title: Gαq ERTU 4

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (version 2.6.0c).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 1.6.2) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (version 1.23.10).
All analyses were performed using the R environment for statistical computing (version 3.6.0).
Assembly: mm10
Supplementary files format and content: counts.txt: 55450 x 20 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: 55450 x 20 matrix of variance-stabilizing-transformed (VST) expression values

growth_protocol: Wild type and cardiac-specific Gαq-overexpressing mice were group housed in the animal facility at Boston University Medical Center. Gαq mice as per Adams et al, PNAS 1998;95:10140-45, as previously decribed by us in Qin et al, Circ Heart Failure 2010;3:306-13.

treatment_protocol: Gαq and wild-type (WT) littermates 4 weeks of age were treated for 16 weeks with or without the SGLT2 inhibitor ertugliflozin (ERTU) formulated in the chow (0.5 mg/g chow).

value: left ventricle

value: FVB/N

value: Gnaq overexpressor (G-alpha-q)

tag: diet

value: ertugliflozin diet (ERTU)


title: SF8628_K27M_rep2

status: Public on Apr 30 2025

type: SRA

city: Austin

first: James

last: Robinson

state: MN

address: 801 16th Ave NE

department: The Hormel Institute

country: USA

institute: University of Minnesota

description:
Library name: ATAC-seq_Sample2
PE42

library_source: genomic

data_processing:
Analysis of ATAC-seq data was very similar to the analysis of ChIP-Seq data. Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations. For differential analysis, reads were counted in all merged peak regions (using Subread), and the replicates for each condition were compared using DESeq2.
Assembly: hg38
Supplementary files format and content: File Format: .bed
Supplementary files format and content: peak files generated using MACS2

molecule: genomic DNA

organism: Homo sapiens

source_name: cell line

growth_protocol: The pediatric glioma cell lines used in this study included SF9427 (RRID: CVCL_E5GC), SF8628 (RRID: CVCL_IT46), SF7761 (RRID: CVCL_IT45), and DIPGXVII/SU-DIPG-XVII (RRID: CVCL_C1MW). Cells were grown in DMEM-high glucose (Sigma Cat. No. D6546), 10% FBS, 2 mM L-Glutamine (EMD Millipore Cat. No. TMS-002-C), 1x Amphotericin, and 1x Penicillin-Streptomycin. Cell lines were cultured under adherent conditions at 37°C and 5% CO₂.

extract_protocol:
Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay.
The cells were then thawed in a 37oC water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al. 2013), with some modifications based on (Corces et al. 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NovaSeq 6000 sequencer (Illumina).

treatment_protocol: To generate EZH1/2 KO (PRC2 loss); EZH1 and EZH2 CRISPR gRNAs were designed using GUIDES software (http://guides.sanjanalab.org/) (35). gRNAs were cloned into the BsmBI digested linear Lenti-Cas9-gRNA-GFP vector (Addgene #124770) as described earlier (Giuliano et al. 2019). Plasmids were propagated by transforming into Stbl3 E. coli. Further, HEK293T cells were transfected with Lenti-Cas9-gRNA-GFP along with packaging plasmids (pMD.2 and PAX) using the calcium phosphate method (36). 24 hrs of post transfection media was changed and virus containing supernatant was collected at 48 to 72 hours post-transfection. Lentivirus were filtered through a 0.45 μm syringe and transduced the target cells with 4-10 μg/mL polybrene. Culture media was changed after 24 hrs of transduction. GFP expressed target cells were sorted and single cell colonies were picked and expanded. The knockout clones were confirmed by western blot and sanger sequencing. We previously created of SF8628 H3.3 WT revertant clones (34) using CRISPR/HDR Cas9 editing to generate SF8628 H3.3 WT revertant cells. A custom gRNA targeted the K27M region of H3F3A. This complex, along with recombinant Cas9, H3F3A WT ssDNA, and a GFP-H3F3A WT HDR repair plasmid, was introduced into cells via electroporation. Colonies were screened for GFP expression using an IncuCyte S3 system and verified by Sanger sequencing and allele-specific PCR with agarose gel analysis.

