title: IL31-5

city: Cambridge

first: Yingnan

last: Han

state: MA

address: 350 Water Street

institute: Sanofi

description: Library name: IL-31--5_001.filtered

data_processing:
De-multiplexed raw sequencing data were converted into gene counts using QIAGEN Omicsoft Array Studio, which filtered out the sequencing reads with low quality and aligned sequencing reads to the mouse reference genome GRCm38
genes with low expression in raw count data were filtered out. TMM normalization and log2 transformation were implemented using edgeR
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file with normalized counts (log2 and TMM normalized) of each sample

source_name: ear pinnae

extract_protocol:
Total RNA from mouse ear pinnae was extracted using Qiagen RNeasy Plus Universal mini kit.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina.

treatment_protocol: IL-4 (R&D Systems, Cat#: 404-ML-100/CF, 0.1 μg/μl, 10 μl), IL-13 (R&D Systems, Cat#: 413-ML-50/CF, 0.1 μg/μl, 10 μl), and IL-31 (R&D Systems, Cat#: 3028-ML-010, 0.1 μg/μl, 10 μl) diluted in PBS, were injected intradermally separately into the mouse right ear pinnae. The control group received PBS injection in the right ear pinnae.

value: ear pinnae


title: IL31-3

status: Public on May 15 2025

type: SRA

country: USA

description: Library name: IL-31--3_001.filtered

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: tissue

tag: treatment


title: IL31-2

description: Library name: IL-31--2_001.filtered


title: transcriptome of blood of patient with COVID-19 delta strain 223

city: Moscow

first: Ivan

middle: Nikolaevitch

last: Vlasov

address: Akademika Kurchatova square, 2

country: Russia

institute: National Research Center «Kurchatov Institute»

description: Library name: 223

data_processing:
3 different pipelines were used in the process of data processing.
Pipeline 1 - Fastq files for each sample were aligned to the GRCh38 genome (Gencode, release 37) using HISAT2 (v2.0.1b) with default parameters. Quality control for each sample was performed by FastQC (v0.11.9) and RSeQC (v4.0.0). Counting reads was done using featureCounts.
Pipeline 2 - Human reference genome assembly GRCh38 (hg38) and gene model annotation files were downloaded from Gencode website (https://www.gencodegenes.org/human/) directly (release 37). Adapters were removed by Cutadapt (v3.4). HISAT2 (v2.2.1) [18] was used with default parameters to building of the index of the reference genome and mapping reads to genome. Quality control for each sample was performed by FastQC (v0.11.9) and RSeQC (v4.0.0). Counts the number of sequencing reads mapping to each gene after the alignment step was done using htseq-count function from HTSeq framework (v.0.6.1).
Pipeline 3 – Ambiguous and low-quality bases were removed from the files obtained during the FASTQ sequencing process. Removal was done with AdapterRemoval V2. The trimmed files were aligned to the human reference genome GRCH38 and GRCH38.92 gene annotation using RSEM with rsem-prepare-reference and rsem-calculate-expression commands  and the -star option to also generate STAR indices.
Assembly: GRCH38
Supplementary files format and content: Processed count files  were obtained using each of 3 pipelines and contains 3 columns with respective pipeline counts.

molecule: polyA RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Total RNA isolation was conducted using a Direct-Zol RNA Mini-Prep Kit (ZymoResearch) according to the manufacturer's recommendations. The concentration of total RNA isolated was measured using a Quant-iT RNA BR Assay Kit and a Qubit fluorimeter (Invitrogen). RNA quality was monitored using an Experion automated electrophoresis system (Bio-Rad Laboratories).
Poly-a fraction of RNA was extracted from total RNA for RNA-seq. Sequencing libraries were prepared using NEBNext® mRNA Library Perp Reagent Set (NEB, USA). Sequencing was performed using HiSeq1500 (Illumina, USA), obtaining no less then 15 mln. reads of 50 length per library.

value: blood

tag: batch

value: Batch 1

tag: age

tag: rin

tag: clinical outcome

value: survived


title: IL13-5

description: Library name: IL-13--5_001.filtered


title: wt_emt3

city: New York

first: Samie

last: Jaffrey

state: New York

address: 1300 York Ave

department: Pharmacology

institute: Weill Cornell Medicine

description: Library name: wt_emt3

data_processing:
Library quality was first analyzed using MultiQC 1.14.  Adaptors were trimmed using TrimGalore-0.6.9 with --stringency 3 and library quality was again assessed using MultiQC 1.14.  The data was then analyzed using the slamdunk all function of the analytical suite SLAM-DUNK 0.4.3 with the default parameters for mapping, quality filtering, and single nucleotide polymorphism identification.  The reference genome hg38 and mm10 was used for mapping and the subsequent analysis. PCR duplicates in the quality filtered reads were collapsed using alleyoop collapse function of SLAM-DUNK 0.4.3.  The 4sU conversion was further assessed using alleyoop rates, alleyoop tccontext, and alleyoop snpeval functions with the default parameters.  alleyoop utrrates was used with a bed file of all exons of each mRNA to analyzed 4sU conversion rates per mRNA.  The quality filtered and PCR duplicate-collapsed mapped reads were further analyzed using GRAND-SLAM 2.0.7b with the default parameters to quantify read counts and perform statistical analysis to infer the ratio of transcripts for each gene that originate from pre-4sU labeling and post labeling.  The results from GRAND-SLAM 2.0.7b was used to calculate mRNA synthesis rate and half-life using grandR 0.2.2.
Assembly: mm10
Supplementary files format and content: The processed data file contains the log2 fold change on half-life, the lower/upper credible interval boundaries of the half-life log2 fold change, and the signed ROPE probability.

