', 'Cell_968', 'Cell_969', 'Cell_970', 'Cell_971', 'Cell_972', 'Cell_973', 'Cell_974', 'Cell_975', 'Cell_976', 'Cell_977', 'Cell_978', 'Cell_979', 'Cell_980', 'Cell_981', 'Cell_982', 'Cell_983', 'Cell_984', 'Cell_985', 'Cell_986', 'Cell_987', 'Cell_988', 'Cell_989', 'Cell_990', 'Cell_991', 'Cell_992', 'Cell_993', 'Cell_994', 'Cell_995', 'Cell_996', 'Cell_997', 'Cell_998', 'Cell_999', 'Cell_1000', 'Cell_1001', 'Cell_1002', 'Cell_1003', 'Cell_1004', 'Cell_1005', 'Cell_1006', 'Cell_1007', 'Cell_1008', 'Cell_1009', 'Cell_1010', 'Cell_1011', 'Cell_1012', 'Cell_1013', 'Cell_1014', 'Cell_1015', 'Cell_1016', 'Cell_1017', 'Cell_1018', 'Cell_1019', 'Cell_1020', 'Cell_1021', 'Cell_1022', 'Cell_1023', 'Cell_1024', 'Cell_1025', 'Cell_1026', 'Cell_1027', 'Cell_1028', 'Cell_1029', 'Cell_1030', 'Cell_1031', 'Cell_1032', 'Cell_1033', 'Cell_1034', 'Cell_1035', 'Cell_1036', 'Cell_1037', 'Cell_1038', 'Cell_1039', 'Cell_1040', 'Cell_1041', 'Cell_1042', 'Cell_1043', 'Cell_1044', 'Cell_1045', 'Cell_1046', 'Cell_1047', 'Cell_1048', 'Cell_1049', 'Cell_1050', 'Cell_1051', 'Cell_1052', 'Cell_1053', 'Cell_1054', 'Cell_1055', 'Cell_1056', 'Cell_1057', 'Cell_1058', 'Cell_1059', 'Cell_1060', 'Cell_1061', 'Cell_1062', 'Cell_1063', 'Cell_1064', 'Cell_1065', 'Cell_1066', 'Cell_1067', 'Cell_1068', 'Cell_1069', 'Cell_1070', 'Cell_1071', 'Cell_1072', 'Cell_1073', 'Cell_1074', 'Cell_1075', 'Cell_1076', 'Cell_1077', 'Cell_1078', 'Cell_1079', 'Cell_1080', 'Cell_1081', 'Cell_1082', 'Cell_1083', 'Cell_1084', 'Cell_1085', 'Cell_1086', 'Cell_1087', 'Cell_1088', 'Cell_1089', 'Cell_1090', 'Cell_1091', 'Cell_1092', 'Cell_1093', 'Cell_1094', 'Cell_1095', 'Cell_1096', 'Cell_1097', 'Cell_1098', 'Cell_1099', 'Cell_1100', 'Cell_1101', 'Cell_1102', 'Cell_1103', 'Cell_1104', 'Cell_1105', 'Cell_1106', 'Cell_1107', 'Cell_1108', 'Cell_1109', 'Cell_1110', 'Cell_1111', 'Cell_1112', 'Cell_1113', 'Cell_1114', 'Cell_1115', 'Cell_1116', 'Cell_1117', 'Cell_1118', 'Cell_1119', 'Cell_1120', 'Cell_1121', 'Cell_1122', 'Cell_1123', 'Cell_1124', 'Cell_1125', 'Cell_1126', 'Cell_1127', 'Cell_1128', 'Cell_1129', 'Cell_1130', 'Cell_1131', 'Cell_1132', 'Cell_1133', 'Cell_1134', 'Cell_1135', 'Cell_1136', 'Cell_1137', 'Cell_1138', 'Cell_1139', 'Cell_1140', 'Cell_1141', 'Cell_1142', 'Cell_1143', 'Cell_1144', 'Cell_1145', 'Cell_1146', 'Cell_1147', 'Cell_1148', 'Cell_1149', 'Cell_1150', 'Cell_1151', 'Cell_1152', 'Cell_1153', 'Cell_1154', 'Cell_1155', 'Cell_1156', 'Cell_1157', 'Cell_1158', 'Cell_1159', 'Cell_1160', 'Cell_1161', 'Cell_1162', 'Cell_1163', 'Cell_1164', 'Cell_1165', 'Cell_1166', 'Cell_1167', 'Cell_1168', 'Cell_1169', 'Cell_1170', 'Cell_1171', 'Cell_1172', 'Cell_1173', 'Cell_1174', 'Cell_1175', 'Cell_1176', 'Cell_1177', 'Cell_1178', 'Cell_1179', 'Cell_1180', 'Cell_1181', 'Cell_1182', 'Cell_1183', 'Cell_1184', 'Cell_1185', 'Cell_1186', 'Cell_1187', 'Cell_1188', 'Cell_1189', 'Cell_1190', 'Cell_1191', 'Cell_1192', 