tag: cell line

tag: cell type

value: Diffuse midline glioma

tag: genotype


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1072

city: Stockholm

first: Eva

last: Hedlund

address: Svante Arrhenius v. 16C

department: Department of Biochemistry and Biophysics

country: Sweden

institute: Stockholm University

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'Cell_1143', 'Cell_1144', 'Cell_1145', 'Cell_1146', 'Cell_1147', 'Cell_1148', 'Cell_1149', 'Cell_1150', 'Cell_1151', 'Cell_1152', 'Cell_1153', 'Cell_1154', 'Cell_1155', 'Cell_1156', 'Cell_1157', 'Cell_1158', 'Cell_1159', 'Cell_1160', 'Cell_1161', 'Cell_1162', 'Cell_1163', 'Cell_1164', 'Cell_1165', 'Cell_1166', 'Cell_1167', 'Cell_1168', 'Cell_1169', 'Cell_1170', 'Cell_1171', 'Cell_1172', 'Cell_1173', 'Cell_1174', 'Cell_1175', 'Cell_1176', 'Cell_1177', 'Cell_1178', 'Cell_1179', 'Cell_1180', 'Cell_1181', 'Cell_1182', 'Cell_1183', 'Cell_1184', 'Cell_1185', 'Cell_1186', 'Cell_1187', 'Cell_1188', 'Cell_1189', 'Cell_1190', 'Cell_1191', 'Cell_1192', 'Cell_1193', 'Cell_1194', 'Cell_1195', 'Cell_1196', 'Cell_1197', 'Cell_1198', 'Cell_1199', 'Cell_1200', 'Cell_1201', 'Cell_1202', 'Cell_1203', 'Cell_1204', 'Cell_1205', 'Cell_1206', 'Cell_1207', 'Cell_1208', 'Cell_1209', 'Cell_1210', 'Cell_1211', 'Cell_1212', 'Cell_1213', 'Cell_1214', 'Cell_1215', 'Cell_1216', 'Cell_1217', 'Cell_1218', 'Cell_1219', 'Cell_1220', 'Cell_1221', 'Cell_1222', 'Cell_1223', 'Cell_1224', 'Cell_1225', 'Cell_1226', 'Cell_1227', 'Cell_1228', 'Cell_1229', 'Cell_1230', 'Cell_1231', 'Cell_1232', 'Cell_1233', 'Cell_1234', 'Cell_1235', 'Cell_1236', 'Cell_1237', 'Cell_1238', 'Cell_1239', 'Cell_1240', 'Cell_1241', 'Cell_1242', 'Cell_1243', 'Cell_1244', 'Cell_1245', 'Cell_1246', 'Cell_1247', 'Cell_1248', 'Cell_1249', 'Cell_1250', 'Cell_1251', 'Cell_1252', 'Cell_1253', 'Cell_1254', 'Cell_1255', 'Cell_1256', 'Cell_1257', 'Cell_1258', 'Cell_1259', 'Cell_1260', 'Cell_1261', 'Cell_1262', 'Cell_1263', 'Cell_1264', 'Cell_1265', 'Cell_1266', 'Cell_1267', 'Cell_1268', 'Cell_1269', 'Cell_1270', 'Cell_1271', 'Cell_1272', 'Cell_1273', 'Cell_1274', 'Cell_1275', 'Cell_1276', 'Cell_1277', 'Cell_1278', 'Cell_1279', 'Cell_1280', 'Cell_1281', 'Cell_1282', 'Cell_1283', 'Cell_1284', 'Cell_1285', 'Cell_1286', 'Cell_1287', 'Cell_1288', 'Cell_1289', 'Cell_1290', 'Cell_1291', 'Cell_1292', 'Cell_1293', 'Cell_1294', 'Cell_1295', 'Cell_1296', 'Cell_1297', 'Cell_1298', 'Cell_1299', 'Cell_1300', 'Cell_1301', 'Cell_1302', 'Cell_1303', 'Cell_1304', 'Cell_1305', 'Cell_1306', 'Cell_1307', 'Cell_1308', 'Cell_1309', 'Cell_1310', 'Cell_1311', 'Cell_1312', 'Cell_1313', 'Cell_1314', 'Cell_1315', 'Cell_1316', 'Cell_1317', 'Cell_1318', 'Cell_1319', 'Cell_1320', 'Cell_1321', 'Cell_1322', 'Cell_1323', 'Cell_1324', 'Cell_1325', 'Cell_1326', 'Cell_1327', 'Cell_1328', 'Cell_1329', 'Cell_1330', 'Cell_1331', 'Cell_1332', 'Cell_1333', 'Cell_1334', 'Cell_1335', 'Cell_1336', 'Cell_1337', 'Cell_1338', 'Cell_1339', 'Cell_1340', 'Cell_1341', 'Cell_1342', 'Cell_1343', 'Cell_1344', 'Cell_1345', 'Cell_1346', 'Cell_1347', 'Cell_1348', 'Cell_1349', 'Cell_1350', 'Cell_1351', 'Cell_1352', 'Cell_1353', 'Cell_1354', 'Cell_1355', 'Cell_1356', 'Cell_1357', 'Cell_1358', 'Cell_1359', 'Cell_1360', 'Cell_1361', 'Cell_1362', 'Cell_1363', 'Cell_1364', 'Cell_1365', 'Cell_1366', 'Cell_1367', 'Cell_1368', 'Cell_1369', 'Cell_1370', 'Cell_1371', 'Cell_1372', 'Cell_1373', 'Cell_1374', 'Cell_1375', 'Cell_1376', 'Cell_1377', 'Cell_1378', 'Cell_1379', 'Cell_1380', 'Cell_1381', 'Cell_1382', 'Cell_1383', 'Cell_1384', 'Cell_1385', 'Cell_1386', 'Cell_1387', 'Cell_1388', 'Cell_1389', 'Cell_1390', 'Cell_1391', 'Cell_1392', 'Cell_1393', 'Cell_1394', 'Cell_1395', 'Cell_1396', 'Cell_1397', 'Cell_1398', 'Cell_1399', 'Cell_1400', 'Cell_1401', 'Cell_1402', 'Cell_1403', 'Cell_1404', 'Cell_1405', 'Cell_1406', 'Cell_1407', 'Cell_1408', 'Cell_1409', 'Cell_1410', 'Cell_1411', 'Cell_1412', 'Cell_1413', 'Cell_1414', 'Cell_1415').

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 bcl2fastq_2.17 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.

value: spinal neuron differentiation

tag: treatment

value: heterogenous protocol

tag: sequencing batch


title: SF8628_K27M_rep1

description:
Library name: ATAC-seq_Sample1
PE42


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1070


title: Gαq ERTU 2

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

source_name: left ventricle

extract_protocol: RNA was isolated from frozen powderized left ventricles and extracted with the Qiagen RNeasy Plus Universal mini kit with an on-column DNAse treatment. The Boston University Microarray and Sequencing Resource Core Facility performed RNA quantity and quality measurements, library preparation, and RNA sequencing. RNA integrity was confirmed via RNA Pico assay for total RNA Bioanalyzer QC analysis (Agilent).

tag: tissue

tag: strain


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1071


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1069


title: Gαq ERTU 3


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1068


title: kasumi-1 cells, (treated 3j-2)

city: Delhi

first: Jaidev

last: Sharma

state: Delhi

address: Indraprastha Institute of Information Technology, Okhla Industrial Estate, Phase III, near Govind Puri Metro Station, New Delhi, Delhi 110020

department: Computational Biology

country: India

description:
Library name: Treated 3j-2
column name in raw_counts_All_Samples.txt: Treated_3j-2

data_processing:
Sequence reads were trimmed by using Fastp
Alignment was performed by using HISAT2
FeatureCount was used to generate the count matrix.
Assembly: hg38
Supplementary files format and content: tab delimited text files includes Raw values for each sample

source_name: Leukemia cell line Kasumi-1

growth_protocol: Kasumi- 1 (ATCC #CRL-2724) cells were routinely cultured in RPMI 1640 (Gibco) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37 ˚C and passaged every 3-4 days. All the cells were maintained at 37 ˚C in a 5% CO2 humidified incubator.

extract_protocol:
RNA was harvested using Qiagen RNeasy kit . 1ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using KAPA RNA HyperPrep Kit with RiboErase (Roche, 08098140702) as per manufacturer's instructions.

treatment_protocol: Kasumi-1 cells were treated(3j) for 24 hr and also untreated control was maintained for the same.

tag: time

value: 24 hr

value: Leukemia cell line Kasumi-1

value: myeloblast cells

value: Treated 3j-2


title: Kasumi-1 cells, (Untreated-1)

institute: Indraprastha Institute of Information Technology

description:
Library name: Control 1
column name in raw_counts_All_Samples.txt :Control_1

value: WT


title: Kasumi-1 cells, (Untreated-2)

description:
Library name: Control 2
column name in raw_counts_All_Samples.txt: Control_2


title: WT ERTU 4

value: wild-type (WT)


title: WT ERTU 3


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1067


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1066


title: kasumi-1 cells, (treated 3j-1)

description:
Library name: Treated 3j-1
column name in raw_counts_All_Samples.txt: Treated_3j-1

value: Treated 3j-1


title: WT ERTU 2


title: Normal endometrium

city: 广州市

first: bo

last: Yao

state: 广东省

address: 广州市天河区黄埔大道西601号暨南大学医学楼

country: China

institute: 暨南大学

description: Library name: Sample 1

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipelineto generate FASTQ files
Assembly: GRCh38
Supplementary files format and content: X2_barcodes.tsv.gz；X3_barcodes.tsv.gz；X4_barcodes.tsv.gz:list of spatial barcodes
Supplementary files format and content: X2_matrix.mtx.gz;X3_matrix.mtx.gz;X4_matrix.mtx.gz:list of spatial matrix
Supplementary files format and content: X2_features.tsv.gz;X3_features.tsv.gz; X4_features.tsv.gz:list of spatial features
Library strategy: Spatial Transcriptomics