source_name: mESC

growth_protocol: mESC cells were grown in KnockOut DMEM (ThermoFisher, 10829018) supplemented with 15% heat-inactivated FBS, 10 U/mL Penicillin-Streptomycin (ThermoFisher, 15140122), 1x GlutaMax (ThermoFisher, 35050061), 500 μM β-mercaptoethanol (ThermoFisher, 21985023), 1x Nonessential amino acids (ThermoFisher, 11140076), 103 U/mL LIF (MilliporeSigma, ESG1107), 3 μM CHIR99021 (ThermoFisher, 501013679), and 1 μM PD0325901 (ThermoFisher, 501013147). Cells were plated on plates coated with EmbryoMax™ 0.1% gelatin solution (MilliporeSigma, ES-006-B) and passaged daily using TrypLE Express (ThermoFisher, 12604039) according to the manufacturer’s instructions.

extract_protocol:
Total RNA was collected using Qiagen RNeasy Mini kit RLT buffer (Qiagen, 74104) supplemented with 1% 𝛽-mercaptoethanol (BME).  Cells were lysed by passing through a 25 1/2-gauge needle, and RNA was isolated following the manufacturer’s instruction with RPE buffer supplemented with 1% BME.
10 µg total RNA was treated with 2,2,2-trifluoroethylamine (TFEE) and sodium periodate (NaIO4) at 45 °C for 1 h to convert 4sU to N4-trifluoroethylcytosine.  RNA was then purified twice using RNAClean beads (Beckman Coulter, A63987). 1 µg of treated RNA was used for RNA-seq library preparation using NEBNext® rRNA Depletion Kit (NEB, E6310X) and NEBNext® Ultra™ II Directional RNA Library Prep Kit (NEB, E7760L).  Library quality was assessed on Agilent TapeStation4200 using D1000 ScreenTape (Agilent, 5067-5584).  Library was quantified on Qubit4 Fluorometer using Qubit 1X dsDNA HS Assay Kit (ThermoFisher, Q33231).

treatment_protocol: Cells were incubated treated with 250 µM 4-thiouridine (4sU, SigmaAldrich, T4509) for 3 hr.

tag: cell line

value: mESC

tag: genotype

value: wildtype


title: CropSeq NTN 2, Sample 2, ADT

city: Hamburg

first: Malte

last: Hellmig

state: Hamburg

address: Martinistraße 52

department: III. Department of Medicine

country: Germany

institute: University Medical Center Hamburg-Eppendorf

description:
Library name: 23_1-Th17-1-ADT
10X Genomics scRNA-seq using Chromium Single Cell 3' v7

library_source: other

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 3.1 and 7.1, 10x Genomics, Pleasanton, CA).
Assembly: GRCh38
Assembly: mm10
Supplementary files format and content: Cellranger output: Tab seperated values files and Matrix table with raw gene counts
Supplementary files format and content: Cellranger output: Character seperated values file of TCR contig annotation
Supplementary files format and content: Cellranger output: Filtered feature-barcode matrices HDF5. JSON object where each protospacer is associated with a list of barcodes.
Library strategy: CITE-seq

molecule: protein

source_name: kidney

extract_protocol:
Kidneys were incubated at 37 °C for 40 min in RPMI 1640 Medium (Thermo Fisher) containing 10% heat inactivated FBS, 1% P/S, 0.4 µg/ml Collagenase D (Roche, Basel, Switzerland) and 0.2 µg/ml DNAse (Roche). Subsequently, tissue was dissociated using the GentleMACS Dissociator and C-Tubes (both Miltenyi Biotec) and leukocytes were isolated using a gradient centrifugation with 37 % Percoll (GE Healthcare). After the centrifugation, cells were washed with DPBS (Gibco). CD4+ T cells were enriched using the EasySep Mouse CD4+ T cell Isolation Kit according to manufacturer’s instructions (Stemcell Technologies, Vancouver, Canada). Enriched cells were sorted by Fluorescence-activated cell sorting (FACS) for CD4+ T cells, GFP signal and eBFP2 signal. For isolation of intestinal lymphocytes, the small intestine was obtained and cut into 1 cm pieces. We separated lamina propria lymphocytes (LPLs) from intraepithelial lymphocytes (IELs) by incubation with 2 mM DTT at 37°C for 30 min and subsequent filtering through a 100 µm cell strainer (Falcon). The IELs in the supernatant were discarded. The remaining parts were transferred into 50 ml tubes (Falcon, Thermo Fischer), containing DPBS, calcium, magnesium (Gibco), washed by rigorous shaking and repeatedly filtered through a 100 µm cell strainer. Further, the pieces were digested with collagenase D (Roche) and DNAse (Roche) at 37°C for 45 min while rotating in a MACS-Mix tube rotator (Miltenyi Biotec). Subsequently, the small intestines were minced in a MACS cell separator (C-tubes, program “intestine 01”) and filtered through a 70 µm cell strainer (Falcon) until the tissue turns white. The cell strainer was washed with RPMI-medium. Lastly, gradient centrifugation with 37% Percoll (GE Healthcare) was performed. Cells were sorted by Fluorescence-activated cell sorting (FACS) for CD4+ T cells, GFP signal and eBFP2 signal.
All steps were performed according to standard protocol of the Chromium Single Cell 3' v3 kit, Chromium  Next GEM Single Cell 3' v3.1