'Cell_1193', 'Cell_1194', 'Cell_1195', 'Cell_1196', 'Cell_1197', 'Cell_1198', 'Cell_1199', 'Cell_1200', 'Cell_1201', 'Cell_1202', 'Cell_1203', 'Cell_1204', 'Cell_1205', 'Cell_1206', 'Cell_1207', 'Cell_1208', 'Cell_1209', 'Cell_1210', 'Cell_1211', 'Cell_1212', 'Cell_1213', 'Cell_1214', 'Cell_1215', 'Cell_1216', 'Cell_1217', 'Cell_1218', 'Cell_1219', 'Cell_1220', 'Cell_1221', 'Cell_1222', 'Cell_1223', 'Cell_1224', 'Cell_1225', 'Cell_1226', 'Cell_1227', 'Cell_1228', 'Cell_1229', 'Cell_1230', 'Cell_1231', 'Cell_1232', 'Cell_1233', 'Cell_1234', 'Cell_1235', 'Cell_1236', 'Cell_1237', 'Cell_1238', 'Cell_1239', 'Cell_1240', 'Cell_1241', 'Cell_1242', 'Cell_1243', 'Cell_1244', 'Cell_1245', 'Cell_1246', 'Cell_1247', 'Cell_1248', 'Cell_1249', 'Cell_1250', 'Cell_1251', 'Cell_1252', 'Cell_1253', 'Cell_1254', 'Cell_1255', 'Cell_1256', 'Cell_1257', 'Cell_1258', 'Cell_1259', 'Cell_1260', 'Cell_1261', 'Cell_1262', 'Cell_1263', 'Cell_1264', 'Cell_1265', 'Cell_1266', 'Cell_1267', 'Cell_1268', 'Cell_1269', 'Cell_1270', 'Cell_1271', 'Cell_1272', 'Cell_1273', 'Cell_1274', 'Cell_1275', 'Cell_1276', 'Cell_1277', 'Cell_1278', 'Cell_1279', 'Cell_1280', 'Cell_1281', 'Cell_1282', 'Cell_1283', 'Cell_1284', 'Cell_1285', 'Cell_1286', 'Cell_1287', 'Cell_1288', 'Cell_1289', 'Cell_1290', 'Cell_1291', 'Cell_1292', 'Cell_1293', 'Cell_1294', 'Cell_1295', 'Cell_1296', 'Cell_1297', 'Cell_1298', 'Cell_1299', 'Cell_1300', 'Cell_1301', 'Cell_1302', 'Cell_1303', 'Cell_1304', 'Cell_1305', 'Cell_1306', 'Cell_1307', 'Cell_1308', 'Cell_1309', 'Cell_1310', 'Cell_1311', 'Cell_1312', 'Cell_1313', 'Cell_1314', 'Cell_1315', 'Cell_1316', 'Cell_1317', 'Cell_1318', 'Cell_1319', 'Cell_1320', 'Cell_1321', 'Cell_1322', 'Cell_1323', 'Cell_1324', 'Cell_1325', 'Cell_1326', 'Cell_1327', 'Cell_1328', 'Cell_1329', 'Cell_1330', 'Cell_1331', 'Cell_1332', 'Cell_1333', 'Cell_1334', 'Cell_1335', 'Cell_1336', 'Cell_1337', 'Cell_1338', 'Cell_1339', 'Cell_1340', 'Cell_1341', 'Cell_1342', 'Cell_1343', 'Cell_1344', 'Cell_1345', 'Cell_1346', 'Cell_1347', 'Cell_1348', 'Cell_1349', 'Cell_1350', 'Cell_1351', 'Cell_1352', 'Cell_1353', 'Cell_1354', 'Cell_1355', 'Cell_1356', 'Cell_1357', 'Cell_1358', 'Cell_1359', 'Cell_1360', 'Cell_1361', 'Cell_1362', 'Cell_1363', 'Cell_1364', 'Cell_1365', 'Cell_1366', 'Cell_1367', 'Cell_1368', 'Cell_1369', 'Cell_1370', 'Cell_1371', 'Cell_1372', 'Cell_1373', 'Cell_1374', 'Cell_1375', 'Cell_1376', 'Cell_1377', 'Cell_1378', 'Cell_1379', 'Cell_1380', 'Cell_1381', 'Cell_1382', 'Cell_1383', 'Cell_1384', 'Cell_1385', 'Cell_1386', 'Cell_1387', 'Cell_1388', 'Cell_1389', 'Cell_1390', 'Cell_1391', 'Cell_1392', 'Cell_1393', 'Cell_1394', 'Cell_1395', 'Cell_1396', 'Cell_1397', 'Cell_1398', 'Cell_1399', 'Cell_1400', 'Cell_1401', 'Cell_1402', 'Cell_1403', 'Cell_1404', 'Cell_1405', 'Cell_1406', 'Cell_1407', 'Cell_1408', 'Cell_1409', 'Cell_1410', 'Cell_1411', 'Cell_1412', 'Cell_1413', 'Cell_1414', 'Cell_1415').