source_name: Normal endometrium

extract_protocol:
Fresh frozen tissue were OCT embedded, and 5um frozen sections were cut with cryostat
Spatial transcriptome sequencing libraries were prepared with 10xGenomics VisiumSpatial Gene Expression Slides & Reagent kit according to manufacturer'sconstruction

value: Normal endometrium


title: Sample #29- Tumor biopsy of responder patient to BCG treatment

city: Jerusalem

first: Francesca

last: Levi-Schaffer

address: Kalman Ya'akov Man Street

country: Israel

institute: The Hebrew University of Jerusalem

description: Library name: VY29

data_processing:
The BCL binary files were converted into FASTQ utilizing illumina package bcl2fastq.
Quality trimming of the reads was done at the 3’ and 5' ends using cutadapt (v2.10) with the quality cutoff 32.  The remaining poly-G sequences were removed from the 3' ends, then adapter sequences (Truseq adapters – forward and reverse) were removed from the 3' ends as well. Following that, poly-A (from the 3' end of R2) and poly-T (from the 5' end of R1) sequences were removed. All these were removed using a minimal overlap of 1 (-O parameter), allowing for read wildcards, and filtering out reads that became shorter than 15 nt (-m parameter). Following that, low quality reads were filtered out using fastq_quality_filter, with a quality threshold of 20 at 90 percent or more of the read's positions.
The processed fastq files were aligned to the Homo sapiens transcriptome and genome using TopHat (v2.1.1). The genome version was GRCh38 with annotations from Ensembl release 99.  Strand information was taken into consideration (--library-type fr-firststrand). Alignment allowed up to 10 mismatches per read, a gap of 5, and a total edit distance of 15.  Paired reads were aligned as such, and reads whose mate was filtered out were aligned as unpaired. The mean distance between read pairs (mate-inner-dist  parameter) was set to -139, and the standard deviation of this distance (--mate-std-dev parameter) was set to 50, based upon QC performed by Macrogen (of Tapestation).
Counting was done using htseq-count (0.12.4). Strand information was taken into consideration (--stranded=’reverse’). An annotation file that lacked information for genes of type IG, TR, Artifact, miRNA, Mt_rRNA, Mt_tRNA, ncRNA, piRNA, pre_miRNA, rRNA, ribozyme, sRNA, scRNA, scaRNA, siRNA, snRNA, snoRNA, tRNA and vaultRNA was used.
At an initial filtering stage, genes that did not have at least 1 count per million in at least 3 samples were filtered out.  Normalization was done with DESeq2 (1.24.0). Differential expression was also calculated in DESeq2 with default parameters (excepting for not using independentFiltering algorithm). Significance threshold was taken as padj<0.1.
Assembly: GRCh38
Supplementary files format and content: An excel file with raw counts, normalized counts and differential expression results.

source_name: Bladder

extract_protocol:
RNA was harvested using RNeasy® Mini Kit, Mineral Oil (Cat. No. M5904) following manufacturer's protocols. . Minimum of 5ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using truseq RNA Library Prep Kit following manufacturer's protocols.

value: Bladder

value: Superficial fragments of non-invasive high-grade papillary urothelial carcinoma. Urothelial carcinoma in situ, involving Von Brunn's nests. High-grade papillary urothelial carcinoma invading the lamina propria, Angiolymphatic invasion seen. High-grade urothelial carcinoma invading the lamina propria/prostatic stroma

value: BCG


title: Sample #28- Tumor biopsy of non responder patient to BCG treatment

description: Library name: VY28

value: Papillary urothelial carcinoma, high grade, with inverted growth pattern. Focal supeficial invasion into the lamina propria


title: Sample #21- Tumor biopsy of responder patient to BCG treatment

description: Library name: VY21

value: Papillary urothelial carcinoma of bladder high grade, with invasion into lamina propria and suspicious vascular invasion. There is focal inverted growth. There is focal tumor necrosis. The detrusor muscle is free of tumor


title: WT ERTU 1

value: left ventricle

value: FVB/N

value: ertugliflozin diet (ERTU)


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1064

value: spinal neuron differentiation

value: heterogenous protocol


title: endometriosis

address: 广州市天河区黄埔大道西601号暨南大学医学楼

description: Library name: Sample 2

source_name: endometriosis

value: endometriosis


title: Gαq CD 5

value: Gnaq overexpressor (G-alpha-q)

value: control diet (CD)


title: Sample #17- Tumor biopsy of non responder patient to BCG treatment

description: Library name: VY17

value: Papillary transitional cell carcinoma, high grade (WHO grade 3) focal invasion into the lamina propria is found


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1063


title: Gαq CD 4


title: Gαq ERTU 1


title: Sample #16- Tumor biopsy of non responder patient to BCG treatment

description: Library name: VY16

value: Superficial fragments of transitional cell carcinoma, papillary high grade (WHO grade 3)


title: Sample #15- Tumor biopsy of responder patient to BCG treatment

description: Library name: VY15

value: Fragments of papillary transitional cell carcinoma, high grade (WHO grade 3).


title: WT ERTU 5

value: wild-type (WT)


title: Sample #10- Tumor biopsy of responder patient to BCG treatment

description: Library name: VY10

value: Bladder

value: Urothelial carcinoma, high grade, with lamina propria invasion. Background focal urothelial carcinoma in situ is seen.


title: Sample #7-Tumor biopsy of non responder patient to BCG treatment

description: Library name: VY7

value: Non-invasive high-grade papillary urothelial carcinoma

value: BCG


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1061


title: Gαq CD 2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1060


title: Gαq CD 3


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1062


title: Gαq CD 1


title: activated A549 cells, OC3

city: Shanghai

first: yuzhen

last: Du

address: West Huanhu Road 3, No.222

department: Laboratory Medicine

institute: Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

description:
Library name: sample6
A_OC_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

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

value: WT

value: activated by osteoclast conditional medium


title: endometriosis associated ovarian cancer

address: 广州市天河区黄埔大道西601号暨南大学医学楼

description: Library name: Sample 3

source_name: endometriosis associated ovarian cancer

value: endometriosis associated ovarian cancer


title: Sample #6-Tumor biopsy of responder patient to BCG treatment

description: Library name: VY6

value: Non-invasive high grade papillary urothelial carcinoma. Urothelial carcinoma in situ.