value: kidney

tag: cell type

value: T cells

value: crescentic glomerulonephritis

tag: library type

value: ADT

tag: adt

value: Features defined in CropSeq_feature_reference.csv


title: CropSeq Colitis 2, Sample 2, CRISPR

description:
Library name: 23_2-Th17-1-CRISPR
10X Genomics scRNA-seq using Chromium Single Cell 3' v7

data_processing:
10x Genomics raw sequencing data were processed using CellRanger software (version 3.1 and 7.1, 10x Genomics, Pleasanton, CA).
Assembly: GRCh38
Assembly: mm10
Supplementary files format and content: Cellranger output: Tab seperated values files and Matrix table with raw gene counts
Supplementary files format and content: Cellranger output: Character seperated values file of TCR contig annotation
Supplementary files format and content: Cellranger output: Filtered feature-barcode matrices HDF5. JSON object where each protospacer is associated with a list of barcodes.

molecule: other

source_name: intestine

value: intestine

value: experimental colitis

value: CRISPR

tag: crispr


title: CropSeq Colitis 2, Sample 3, CRISPR

description:
Library name: 23_2-Th17-2-CRISPR
10X Genomics scRNA-seq using Chromium Single Cell 3' v7


title: wt_emt1

description: Library name: wt_emt1


title: CropSeq NTN 2, Sample 2, CRISPR

description:
Library name: 23_1-Th17-1-CRISPR
10X Genomics scRNA-seq using Chromium Single Cell 3' v7


title: CropSeq NTN 2, Sample 1, GEX

description:
Library name: 23_1-Control-GEX
10X Genomics scRNA-seq using Chromium Single Cell 3' v7

library_source: transcriptomic single cell

value: mRNA


title: transcriptome of blood of patient with COVID-19 delta strain 222

description: Library name: 222

value: deceased


title: ko_ctrl3

description: Library name: ko_ctrl3


title: CropSeq NTN 2, Sample 3, CRISPR

description:
Library name: 23_1-Th17-2-CRISPR
10X Genomics scRNA-seq using Chromium Single Cell 3' v7


title: CropSeq NTN 2, Sample 3, GEX

description:
Library name: 23_1-Th17-2-GEX
10X Genomics scRNA-seq using Chromium Single Cell 3' v7


title: CropSeq NTN 2, Sample 1, ADT

description:
Library name: 23_1-Control-ADT
10X Genomics scRNA-seq using Chromium Single Cell 3' v7


title: CropSeq NTN 2, Sample 4, GEX

description:
Library name: 23_1-Th17-3-GEX
10X Genomics scRNA-seq using Chromium Single Cell 3' v7


title: IL13-1

description: Library name: IL-13--1_001.filtered


title: transcriptome of blood of patient with COVID-19 delta strain 191

description: Library name: 191


title: IL4-5

description: Library name: IL-4--5_001.filtered


title: transcriptome of blood of patient with COVID-19 delta strain 184

description: Library name: 184


title: IL4-4

description: Library name: IL-4--4_001.filtered


title: IL31-4

description: Library name: IL-31--4_001.filtered


title: transcriptome of blood of patient with COVID-19 delta strain 183

description: Library name: 183


title: IL31-1

description: Library name: IL-31--1_001.filtered


title: CropSeq Colitis 2, Sample 2, GEX

description:
Library name: 23_2-Th17-1-GEX
10X Genomics scRNA-seq using Chromium Single Cell 3' v7