title: Brain, BCAS, 28d, rep6

description: Library name: BCAS+PBS6


title: Brain, BCAS+ND-Exos1, 28d, rep4

description: Library name: BCAS+ND-Exos4


title: VEXAS14_PBMC2_TCR

description: 10x Genomics


title: Brain, BCAS, 28d, rep5

description: Library name: BCAS+PBS5


title: T8P7_P1_d11_NORM_2_S8 [Sample 67]

description: Triple hypoxic experiment: Day 11_Passage 1_Normoxic control _replicate 2

value: Day 11_Passage 1_Normoxic control


title: T8P7_P1_d11_NORM_1_S7 [Sample 68]

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


title: VEXAS14_PBMC1_TCR

description: 10x Genomics


title: Brain, BCAS, 28d, rep4

description: Library name: BCAS+PBS4


title: T8P7_P1_d11_NORM_3_S9 [Sample 66]

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


title: Brain, BCAS, 28d, rep2

description: Library name: BCAS+PBS2


title: T8P7_P1_d6_HYP_1_S4 [Sample 65]

description: Triple hypoxic experiment: Day 6_Passage 1_Hypoxic injured Tubuloid _replicate 3


title: Brain, BCAS, 28d, rep3

description: Library name: BCAS+PBS3


title: VEXAS13_PBMC2_TCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_172


title: VEXAS13_PBMC1_TCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_171


title: Brain, BCAS, 28d, rep1

description: Library name: BCAS+PBS1


title: T8P7_P1_d6_HYP_2_S5 [Sample 64]

description: Triple hypoxic experiment: Day 6_Passage 1_Hypoxic injured Tubuloid _replicate 2


title: VEXAS12_PBMC2_TCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_170


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_169


title: T8P7_P1_d6_HYP_3_S6 [Sample 63]

description: Triple hypoxic experiment: Day 6_Passage 1_Hypoxic injured Tubuloid _replicate 1


title: Brain, control, 28d, rep6

description: Library name: Sham+PBS6


title: VEXAS12_PBMC1_TCR

description: 10x Genomics


title: T8P7_P1_d6_NORM_1_S1 [Sample 62]

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

value: Day 6_Passage 1_Normoxic control


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_168


title: VEXAS11_PBMC2_TCR

description: 10x Genomics


title: Brain, control, 28d, rep4

description: Library name: Sham+PBS4


title: Brain, control, 28d, rep5

description: Library name: Sham+PBS5


title: T8P7_P1_d6_NORM_2_S2 [Sample 61]

description: Triple hypoxic experiment: Day 6_Passage 1_Normoxic control _replicate 2


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_166


title: VEXAS11_PBMC1_TCR

description: 10x Genomics


title: VEXAS10_PBMC2_TCR

description: 10x Genomics


title: T8P7_P1_d6_NORM_3_S3 [Sample 60]