title: Sample #4- Tumor biopsy of responder patient to BCG treatment

description: Library name: VY4

value: Non-invasive high grade papillary urothelial carcinoma Multifocal urothelial carcinoma in situ. Muscularis propria is not identified


title: activated A549 cells, OC2

description:
Library name: sample5
A_OC_2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1065

value: spinal neuron differentiation

value: heterogenous protocol


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1059


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1058


title: dormant A549 cells, SF3

description:
Library name: sample3
A_SF_3

value: inducing dormancy


title: WT CD 4

value: left ventricle

value: FVB/N

value: control diet (CD)


title: WT CD 3


title: Sample #19- Tumor biopsy of non responder patient to BCG treatment

description: Library name: VY19

value: Papillary transitional cell carcinoma of urinary bladder, high grade (WHO grade 3) with extensive inverted growth, non-invasive.


title: dormant A549 cells, SF2

description:
Library name: sample2
A_SF_2


title: dormant A549 cells, SF1

description:
Library name: sample1
A_SF_1


title: WT CD 2

value: wild-type (WT)


title: H929 shRBM39 3

first: Hua

last: Yan

address: 197 Ruijin 2nd Road

institute: Ruijin Hospital

description: Library name: Sample 6

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

extract_protocol:
RNA was harvested using TRIzol regent. Total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were performed using SMARTER mRNA-Seq Library Prep Kit following manufacture's protocols.

value: plasma cell


title: H929 shRBM39 2

description: Library name: Sample 5


title: WT CD 1


title: H929 shRBM39 1

description: Library name: Sample 4


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1056


title: H929 scr 3

description: Library name: Sample 3


title: H929 scr 2

description: Library name: Sample 2


title: QWBMP-3

city: Lexington

first: Qingding

last: Wang

address: 760 Press Ave

institute: University of Kentucky

data_processing:
The adaptors and low-quality sequences were trimmed from the miRNA-seq reads using bbmap (v38.73), discarding reads with length less than 15 nucleotides and longer than 27 nucleotides.
For quantification of mature miRNAs documented in miRBase, sequencing reads were first mapped to the reference genome using the mapper.pl script in the miRDeep2 (v0.1.3) package. The quantifier.pl script was used with default settings to quantify the number of reads mapped to mature miRNAs.
The R package EdgeR was used to identify differentially expressed genes between different experimental contrasts.
Assembly: mirbase mmu version 22
Supplementary files format and content: miRNA_count_mat.xlsx: miRNA count matrix

source_name: Intestine

growth_protocol: Mouse intestinal crypts were isolated and cultured for growing organoids in IntestiCult™ Organoid Growth Medium (Mouse, stem cell tech Catalog # 06005).

extract_protocol:
RNA was isolated using a mirVana miRNA Isolation Kit (Thermo Fisher Scientific).
To construct the library, NEBNext Small RNA Sample Library Preparation kit (NEB, Ipswich, MA) was used.

treatment_protocol: The organoids were treated with BMP4 (0.5 µg/ml) for 4 days.

value: Intestine

value: Intestinal epithelium


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1055


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1054


title: H929 scr 1

description: Library name: Sample 1


title: HCC827,shCEACAM6

city: Hsinchu

first: Ming-Yi

last: Zheng

address: College of Life Science, No. 101, Section 2, Kuang Fu Road

department: college of life science and medicine

country: Taiwan

institute: NATIONAL TSING HUA UNIVERSITY

description:
Library name: SAMPLE2
HCC_CEA6KD

data_processing:
The raw data, generated by high-throughput sequencing (Illumina NovaSeq 6000 platform), were initially converted into raw sequenced reads using CASAVA base calling and were stored in FASTQ format. To ensure data quality, FastQC and MultiQC were used to perform quality checks on the fastq files. Subsequently, Trimmomatic was employed to filter out low-quality reads, trim adapter sequences, and eliminate poor-quality bases from the obtained raw paired-end reads. The resulting high-quality data, referred to as "clean reads", was used for downstream analysis. The read pairs from each sample were then mapped to the corresponding reference genome (H. sapiens, GRCh38) using HISAT2, and the number of reads mapped to individual genes was counted using featureCounts .
Assembly: hsa_GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA extraction by Trizol. RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, no gDNA contamination.
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.

value: CEACAM6 knockdown


title: activated A549 cells, OC1

description:
Library name: sample4
A_OC_1

value: WT


title: QWBMP-2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1053


title: HCC827,SC

description:
Library name: SAMPLE1
HCC_SC


title: MCF7, paclitaxel-resistant, 3

city: Daejeon

first: Hyun Uk

last: Kim

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

description: Library name: PR_3

data_processing:
FastQC (version 0.11.7) was used to access quality of Illumina paired-end reads.
Trimmomatic (version 0.38) was used to trim adapter sequences and low-quality bases from the reads (LEADING=3, TRAILING=3, SLIDINGWINDOW: sindowSize=4; requiredQuality=15, MINLEN=36).
HISAT2 (version 2.1.0) was used to align trimmed reads on human genome (GRCh37).
StringTie (version 2.1.3b) was used to estimate raw counts and FPKMs of genes (-e).
Assembly: GRCh37
Supplementary files format and content: tab-seperated text file includes raw counts for each sample.
Supplementary files format and content: csv files include FPKM values for each sample.

source_name: Breast

growth_protocol: The MCF7, doxorubicin-resistant MCF7(MCF7/DXR), and paclitaxel-resistant MCF7(MCF7/PR) cells were cultured in high‐glucose Dulbecco's modified Eagle medium (Welgene) with 10% fetal bovine serum (Welgene) and 1% penicillin-streptomycin (Welgene) at 37 °C in a humidified incubator with 5% CO2. To preserve their drug-resistant properties, MCF7/DXR and MCF7/PR cells were maintained in the medium containing 0.345 μM doxorubicin and 0.1 μM paclitaxel, respectively.

extract_protocol:
Cultured cells were lysed with 1 ml TRIzol (Ambion), and after adding 200 µl chloroform, the samples were vortexed and centrifuged at 12000 rpm for 15 min at 4 °C. The supernatant was mixed with 30 µl NaOAc, 0.5 µl glycoblue, and 500 µl IPA, then incubated overnight at -20 °C. The pellet was collected by centrifugation at 15000 rpm for 1 h at 4 °C, washed twice with 75% EtOH, dried, and dissolved in 42 µl TDW. For DNA removal, 2 µl DNase I (Takara), 1 µl RNase inhibitor, and 5 µl DNase buffer were added and incubated at 37 °C for 30 min. The sample was purified with 150 µl TDW and 200 µl acid phenol, followed by ethanol precipitation overnight. The pellet was washed with 75% EtOH, dried, and dissolved in TDW.
RNA libraries for RNA-seq was prepared using Illumina's TruSeq stranded mRNA LT Sample Prep Kit following the manufacturer’s protocols.

value: Breast

value: paclitaxel-resistant


title: MCF7, doxorubicin-resistant, 3

description: Library name: DXR_3

value: doxorubicin-resistant


title: MCF7, paclitaxel-resistant, 2

description: Library name: PR_2


title: QWBMP-1


title: MCF7, paclitaxel-resistant, 1

description: Library name: PR_1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1051