title: IL13-4

description: Library name: IL-13--4_001.filtered


title: IL13-3

description: Library name: IL-13--3_001.filtered


title: IL4-3

description: Library name: IL-4--3_001.filtered


title: transcriptome of blood of patient with COVID-19 delta strain 172

description: Library name: 172


title: transcriptome of blood of patient with COVID-19 delta strain 213

description: Library name: 213


title: IL4-2

description: Library name: IL-4--2_001.filtered


title: PBS-4

description: Library name: PBS--4_001.filtered

value: PBS


title: IL4-1

description: Library name: IL-4--1_001.filtered

value: ear pinnae


title: transcriptome of blood of patient with COVID-19 delta strain 166

description: Library name: 166

value: blood


title: PBS-3

description: Library name: PBS--3_001.filtered


title: siDFs_emt_2

description: Library name: siDFs_emt_2

data_processing:
Library quality was first analyzed using MultiQC 1.14.  Adaptors were trimmed using TrimGalore-0.6.9 with --stringency 3 and library quality was again assessed using MultiQC 1.14.  The data was then analyzed using the slamdunk all function of the analytical suite SLAM-DUNK 0.4.3 with the default parameters for mapping, quality filtering, and single nucleotide polymorphism identification.  The reference genome hg38 and mm10 was used for mapping and the subsequent analysis. PCR duplicates in the quality filtered reads were collapsed using alleyoop collapse function of SLAM-DUNK 0.4.3.  The 4sU conversion was further assessed using alleyoop rates, alleyoop tccontext, and alleyoop snpeval functions with the default parameters.  alleyoop utrrates was used with a bed file of all exons of each mRNA to analyzed 4sU conversion rates per mRNA.  The quality filtered and PCR duplicate-collapsed mapped reads were further analyzed using GRAND-SLAM 2.0.7b with the default parameters to quantify read counts and perform statistical analysis to infer the ratio of transcripts for each gene that originate from pre-4sU labeling and post labeling.  The results from GRAND-SLAM 2.0.7b was used to calculate mRNA synthesis rate and half-life using grandR 0.2.2.
Assembly: hg38
Supplementary files format and content: The processed data file contains the log2 fold change on half-life, the lower/upper credible interval boundaries of the half-life log2 fold change, and the signed ROPE probability.

source_name: HeLa

growth_protocol: HeLa cells were grown at 37°C in 5% CO2 using DMEM (ThermoFisher, 11995065) supplemented with 10% FBS and 10 U/mL penicillin-streptomycin (ThermoFisher, 15140122).  Cells were passaged every 3-4 days using with TrypLE Express (ThermoFisuer, 12604039) according to the manufacturer’s instructions.

treatment_protocol: Cells were incubated treated with 500 µM 4-thiouridine (4sU, SigmaAldrich, T4509) for 1.5 hr.

value: HeLa

value: Control knockdown


title: IL13-2

description: Library name: IL-13--2_001.filtered


title: transcriptome of blood of patient with COVID-19 delta strain 207

description: Library name: 207

value: Batch 1

value: survived


title: transcriptome of blood of patient with COVID-19 delta strain 201

description: Library name: 201


title: transcriptome of blood of patient with COVID-19 delta strain 171

description: Library name: 171


title: transcriptome of blood of patient with COVID-19 delta strain 163

description: Library name: 163


title: PBS-2

description: Library name: PBS--2_001.filtered


title: BMFA3v1, Smad4 KO, TGFb-treated, replicate 2

city: Dallas

first: Rolf

middle: A

last: Brekken

state: TX

address: 6000 Harry Hines Blvd, MC8593

department: Surgery

institute: UT Southwestern

description:
Library name: BM8
SMAD4 KO+TGFB in columns B, C, F shows counts for BM7, BM8, and averaged counts, respectively; SMAD4 KO-TGFB in columns D, E, and G shows conts for BM5, BM6, and averaged counts, respectively;
KO_TGFbvsKO_deg_all_BMFA3.xlsx

data_processing:
data processing was conducted by Novogene
Assembly: genome bild/assembly was conducted by Novogene
Supplementary files format and content: .xlsx; contains statistical analysis of DEG

source_name: tumor

growth_protocol: The cells were grown in DMEM-10%FBS in hunidified atmosphere with 5%CO2 at 37C. For the experiment the cells were plated into 6-well plates 24h before the treatment.

extract_protocol:
Total RNA was extracted with RNeasyPlus kit (Qiagen)
mRNA enrichment and library preparation was conducted by Novogene

treatment_protocol: The cells were treated with 30ng/ml TGFb  for 48h

value: tumor

value: derived from KFC (KrasLSL-G12D/+; Trp53fl/fl; Pdx1Cre/+) mice

value: SMAD4 CRISPR Cas9 KO

value: 30ng/ TGFb, 48h


title: siDFs_emt_1

description: Library name: siDFs_emt_1


title: siNC_emt_3

description: Library name: siNC_emt_3


title: BMFA3v1, Smad4KO,untreated, replicate 2

description:
Library name: BM6
SMAD4 KO (-) in columns B, C, F shows counts for BM5, BM6, and averaged for BM5 and BM6, respectively; SMAD4 WT (-) in columns D, E, and G shows conts for BM1, BM2, and averaged for BM3 and BM4, respectively. SMAD4 KO+TGFB in columns B, C, F shows counts for BM7, BM8, and averaged counts, respectively; SMAD4 KO-TGFB in columns D, E, and G shows conts for BM5, BM6, and averaged counts, respectively;
KOvsEV_deg_all_BMFA3.xlsx
KO_TGFbvsKO_deg_all_BMFA3.xlsx