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


title: Brain, control, 28d, rep2

description: Library name: Sham+PBS2


title: Brain, control, 28d, rep3

description: Library name: Sham+PBS3


title: T8P7_P2_d11_HYPx1_1_S22 [Sample 59]

description: Triple hypoxic experiment: Day 11_Passage 2_Tubuloid injured 1 time with hypoxia _replicate 3


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_164


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_167


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_165


title: T8P7_P2_d11_HYPx1_2_S23 [Sample 58]

description: Triple hypoxic experiment: Day 11_Passage 2_Tubuloid injured 1 time with hypoxia _replicate 2


title: VEXAS10_PBMC1_TCR

description: 10x Genomics


title: Brain, control, 28d, rep1

description: Library name: Sham+PBS1


title: VEXAS9_PBMC_TCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_163


title: High Fat Diet.027

city: Leiden

first: Robert

last: Kleemann

address: Sylviusweg 71

country: Netherlands

institute: The Netherlands Organisation for Applied Scientific Research

description: Library name: 105170-001-027

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

source_name: Hippocampus

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

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

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

value: Hippocampus

value: HFD

tag: treatmdescript

value: High Fat Diet

tag: animalnr


title: Lung HDM Influenza rep 9

city: Groningen

first: Barbro

middle: N

last: Melgert

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

institute: University of Groningen

description: Library name: 104532-001-070

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

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.

value: Lung

value: Mixed cells from whole lung

value: Wildtype C57Bl6

value: HDM Influenza

tag: batch


title: Healthy7_PBMC_TCR

description: 10x Genomics

value: Healthy

tag: tissue

value: Human peripheral blood

value: PBMCs

value: Male

value: VDJ (TCR)


title: T8P7_P2_d11_HYPx1_3_S24 [Sample 57]

description: Triple hypoxic experiment: Day 11_Passage 2_Tubuloid injured 1 time with hypoxia _replicate 1

value: Adult kidney organoid

value: female

value: Tubuloids derived from d20 kidney organoids

value: Derived from GM04522 fibroblasts (Coriell Inst)

tag: treatment


title: T8P7_P2_d11_HYPx3_1_S28 [Sample 56]

description: Triple hypoxic experiment: Day 11_Passage 2_Tubuloid injured 3 times with hypoxia _replicate 3


title: Healthy4_PBMC_TCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_162

tag: cell line

value: spinal neuron differentiation

value: heterogenous protocol


title: Lung HDM Influenza rep 7

description: Library name: 104532-001-047

tag: cell type


title: T8P7_P2_d11_HYPx3_2_S29 [Sample 55]

description: Triple hypoxic experiment: Day 11_Passage 2_Tubuloid injured 3 times with hypoxia _replicate 2

tag: genotype


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_160

tag: sequencing batch


title: Lung HDM Influenza rep 6

description: Library name: 104532-001-046


title: Healthy2_PBMC_TCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_161


title: T8P7_P2_d11_NORM_1_S16 [Sample 53]

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

value: Day 11_Passage 2_Normoxic control


title: Lung HDM Influenza rep 5

description: Library name: 104532-001-045


title: Healthy1_PBMC_TCR

description: 10x Genomics


title: T8P7_P2_d11_HYPx3_3_S30 [Sample 54]

description: Triple hypoxic experiment: Day 11_Passage 2_Tubuloid injured 3 times with hypoxia _replicate 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_159

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'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: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_158


title: Lung HDM Influenza rep 4

description: Library name: 104532-001-044


title: T8P7_P2_d11_NORM_2_S17 [Sample 52]

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


title: Lung HDM Influenza rep 3

description: Library name: 104532-001-043


title: VEXAS17_PBMC2_BCR

description: 10x Genomics

value: VEXAS

value: VDJ (BCR)


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_157


title: T8P7_P2_d11_NORM_3_S18 [Sample 51]

description: Triple hypoxic experiment: Day 11_Passage 2_Normoxic control _replicate 1


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_156


title: T8P7_P2_d6_HYPx1_1_S19 [Sample 50]

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


title: VEXAS17_PBMC1_BCR

description: 10x Genomics


title: Lung HDM Influenza rep 2

description: Library name: 104532-001-042

value: Lung

value: Mixed cells from whole lung


title: Lung HDM Influenza rep 8

description: Library name: 104532-001-048

value: Wildtype C57Bl6

value: HDM Influenza


title: Healthy3_PBMC_TCR

description: 10x Genomics

value: Healthy

value: Human peripheral blood


title: Lung HDM rep 9

description: Library name: 104532-001-069

value: HDM


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_154


title: VEXAS16_PBMC1_BCR

description: 10x Genomics

value: PBMCs

value: Male


title: T8P7_P2_d6_HYPx3_1_S25 [Sample 47]