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1052


title: MCF7, doxorubicin-resistant, 2

description: Library name: DXR_2


title: MCF7, doxorubicin-resistant, 1

description: Library name: DXR_1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1057


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1050


title: MCF7, parental, 3

description: Library name: MCF7_3

value: sensitive


title: QWcon-1

value: PBS


title: QWcon-2


title: MCF7, parental, 2

description: Library name: MCF7_2


title: iPSC-VSMC NNKO Line HE56 (bio rep 2)

city: Madison

first: Valentina

last: Lo Sardo

state: Wisconsin

address: 1111 Highland avenue

department: Cell and Regenerative Biology

institute: University of Wisconsin-Madison

description:
Library name: HE56
Terminally differentiated (day 17) VSMC

data_processing:
Data was demultiplexed with 10x Genomic's Cell Ranger mkfastq command wrapped around Illumina's bcl2fastq and aligned, filtered, barcodes counted, UMI counted, and gene expression estimated with the Cell ranger pipeline.
Quality control, normalization, PCA, and clustering were performed with Seurat V4.3.0. See 'Methods' section for details.
Assembly: NCBI:GCA_000001405.27
Supplementary files format and content: .rds file is a Seurat object containing the cleaned, normalized, and clustered data for all samples. Sample and genotype labels are preserved to allow for subsetting.

source_name: cultured cells

growth_protocol: iPSC were differentiated to VSMC according to Cheung et al. 2014

extract_protocol:
RNA was harvested using a 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kit v3.1
Libraries constructed using a 10x Genomics Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 and a single-cell G Chip Kit (Lot# 161273)

value: cultured cells

value: iPSC-derived VSMC

value: 9p21.3 CAD risk locus homozygous risk cells


title: Huh7.5 infected with poliovirus for 6h, biological replicate 2

city: CHAPEL HILL

first: Jason

last: Whitmire

state: NC

address: 5062 Genetic Medicine Bldg

institute: UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL

description: Library name: PV-2

data_processing:
Map the reads to the reference transcriptome using Minimap2
Determine the length of the poly(A) tails using Nanopolish
Assembly: hg38, HAV/18f, PV/Mahoney
Supplementary files format and content: tsv files of the poly(A) tail length of each transcript in each sample

extract_protocol:
RNeasy column (Qiagen)
in house protocol (PMID 37085578)

tag: agent

value: poliovirus


title: Huh7.5 infected with poliovirus for 6h, biological replicate 1

description: Library name: PV-1


title: iPSC-VSMC NNKO Line HE50 (bio rep 1)

description:
Library name: HE50
Terminally differentiated (day 17) VSMC


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1049

value: spinal neuron differentiation

value: heterogenous protocol


title: iPSC-VSMC NN Line HE17 (bio rep 2)

description:
Library name: HE17
Terminally differentiated (day 17) VSMC


title: Huh7.5 infected with HAV, treated with RG7834 control, experiment 2

description: Library name: RG7834-2

value: HAV

value: RG7834 control


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1047


title: iPSC-VSMC NN Line HE14 (bio rep 1)

description:
Library name: HE14
Terminally differentiated (day 17) VSMC


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1048


title: iPSC-VSMC RRKO Line CWB46 (bio rep 2)

description:
Library name: cwb46
Terminally differentiated (day 17) VSMC


title: QWcon-3

value: Intestine


title: iPSC-VSMC RR Line C2-3 (bio rep 2)

description:
Library name: c2_3
Terminally differentiated (day 17) VSMC


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1046


title: Huh7.5 infected with HAV, treated with DMSO control, experiment 2

description: Library name: DMSO-2

value: DMSO


title: iPSC-VSMC RR Line C1-2 (bio rep 1)

description:
Library name: c1_2
Terminally differentiated (day 17) VSMC


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1045


title: iPSC-VSMC RRKO Line C1-9 (bio rep 1)

description:
Library name: c1_9
Terminally differentiated (day 17) VSMC


title: MCS, MMC+/GDF+, rep4

city: Moscow

first: Liya

last: Kondratyeva

address: Ulitsa Miklukho Maklaya, 16/10

country: Russia

institute: Institute of bioorganic chemistry of the Russian Academy of Sciences

description: Library name: 16_S40

data_processing:
The raw reads were mapped on the murine reference genome (GRCh38/hg38) using HISAT2 v2.2.1
The featureCounts tool (v.2.0.1) was used for counting reads to GENCODE release V38 annotated genes.
Assembly: hg38
Supplementary files format and content: .txt format, matrix table with featureCounts read counts

source_name: Adipose

growth_protocol: Experiments were conducted using immortalized standard line of MSCs ASC52telo (ATCC® SCRC-4000™). The cells were expanded in α-MEM (Gibco, Life Technologies, Carlsbad, CA, USA) with 50 U/mL penicillin-streptomycin (PanEco, Moscow, Russia), and 10% fetal bovine serum (FBS) (HyClone, Logan, UT, USA) at standard conditions (5% CO2, 37 °C).

extract_protocol:
Total RNA was isolated from MSCs by phenol-chloroform extraction using the ExtractRNA reagent (Evrogen, Russia), followed by treatment with DNase I. mRNA-enriched fractions were obtained using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England Biolabs, Ipswich, MA, USA) with magnetic beads.
For cDNA library construction, the "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB) was used in conjunction with the "NEBNext Multiplex Oligos for Illumina"

treatment_protocol: Mitomycin C (MmC) was used to obtain stress-induced senescent MSC. A Petri dish was seeded with 250,000 cells. Cells (90–100% confluence) were incubated in complete growth medium containing 1.5 μg/mL MmC (SigmaeAldrich, St. Louis, MO, USA) for 18 h, and then washed twice with PBS, and cultured. During the following 10 days after MmC treatment, recombinant GDF11 protein (ab218080, Abcam, Waltham, MA, USA) was added to both senescent and intact MSCs to final concentariton 10 ng/mL. MSC without MmC or without GDF11 served as the control.

value: Adipose

value: MSCs

value: wt

value: +MMC +GDF

tag: batch


title: Huh7.5 infected with HAV, treated with RG7834 control, experiment 1

description: Library name: RG7834-1


title: MCF7, parental, 1

description: Library name: MCF7_1

value: Breast


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1044


title: MCS, MMC-/GDF+, rep4

description: Library name: 14_S31


title: MCS, MMC-/GDF-, rep4

description: Library name: 13_S26

value: no treatment


title: Huh7.5 infected with HAV, treated with DMSO control, experiment 1

description: Library name: DMSO-1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1043


title: MCS, MMC+/GDF+, rep3

description: Library name: 12_S20


title: iPSC_organoid_control d25_R3

city: Clayton

first: Nitika

last: Kandhari

state: VIC

address: Wellington Road

country: Australia

institute: Monash University

description: raw-counts.csv

data_processing:
Raw fastq files have been analysed with nfcore/RNAseq pipeline using STAR with STAR aligner option (Dobin et al., 2013) mapping raw reads to the mus musculus GRCm38-mm10 (GCF_000001635.20, NCBI) reference genome, reads were quantified with salmon.
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
Supplementary files format and content: raw gene counts, text file, comma 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: iPSC_kidney organoid