value: untreated


title: siDFs_ctrl_3

description: Library name: siDFs_ctrl_3


title: PBS-1

description: Library name: PBS--1_001.filtered


title: siNC_emt_1

description: Library name: siNC_emt_1


title: siNC_ctrl_2

description: Library name: siNC_ctrl_2


title: BMFA3v1, empty vector controrol, TGFb-treated, replicate 2

description:
Library name: BM4
SMAD4 WT+TGFB in columns B, C, F shows counts for BM3, BM4, and averaged counts, respectively; SMAD4 WT-TGFB in columns D, E, and G shows conts for BM1, BM2, and averaged counts, respectively;
EV_TGFbvsEV_deg_all_BMFA3.xlsx

value: WT


title: siNC_ctrl_1

description: Library name: siNC_ctrl_1


title: siDFs_ctrl_2

description: Library name: siDFs_ctrl_2


title: BMFA3v1, empty vector controrol, untreated, replicate 1

description:
Library name: BM1
SMAD4 KO (-) in columns B, C, F shows counts for BM5, BM6, and averaged counts, respectively; SMAD4 WT (-) in columns D, E, and G shows conts for BM1, BM2, and averaged counts, respectively. SMAD4 WT+TGFB in columns B, C, F shows counts for BM3, BM4, and averaged counts, respectively; SMAD4 WT-TGFB in columns D, E, and G shows conts for BM1, BM2, and averaged counts, respectively;
KOvsEV_deg_all_BMFA3.xlsx
EV_TGFbvsEV_deg_all_BMFA3.xlsx


title: BMFA3v1, empty vector controrol, TGFb-treated, replicate 1

description:
Library name: BM3
SMAD4 WT+TGFB in columns B, C, F shows counts for BM3, BM4, and averaged counts, respectively; SMAD4 WT-TGFB in columns D, E, and G shows conts for BM1, BM2, and averaged counts, respectively;
EV_TGFbvsEV_deg_all_BMFA3.xlsx


title: siNC_emt_2

description: Library name: siNC_emt_2


title: siDFs_emt_3

description: Library name: siDFs_emt_3


title: siNC_ctrl_3

description: Library name: siNC_ctrl_3


title: siDFs_ctrl_1

description: Library name: siDFs_ctrl_1


title: 6620c1, Smad4 KO, TGFb-treated, replicate 3

description:
Library name: KO6620_TGF_3
Column names correpond to raw data file names. Columns H and I show averaged counts.
KO_TGFbvsKO_deg_all_6620c1.xls

value: derived from KPCY (KrasG12D/+; Trp53LSL-R172H/+; Pdx1Cre/+; Rosa26-YFP) mice


title: PBS-5

description: Library name: PBS--5_001.filtered


title: 6620c1, Smad4 KO, TGFb-treated, replicate 2

description:
Library name: KO6620_TGF_2
Column names correpond to raw data file names. Columns H and I show averaged counts.
KO_TGFbvsKO_deg_all_6620c1.xls


title: BMFA3v1, empty vector controrol, untreated, replicate 2

description:
Library name: BM2
SMAD4 KO (-) in columns B, C, F shows counts for BM5, BM6, and averaged counts, respectively; SMAD4 WT (-) in columns D, E, and G shows conts for BM1, BM2, and averaged counts, respectively. SMAD4 WT+TGFB in columns B, C, F shows counts for BM3, BM4, and averaged counts, respectively; SMAD4 WT-TGFB in columns D, E, and G shows conts for BM1, BM2, and averaged counts, respectively;
KOvsEV_deg_all_BMFA3.xlsx
EV_TGFbvsEV_deg_all_BMFA3.xlsx


title: HeLa_-AA_mRNAseq_biological-replicate2

city: Los Angeles

first: Siavash

middle: K

last: Kurdistani

state: CA

address: 615 Charles E Young Dr South

department: Biological Chemistry

institute: UCLA

description: Library name: Sample 5

data_processing:
FASTQ of the paired-end reads used for mapping with RNA star alignment
Differential expression analysis performed with DESeq2
Assembly: hg19
Supplementary files format and content: csv

growth_protocol: HeLa cells were maintained in DMEM (Cellgro #10-013-CV) supplemented with 10% fetal bovine serum (FBS) (Thermo Fisher HyClone #SV30014.03).

extract_protocol:
Total RNA was extracted using the Trizol reagents (Ambion #15596026) and treated with TURBO DNase (Ambion #AM2239).
Prior to preparing RNA-seq libraries for Illumina NovaSeq sequencing, contaminating DNA was digested using Turbo DNase (Thermo Fisher). RNA quality was assessed by Agilent 2200 Tapestation. Stranded mRNA (Poly-A) libraries were constructed with automated NGS library construction and sequenced by UCLA Technology Center for Genomics & Bioinformatics

treatment_protocol: Media containing complete amino acids (AA) were made from DMEM powder (US Biological #D9802) and supplemented with an additional 3.5 g/L D-glucose (for a total of 4.5 g/L), 1 mM sodium pyruvate (Gibco #11360070), 3.7 g/L sodium bicarbonate, and 0.0159 g/L sodium phenol red (US Biological #P4040). Media without AA were made from DMEM without amino acids powder (US Biological #D9800-013) and supplemented with an additional 3.5 g/L D-glucose, 1 mM sodium pyruvate (Gibco #11360070), and 3.7 g/L sodium bicarbonate. pH of media was adjusted to 7.2 by the addition of HCl before being filter sterilized and supplemented with 10% dialyzed FBS (Gibco #26400-044).