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

value: Adult kidney organoid

value: female


title: VEXAS15_PBMC2_BCR

description: 10x Genomics


title: VEXAS16_PBMC2_BCR

description: 10x Genomics


title: T8P7_P2_d6_HYPx1_2_S20 [Sample 49]

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

value: Tubuloids derived from d20 kidney organoids

value: Derived from GM04522 fibroblasts (Coriell Inst)


title: Lung HDM rep 8

description: Library name: 104532-001-040


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_155

value: spinal neuron differentiation

value: heterogenous protocol


title: Lung HDM Influenza rep 1

description: Library name: 104532-001-035


title: VEXAS15_PBMC1_BCR

description: 10x Genomics

value: VEXAS


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_153


title: VEXAS14_PBMC2_BCR

description: 10x Genomics

value: VDJ (BCR)


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_152


title: T8P7_P2_d6_HYPx3_2_S26 [Sample 46]

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


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_151


title: Lung HDM rep 7

description: Library name: 104532-001-039

value: Lung


title: Lung HDM rep 6

description: Library name: 104532-001-038

value: Mixed cells from whole lung


title: T8P7_P2_d6_HYPx3_3_S27 [Sample 45]

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


title: VEXAS13_PBMC2_BCR

description: 10x Genomics


title: Lung HDM rep 5

description: Library name: 104532-001-037

value: Wildtype C57Bl6


title: T8P7_P2_d6_NORM_1_S13 [Sample 44]

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

value: Day 6_Passage 2_Normoxic control


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_149


title: VEXAS14_PBMC1_BCR

description: 10x Genomics


title: Lung HDM rep 4

description: Library name: 104532-001-036


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_150


title: VEXAS13_PBMC1_BCR

description: 10x Genomics


title: T8P7_P2_d6_NORM_2_S14 [Sample 43]

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


title: T8P7_P2_d6_HYPx1_3_S21 [Sample 48]

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


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_148


title: Lung HDM rep 3

description: Library name: 104532-001-041


title: VEXAS12_PBMC2_BCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_147


title: Lung HDM rep 2

description: Library name: 104532-001-034


title: T8P7_P3_d11_HYPx1_1_S40 [Sample 41]

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


title: VEXAS12_PBMC1_BCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_146


title: Lung HDM rep 1

description: Library name: 104532-001-033


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_145


title: T8P7_P3_d11_HYPx1_3_S42 [Sample 39]

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


title: VEXAS11_PBMC2_BCR

description: 10x Genomics


title: VEXAS11_PBMC1_BCR

description: 10x Genomics


title: Lung Influenza rep 8

description: Library name: 104532-001-016

value: Influenza


title: T8P7_P3_d11_HYPx3_1_S46 [Sample 38]

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


title: T8P7_P3_d11_HYPx3_2_S47 [Sample 37]

description: Triple hypoxic experiment: Day 11_Passage 3_Tubuloid injured 3 times with hypoxia _replicate 2


title: VEXAS10_PBMC2_BCR

description: 10x Genomics

value: Human peripheral blood


title: VEXAS10_PBMC1_BCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_142


title: VEXAS9_PBMC_BCR

description: 10x Genomics


title: Diff_D2_Protocol_P1_Line_DF6-9-9T.B_FUS_R495X_Cell_141


title: Lung Influenza rep 5

description: Library name: 104532-001-013


title: T8P7_P2_d6_NORM_3_S15 [Sample 42]

description: Triple hypoxic experiment: Day 6_Passage 2_Normoxic control _replicate 1


title: T8P7_P3_d11_NORM_2_S34 [Sample 35]

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

value: Day 11_Passage 3_Normoxic control


title: Healthy7_PBMC_BCR

description: 10x Genomics

value: Healthy

value: PBMCs


title: Lung Influenza rep 4

description: Library name: 104532-001-012


title: T8P7_P3_d11_HYPx1_2_S41 [Sample 40]

description: Triple hypoxic experiment: Day 11_Passage 3_Tubuloid injured 1 time with hypoxia _replicate 2

value: Adult kidney organoid