tag: gender

value: female

value: Kidney


title: MCS, MMC+/GDF-, rep4

description: Library name: 15_S36

value: +MMC


title: MCS, MMC+/GDF-, rep3

description: Library name: 11_S14


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1042


title: MCS, MMC-/GDF-, rep3

description: Library name: 9_S2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1041


title: iPSC_organoid_control d25_R1

description: raw-counts.csv


title: MCS, MMC+/GDF+, rep2

description: Library name: 8_S39


title: MCS, MMC+/GDF-, rep2

description: Library name: 7_S35


title: iPSC_organoid_control d25_R2

description: raw-counts.csv


title: iPSC_organoid_control d20_R3

description: raw-counts.csv


title: MCS, MMC-/GDF+, rep2

description: Library name: 6_S30


title: MCS, MMC-/GDF-, rep2

description: Library name: 5_S25


title: iPSC_organoid_control d20_R2

description: raw-counts.csv


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1038


title: MCS, MMC+/GDF+, rep1

description: Library name: 4_S19


title: MCS, MMC+/GDF-, rep1

description: Library name: 3_S13


title: iPSC_organoid_control d20_R1

description: raw-counts.csv


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1039


title: MCS, MMC-/GDF+, rep1

description: Library name: 2_S7


title: MCS, MMC-/GDF-, rep1

description: Library name: 1_S1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1037


title: Adult Kidney Tissue donor 3

description: raw-counts.csv

source_name: Nephrectomy - male

value: Adult Kidney_Nephrectomy

value: male


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1036

value: spinal neuron differentiation

value: heterogenous protocol


title: Adult Kidney Tissue donor 2

description: raw-counts.csv


title: Aging_Tfh_bulk RNA-seq 3

first: Cody

last: Nelson

address: 221 Longwood Ave

institute: Brigham and Women's Hospital

description:
Library name: Aging_Tfh3
Aging_bulkRNAseq

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

source_name: CD4 T cells

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

value: CD4 T cells

value: Human CD4 T cell

value: Blood

tag: sample group


title: Aging_Tfh_bulk RNA-seq 2

description:
Library name: Aging_Tfh2
Aging_bulkRNAseq


title: Aging_Tfh_bulk RNA-seq 1

description:
Library name: Aging_Tfh1
Aging_bulkRNAseq


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1035


title: Control_Tfh_bulk RNA-seq 3

description:
Library name: Control_Tfh3
Aging_bulkRNAseq


title: MCS, MMC-/GDF+, rep3

description: Library name: 10_S8

value: Adipose


title: Adult Kidney Tissue donor 1

description: raw-counts.csv

source_name: Nephrectomy - female


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1040

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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title: Control_Tfh_bulk RNA-seq 2

description:
Library name: Control_Tfh2
Aging_bulkRNAseq


title: Control_Tfh_bulk RNA-seq 1

description:
Library name: Control_Tfh1
Aging_bulkRNAseq


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_FUS_P525L_homozygous_Cell_1034


title: BRI-2229_TCR_Library

description: Library name: BRI-2229


title: Human Fetal tubuloid 399P1

description: raw-counts.csv

source_name: Human Foetal Kidney- Female

value: Kidney Tubuloid


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1033

value: Control


title: BRI-2227_GEX_HTO_Library

description: Library name: BRI-2227_Hashing


title: Human Fetal tubuloid 389P1

description: raw-counts.csv


title: BRI-2077_TCR_Library

description: Library name: BRI-2077


title: Human Fetal tubuloid 369P2

description: raw-counts.csv


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1032


title: BRI-1739_TCR_Library

description: Library name: BRI-1739


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1031


title: slide4_ptN_tubules_MCD

city: Seattle

first: Shreeram

last: Akilesh

state: WA

address: 1959 NE Pacific St, Box 356100

department: Laboratory Medicine and Pathology

institute: University of Washington

library_source: other

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

molecule: other

source_name: Kidney

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

tag: donor

value: N

tag: geomx dsp_probe_set

value: Human NGS Whole Transcriptome Atlas RNA_1.0

tag: disease

value: MCD

tag: slide number

tag: roi histology

value: tubules


title: BRI-1737_GEX_HTO_Library

description: Library name: BRI-1737_Hashing

tag: cell line


title: BRI-2075_GEX_HTO_Library

description: Library name: BRI-2075_Hashing

tag: cell type


title: hiPSCNeurons_ChIP_IgG_rep2

city: Bethesda

first: Pedro

middle: P

last: Rocha

state: Maryland

address: 6 Center Drive Building 6B 2B220

department: NICHD

institute: National Institutes of Health

data_processing:
Analysis of ChIPseq data was done as described in (Chakraborty et al., 2023). Reads were aligned with Bowtie2 (version 2.5.3) (Langmead and Salzberg, 2012) to the hg38 genome, with the following parameters (-N 1 --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 -x). Reads that aligned to the hg38 encode blacklist regions were removed using Samtools 1.19 (Li et al., 2009). Duplicate reads were removed with picard (version 3.2.0 broadinstitute.github.io/picard/). Samples that were sequenced in multiple runs were merged before duplicate removal. Peak calling was done using MACS (version 2.2.7.1) (Zhang et al., 2008) after merging biological replicates and using IgG as a control. For visualization, biological replicate signal was merged into a single bigwig file. These files were created using Deeptools (v3.5.5) (Ramirez et al., 2014) with the bamCoverage function using RPKM normalization, bin size 5. For analyzing differential binding between, we used Diffbind (DiffBind 3.14.0) (Ross-Innes et al., 2012). A consensus peakset was created using the peaks identified with the two conditions to be compared and differentially enriched peaks were identified using the DESeq2 method. Signal was analyzed using the summit method and a 400bp bin centered on the summit. Peaks were considered as differentially enriched when the log2FC was larger than one and adjusted p value smaller than 0.05. Heatmaps representing signal strength were generated using deeptools on the peaks that showed no significant difference between JUN and ATF2, peaks with more enrichment of JUN, and peaks with higher enrichment of ATF2. Heatmaps comparing the the effect of Vincristine and phosphorylation mutants were generated by plotting the signal on a file containing a merge of all peaks identified in either all JUN samples or all ATF2 samples. To assign peaks to genes we used GREAT analysis (v4.0.4) (Tanigawa et al., 2022) using the same list of peaks used for the Diffbind. The whole hg38 genome was used as background and Basal plus extension association rule was used with the default 5kb upstream, 1kb downstream setting. Extension distance was changed from 1Mb to 50kb for higher stringency.
Assembly: hg38
Supplementary files format and content: bigwig, genomic enrichment