value: Wild type

value: without AA


title: HeLa_-AA_mRNAseq_biological-replicate3

description: Library name: Sample 6


title: HeLa_+AA_mRNAseq_biological-replicate3

description: Library name: Sample 3

value: AA


title: HeLa_+AA_mRNAseq_biological-replicate2

description: Library name: Sample 2


title: 6620c1, Smad4 KO, TGFb-treated, replicate 1

description:
Library name: KO6620_TGF_1
Column names correpond to raw data file names. Columns H and I show averaged counts.
KO_TGFbvsKO_deg_all_6620c1.xls


title: HeLa_-AA_mRNAseq_biological-replicate1

description: Library name: Sample 4


title: BMFA3v1, Smad4KO,untreated, replicate 1

description:
Library name: BM5
SMAD4 KO (-) in columns B, C, F shows counts for BM5, BM6, and averaged for BM5 and BM6, respectively; SMAD4 WT (-) in columns D, E, and G shows conts for BM1, BM2, and averaged for BM3 and BM4, respectively. SMAD4 KO+TGFB in columns B, C, F shows counts for BM7, BM8, and averaged counts, respectively; SMAD4 KO-TGFB in columns D, E, and G shows conts for BM5, BM6, and averaged counts, respectively;
KOvsEV_deg_all_BMFA3.xlsx
KO_TGFbvsKO_deg_all_BMFA3.xlsx


title: 6620c1, Smad4KO,untreated, replicate 2

description:
Library name: KO6620_2
Column names correpond to raw data file names. Columns H and I show averaged counts.
KOvsEV_deg_all_6620c1.xls
KO_TGFbvsKO_deg_all_6620c1.xls


title: BMFA3v1, Smad4 KO, TGFb-treated, replicate

description:
Library name: BM7
SMAD4 KO+TGFB in columns B, C, F shows counts for BM7, BM8, and averaged counts, respectively; SMAD4 KO-TGFB in columns D, E, and G shows conts for BM5, BM6, and averaged counts, respectively;
KO_TGFbvsKO_deg_all_BMFA3.xlsx


title: 6620c1, Smad4KO,untreated, replicate 3

description:
Library name: KO6620_3
Column names correpond to raw data file names. Columns H and I show averaged counts.
KOvsEV_deg_all_6620c1.xls
KO_TGFbvsKO_deg_all_6620c1.xls


title: 6620c1, Smad4KO,untreated, replicate 1

description:
Library name: KO6620_1
Column names correpond to raw data file names. Columns H and I show averaged counts.
KOvsEV_deg_all_6620c1.xls
KO_TGFbvsKO_deg_all_6620c1.xls


title: Patient sample 11, ADT

description:
Library name: P152-ADT
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: kidney

value: T cells

tag: disease

value: anca associated vasculitis

value: ADT

value: Features defined in ANCA_feature_reference.csv


title: HeLa_+AA_mRNAseq_biological-replicate1

description: Library name: Sample 1

value: HeLa


title: 6620c1, empty vector controrol, TGFb-treated, replicate 2

description:
Library name: EV6620_TGF_2
Column names correpond to raw data file names. Columns H and I show averaged counts.
EV_TGFbvsEV_deg_all_6620c1.xls


title: 6620c1, empty vector controrol, untreated, replicate 3

description:
Library name: EV6620_3
Column names correpond to raw data file names. Columns H and I show averaged counts.
KOvsEV_deg_all_6620c1.xls
EV_TGFbvsEV_deg_all_6620c1.xls


title: 6620c1, empty vector controrol, TGFb-treated, replicate 1

description:
Library name: EV6620_TGF_1
Column names correpond to raw data file names. Columns H and I show averaged counts.
EV_TGFbvsEV_deg_all_6620c1.xls


title: Patient sample 10, ADT

description:
Library name: P150-ADT
10X Genomics scRNA-seq using Chromium Single Cell 5'


title: Patient sample 11, TCR

description:
Library name: P152-TCR
10X Genomics scRNA-seq using Chromium Single Cell V(D)J

value: TCR


title: 6620c1, empty vector controrol, untreated, replicate 1

description:
Library name: EV6620_1
Column names correpond to raw data file names. Columns H and I show averaged counts.
KOvsEV_deg_all_6620c1.xls
EV_TGFbvsEV_deg_all_6620c1.xls

value: tumor


title: Patient sample 10, TCR

description:
Library name: P150-TCR
10X Genomics scRNA-seq using Chromium Single Cell V(D)J


title: Patient sample 11, GEX

description:
Library name: P152-GEX
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: mRNA


title: Patient sample 9, TCR

description:
Library name: P143-TCR
10X Genomics scRNA-seq using Chromium Single Cell V(D)J


title: 6620c1, empty vector controrol, untreated, replicate 2

description:
Library name: EV6620_2
Column names correpond to raw data file names. Columns H and I show averaged counts.
KOvsEV_deg_all_6620c1.xls
EV_TGFbvsEV_deg_all_6620c1.xls


title: Patient sample 8, ADT

description:
Library name: P140-ADT
10X Genomics scRNA-seq using Chromium Single Cell 5'


title: Patient sample 10,GEX

description:
Library name: P150-GEX
10X Genomics scRNA-seq using Chromium Single Cell 5'


title: traf6-ko-q820-5308-as-23

city: Ann Arbor

first: Scott

last: Soleimanpour

state: MI

address: 1000 Wall St

department: Metabolism, Endocrinology, and Diabetes

institute: University of Michigan

description:
Library name: Traf6 KO HFD 2
column name is raw-count-all-expressions.txt: Traf6 KO HFD Q820

data_processing:
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR (v2.6.1b) and assigned count estimates to genes with RSEM (v1.3.1).
Alignment options followed ENCODE standards for RNA-seq. FastQC was used in an additional post-alignment step to ensure that only high-quality data were used for expression quantitation and differential expression. Data were pre-filtered to remove genes with 0 counts in all samples.
Assembly: GRCm38
Supplementary files format and content: tab-delimited texted file includes raw counts for each sample

source_name: Pancreas

growth_protocol: After isolation, islets were left to recover for 24 hours in RPMI-1640 media supplemented with 100 U/mL penicillin/streptomycin, 10% FBS, 1 mM HEPES, 2 mM L-Glutamine, 100 U/mL antibiotic/antimycotic and 10 mM sodium pyruvate

extract_protocol:
RNA was harvested using E.Z.N.A.® Tissue DNA Kit (Omega biotek)
Libraries were constructed and subsequently subjected to 151 bp paired-end cycles on the NovaSeq-6000 platform (Illumina).

treatment_protocol: Prior to islet isolation, mice were placed on 60% high-fat diet (Research Diets Inc) for 15 weeks

value: Pancreas

value: Isolated islets

value: Traf6 KO

value: 15-week HFD


title: traf6-ko-s267-5308-as_62

description:
Library name: Traf6 KO HFD 3
column name is raw-count-all-expressions.txt: Traf6 KO HFD S267


title: traf6-ko-hfd-q819-5308-as-22

description:
Library name: Traf6 KO HFD 1
column name is raw-count-all-expressions.txt: Traf6 KO HFD Q819


title: Patient sample 8, TCR

description:
Library name: P140-TCR
10X Genomics scRNA-seq using Chromium Single Cell V(D)J


title: Patient sample 9, GEX

description:
Library name: P143-GEX
10X Genomics scRNA-seq using Chromium Single Cell 5'


title: 6620c1, empty vector controrol, TGFb-treated, replicate 3

description:
Library name: EV6620_TGF_3
Column names correpond to raw data file names. Columns H and I show averaged counts.
EV_TGFbvsEV_deg_all_6620c1.xls

value: derived from KPCY (KrasG12D/+; Trp53LSL-R172H/+; Pdx1Cre/+; Rosa26-YFP) mice

value: WT

value: 30ng/ TGFb, 48h


title: control-hfd-s214-5308-as-43

description:
Library name: Control HFD 4
column name is raw-count-all-expressions.txt: Control HFD S214

value: Control


title: Patient sample 8, GEX

description:
Library name: P140-GEX
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: kidney


title: control-hfd-q952-5308-as-20

description:
Library name: Control HFD 2
column name is raw-count-all-expressions.txt: Control HFD Q952


title: Patient sample 7, TCR

description:
Library name: P139-TCR
10X Genomics scRNA-seq using Chromium Single Cell V(D)J

value: T cells


title: control-hfd-q821-5308-as-18

description:
Library name: Control HFD 1
column name is raw-count-all-expressions.txt: Control HFD Q821