source_name: iNeurons differentiated from human iPSCs

growth_protocol: i3-iPSCs were dissociated using Accutase (Life Technologies, cat. no. A1110501). Cells were plated in Matrigel-coated (1:100 Corning) plates in sensory neuronal induction media on day 0 (1:1 mix of Neurobasal (ThermoFisher cat. no. 21103049) and DMEM/F12 medium (ThermoFisher cat. no. 11320-033) supplemented with1× MEM nonessential amino acids (NEAA) (ThermoFisher, cat. no. 11140050), 10 μM ROCK inhibitor (Y-27632; Selleckchem, cat. no. S1049), 2 μg/ml doxycycline (Clontech, cat. no. 631311), 1X N2 supplement (Life Technologies, cat. no. 17502048), 1× B27 Plus Supplement (ThermoFisher ScienJfic, cat. no. A3582801). Induction media was changed daily for 2 days. On day 3 of differentiation, cells were dissociated using Accutase and plated in dishes coated with Polyethyleneimine (Sigma, cat. no. 408727-100ML) and laminin (15ng/ml Corning, cat. no. 354232). Cells were plated in sensory neuronal maturation media (1:1 mix of Neurobasal (ThermoFisher cat. no. 21103049) and DMEM/F12 medium supplemented with1× MEM nonessenJal amino acids (NEAA) (ThermoFisher, cat. no. 11140050), 2 μg/ml doxycycline (Clontech, cat. no. 631311), 1X N2 supplement (Life Technologies, cat. no. 17502048), 1× B27 Plus Supplement (ThermoFisher ScienJfic, cat. no. A3582801), 10 ng/ml BDNF (PeproTech, cat. no. 450-02), 10 ng/ml NT-3 (PeproTech, cat. no. 450-03), 10 ng/ml GDNF (PeproTech, cat. no. 450-10 – 100 μg), 10 ng/ml NGF (R&D systems, cat. no. 256-GF-100), 1 mg/ml mouse laminin (Invitrogen, cat. no. 23017015). Half of the neuronal maturation media was removed and replenished with fresh media every 2-3 days.

extract_protocol:
Cell pellets were thawed on ice for 10 minutes. Cells were lysed and sonicated using the truChIP Chromatin Shearing Kit (Covaris 520154) according to the manufacturer’s instructions. Chromatin was sonicated in Covaris milliTUBE 1 ml AFA tubes under the following conditions: 30 minutes total, PIP 75, duty factor 15%, CPB 1000, using a Covaris ME220 sonicator. Sonicated samples were centrifuged at 20,000 g for 15 minutes at 4°C, and the supernatant was collected. Chromatin concentration was determined using the Qubit high sensitivity DNA kit. A 20 µg aliquot of chromatin was used per 1 ml ChIP reaction, adjusted with RIPA buffer. For immunoprecipitation, 30 µl of Protein A/G beads conjugated with 2 µg of antibody (pre-incubated with beads resuspended in 500 µl RIPA for 3 hours) was added, and the mixture was incubated overnight at 4°C on a rotating platform. The beads were then washed once with low-salt wash buffer, twice with high-salt wash buffer, twice with lithium chloride wash buffer, and twice with 1X TE buffer. Chromatin was eluted in 200 µl of freshly prepared direct elution buffer supplemented with 2 µl RNase A (10 mg/ml) and incubated on a thermomixer at 65°C and 800 rpm overnight. The following day, beads were removed, and the supernatant was treated with 3 µl Proteinase K (20 mg/ml) at 55°C and 1200 rpm for 2 hours to reverse crosslinks. DNA was purified using the Zymo DNA Clean and Concentrator kit (Zymo, D4033) and eluted in 20 µl deionized water.
ChIP-seq libraries were prepared following the SMARTer ThruPlex TAKARA Library Prep kit. 10 µl of purified DNA was used per sample. The DNA was prepared with Template Preparation D Buffer (2 µl) and Template Preparation D Enzyme (1 µl) and subjected to end repair and A-tailing in a thermocycler. Library synthesis was performed by adding Library Synthesis D Buffer (1 µl) and Library Synthesis D Enzyme (1 µl) followed by library amplification using Library Amplification D Buffer (25 µl), Library Amplification D Enzyme (1 µl), Nuclease-free water (4 µl), and an Illumina-compatible indexed primer (5 µl). Amplification consisted of an initial extension at 72°C for 3 minutes, denaturation at 98°C for 2 minutes, followed by 4 cycles of 98°C for 20 seconds, 67°C for 20 seconds, and 72°C for 10 seconds for index addition, and 12 cycles of 98°C for 20 seconds and 72°C for 10 seconds for amplification. Libraries were cleaned using a SPRIselect bead double size selection and sequenced on a NovaSeq platform using PE50.

treatment_protocol: iNeurons were dissociated using Accutase, scraped off the plate, and transferred to a conical tube. After two PBS washes, cells were resuspended in 9.375 ml of BrainPhys media. To fix the cells, 625 µL of 16% formaldehyde was added to achieve a final concentration of 1% and incubated for 10 minutes at 37°C. The reaction was quenched by adding 1.42 M glycine, mixing by inversion, and incubating for 5 minutes at room temperature. Cells were pelleted by centrifugation at 2000 g for 5 minutes at 4°C and washed twice with cold PBS. Cell pellets were then counted, flash frozen in aliquots of 20M cells per tube, and stored at −80°C.

value: hiPSC

tag: genotype

value: WT


title: hiPSCNeuronsJUNAA_vinc_ChIP_FLAG_rep1

value: iNeurons differentiated from human iPSCs

tag: treatment

value: vincristine


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1030

first: Eva

last: Hedlund

institute: Stockholm University

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).

tag: sequencing batch


title: hiPSCNeuronsJUNAA_ctrl_ChIP_FLAG_rep1

value: DMSO


title: slide4_ptN_glomerulus_MCD_rep1

tag: tissue

value: Kidney

value: glomerulus


title: hiPSCNeuronsJUNAA_ctrl_ChIP_FLAG_rep2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1028

value: spinal neuron differentiation

value: heterogenous protocol


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1029


title: hiPSCNeuronsJUNWT_vinc_ChIP_FLAG_rep2


title: slide4_ptM_glomerulus_MCD_rep6

value: M


title: slide4_ptM_glomerulus_MCD_rep7


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1027


title: hiPSCNeuronsJUNWT_ctrl_ChIP_FLAG_rep2


title: slide4_ptM_glomerulus_MCD_rep5


title: hiPSCNeuronsJUNWT_ctrl_ChIP_FLAG_rep1


title: hiPSCNeuronsATF2AA_vinc_ChIP_FLAG_rep2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1026


title: hiPSCNeuronsATF2AA_vinc_ChIP_FLAG_rep1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1025


title: slide4_ptM_glomerulus_MCD_rep4


title: hiPSCNeuronsATF2AA_ctrl_ChIP_FLAG_rep2


title: hiPSCNeuronsATF2AA_ctrl_ChIP_FLAG_rep1


title: slide4_ptM_tubules_MCD


title: hiPSCNeuronsATF2WT_vinc_ChIP_FLAG_rep1


title: hiPSCNeuronsJUNAA_vinc_ChIP_FLAG_rep2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1023


title: hiPSCNeuronsATF2WT_ctrl_ChIP_FLAG_rep2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1024


title: slide4_ptM_glomerulus_MCD_rep3


title: hiPSCNeuronsATF2WT_vinc_ChIP_FLAG_rep2


title: hiPSCNeuronsATF2WT_ctrl_ChIP_FLAG_rep1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1022


title: H460_shNRF2_24hr_rep2

city: South San Francisco

first: Scott

last: Foster

address: Genentech

institute: Genentech

data_processing:
Reads were aligned to the GRCh38 genome using GSNAP and genes were counted using the HTSeqGenie Bioconductor package.
GSNAP: version ‘2013-10-10-v2’, allowing maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 --pairmax-rna=200000 --clip-overlap')
Assembly: GrCH38/hg38
Supplementary files format and content: Tab delimited file, contains Ensemble ID, counts and RPKM

extract_protocol:
RNA isolation was performed using the RNeasy Plus Mini Kit (Qiagen) and reverse transcription was performed using the High-Capacity cDNA Reverse Transcription Kit (Thermo) according to the manufacturer’s protocol.
Library construction was performed by Arpeggio Biosciences as describe in Mahat et al. 2016. PMID:  27442863, DOI: 10.1038/nprot.2016.086

value: Non-Small Cell Lung Cancer

value: shNRF2, 500ng/mL dox

tag: timepoint

tag: replicate


title: hiPSCNeuronsJUNWT_vinc_ChIP_FLAG_rep1


title: slide4_ptM_glomerulus_MCD_rep1


title: H460_shNRF2_24hr_rep1


title: slide3_ptL_glomerulus_MCD_rep7

value: L


title: H460_shNRF2_6hr_rep2


title: H460_shNRF2_6hr_rep1


title: hiPSCNeurons_ChIP_IgG_rep1


title: slide3_ptL_glomerulus_MCD_rep6


title: H460_shNRF2_3hr_rep2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1020

address: Svante Arrhenius v. 16C

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 bcl2fastq_2.17 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: Control


title: slide3_ptL_glomerulus_MCD_rep5

value: Human NGS Whole Transcriptome Atlas RNA_1.0


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1019


title: H460_shNRF2_3hr_rep1


title: H460_shNRF2_0hr_rep1

value: shNRF2, no dox


title: slide4_ptM_glomerulus_MCD_rep2

value: MCD


title: A549_shNRF2_24hr_rep2


title: slide3_ptL_glomerulus_MCD_rep4


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1017


title: A549_shNRF2_24hr_rep1


title: slide3_ptL_glomerulus_MCD_rep3


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1021


title: A549_shNRF2_6hr_rep2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1016


title: A549_shNRF2_3hr_rep2


title: A549_shNRF2_3hr_rep1


title: slide3_ptL_glomerulus_MCD_rep2


title: slide3_ptL_glomerulus_MCD_rep1


title: slide3_ptK_glomerulus_MCD_rep7

value: K


title: A549_shNRF2_6hr_rep1


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1015


title: A549_shNRF2_0hr_rep2


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1013


title: A549_shNRF2_0hr_rep1


title: THP-1,OE4

city: 武汉

first: yi

last: he

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院

data_processing:
Trimmomatic software were used to remove adapter and low quality reads. [Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30(15):2114–20.]
Quality control:Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome:STAR is used to align clean reads to reference genome.
Quantification of gene expression level:HTSeq v0.6.0 was used to count the reads numbers mapped to each gene.
Assembly: hg38
Supplementary files format and content: a matrix table include read counts for each sample

extract_protocol:
Total RNA was extracted using TRIzol Reagent.A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) . RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA). RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq6000 platform and 150 bp paired-end reads were generated.

value: overexpression of tRF-Gly-GCC-06


title: slide3_ptK_glomerulus_MCD_rep6


title: THP-1,OE2

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: H460_shNRF2_0hr_rep2


title: THP-1,OE1

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1018

city: Stockholm


title: slide3_ptK_glomerulus_MCD_rep5


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1012


title: THP-1,control4

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院

value: control


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1011


title: THP-1,control3

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: slide3_ptK_glomerulus_MCD_rep4


title: THP-1,control2

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: slide3_ptL_tubules_MCD

value: tubules


title: THP-1,control1

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1010


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1009


title: RBE DMSO DMSO Replicate 3

city: Chapel Hill

first: John

middle: P.

last: Morris IV

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

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

institute: University of North Carolina at Chapel Hill

data_processing:
Fastq Files were processed using Partek Flow Web Software Version 10.0.23.0720.
Bases were trimmed to min quality level (Phred) of 20 from the 3' end and minimum read length threshold was set to 25 bp.
Reads were mapped with STAR - 2.7.8a to hg19.
Reads were counted using HTSeq - 0.11.0.
Reads were normalized with DESeq2 filtering out features with lowest average coverage less than 1.0 and significance was determined using correction for multiple testing with the FDR step-up adjusted p-value.
Assembly: hg19
Supplementary files format and content: Tab-delimited text file containing raw counts for each sample

source_name: Liver/Bile Duct

growth_protocol: RBE cell lines were passaged in sterile tissue culture plates containing RPMI media supplemented with 10% FBS (Gemini) and 1% Penicillin Streptomycin in a humidified incubator at 5% CO2 and 37 C.

extract_protocol:
Cells were scraped into lysis buffer and homogenized using QIAShredders (Qiagen). RNA was extracted using the RNeasy mini kit.
The mRNA library preparation (poly A enrichment) was performed with Novogene Co. polyA capture was used to isolate mRNAs followed by cDNA preparation with reverse transcription.
RNA-seq with Novogene
NovaSeq PE150

treatment_protocol: RBE cholangiocarcinoma cells were treated with 5 uM AG-120 for 22 days to block production of 2-HG followed by activation of p53 using 5 uM MDM2 inhibitor Nutlin for 72 hours.

value: Liver/Bile Duct

value: RBE

value: 22 days of 5 uM DMSO


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1008

value: spinal neuron differentiation


title: RBE DMSO DMSO Replicate 2


title: RBE DMSO Nutlin Replicate 1

value: 22 days of 5 uM DMSO + 72 hours of 5 uM Nutlin


title: slide3_ptK_glomerulus_MCD_rep2

value: Kidney

value: glomerulus


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1014

value: heterogenous protocol


title: RBE DMSO Nutlin Replicate 2


title: RBE AG-120 Nutlin Replicate 3

value: 22 days of 5 uM AG-120 + 72 hours of 5 uM Nutlin


title: THP-1,OE3

address: 武汉市蔡甸区同济医院科研大楼

institute: 华中科技大学附属同济医院


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1007

value: Control


title: Diff_D1_Protocol_P1_Line_DF6-9-9T.B_Control_Cell_1006