title: mouse eye

first: Ziyu

last: Lu

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

description: Library name: mouse eye

library_source: genomic single cell

data_processing:
Base calls were converted to fastq format and demultiplexed using Illumina’s bcl2fastq/v2.19.0.316 tolerating one mismatched base in barcodes (edit distance (ED) <= 1). For sequence processing, indexed Tn5 barcodes and ligation barcodes were extracted, and corrected to their nearest barcode (edit distance (ED) <= 1). Reads with uncorrected barcodes (ED >= 2) were removed. Tn5 adaptors were removed from the 5’-end and clipped from the 3’-end using trim_galore/v0.4.1. Trimmed reads were mapped to the mouse genome (mm10) using STAR/v2.5.2b with default settings. Aligned reads were filtered using samtools/v1.4.1 to retain reads mapped in proper pairs with quality score MAPQ > 30 and to keep only the primary alignment. Duplicates were removed by Picard MarkDuplicates/v2.25.271 per PCR sample. Deduplicated bam files were converted to bedpe format using bedtools/v2.30.072, which were further converted to offset-adjusted (+4 bp for plus strand and -5 bp for minus) fragment files (.bed). Fragment files were inputted for all downstream analyses with SnapATAC2/v2.5.1, including doublet removal, dimension reduction, unsupervised clustering, and cell annotation. After cell annotation, reads from each main cell type of each tissue were aggregated. Then, Tn5-corrected single-base insertions were extracted and subjected to peak calling using macs3/v3.0.0b3 for each group separately, with these parameters: --nomodel --extsize 200 --shift -100 -q 0.1. Peak summits were extended by 250bp on either side and then merged iteratively. Specifically, the peak with the smallest p-value was kept and any peak that directly overlapped with it was removed. Then, this process was iterated to the next most significant peak and so on until all peaks were either kept or removed due to direct overlap with a more significant peak. The peak count matrix and the gene activity matrix were generated using the SnapATAC2 function snapatac2.pp.make_peak_matrix and snapatac2.pp.make_gene_matrix.
Assembly: mouse reference genome (mm10)
Supplementary files format and content: Processed data files include a peak count matrix and a gene count matrix in h5ad format for each tissue.

molecule: genomic DNA

source_name: eye

extract_protocol:
Dissected mouse tissue samples were snap-frozen in liquid nitrogen and stored at -80C. For nuclei extraction, frozen tissues were placed inside aluminum foil, and smashed into powders with a hammer on dry ice. Then, transfer the powdered tissue into 10-20 mL nuclei lysis buffer [10 mM Tris-HCl pH 7.5 (VWR, 97062-936), 10 mM NaCl (VWR, 97062-858), 3 mM MgCl2 (VWR, 97062-848), 0.025% IGEPAL CA-630 (VWR, IC0219859650), 0.1% Tween-20 (Sigma, P9416-100ML), 1x cOmplete, EDTA-free Protease Inhibitor Cocktail (Sigma, 11873580001)], briefly vortex, and incubate for 10-15 minutes at 4C on a rotator. Extracted nuclei were then filtered through 40 m cell strainers (VWR, 470236-276), stained with 4',6-diamidino-2-phenylindole staining (DAPI, Invitrogen D1306), and sorted for singlets.
On the same day of the library preparation, perform nuclei extraction, stain the nuclei with 4',6-diamidino-2-phenylindole staining (DAPI, Invitrogen D1306), and FAC sort for singlets. Spin down the sorted nuclei at 500g for 5 minutes, resuspend in nuclei buffer [10 mM Tris-HCl pH 7.5 (VWR, 97062-936), 10 mM NaCl (VWR, 97062-858), 3 mM MgCl2 (VWR, 97062-848), 0.025% IGEPAL CA-630 (VWR, IC0219859650), 0.1% Tween-20 (Sigma, P9416-100ML), 1x cOmplete, EDTA-free Protease Inhibitor Cocktail (Sigma, 11873580001)] to a final concentrations of 1000~2000 nuclei/µL. Nuclei were mixed in a 1:1 ratio with 2X TD buffer [20 mM Tris-HCl pH 7.5, 20 mM MgCl2, 20% Dimethylformamide (Fisher, AC327175000)] and dispensed 10 µL into each well of four 96-well plates. 1 µL barcoded Tn5 was loaded into each well. Tagmentation reaction was performed at 37°C for 30 minutes with gentle shaking at 300 rpm and stopped by adding 11 µL of 2X Stop buffer [40 mM EDTA (VWR, 37062-656), 1 mM Spermidine (Sigma, S0266-1G)] to each well. Samples were pooled and washed twice and resuspended resuspended in nuclei buffer. 5 µL of resuspended nuclei were distributed into each well of 96-well plates. 2 µL indexed EasySci P5 ligation adapters and 3 µL ligation mix [1 µL nuclease-free water, 1 µL 10X T4 DNA ligase buffer, 1 µL T4 DNA ligase (NEB, M0202L)] were added to each well. Ligation was performed at room temperature for 30 minutes with medium-speed rocking (350g) and stopped by adding 2 µL of 18 mM EDTA to each well. After that, nuclei were pooled, washed, resuspended using nuclei buffer, and subjected to another round of FAC sort based on DAPI staining to remove doublets. Then, sorted nuclei were distributed into PCR plates as 5 uL per well. Proteinase K treatment was performed by mixing each well with 0.25 μL 18.9 mg/mL proteinase K (Sigma, 3115828001), 0.25 µL 1% SDS, and 0.5 µL EB buffer, and plates were incubated at 65°C for 16 hours. Then, 2 μL 10% Tween-20 was added to each well to quench the SDS. Following on, 1 μL of 10 μM universal P5 primer (5′-AATGATACGGCGACCACCGAGATCTACAC-3′, IDT), 1 μL of 10 μM indexed P7 primer (5’-CAAGCAGAAGACGGCATACGAGAT[i7]GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3’, IDT) and 10 μL NEBNext High-Fidelity 2X PCR Master Mix (NEB M0541L) were added into each well. Amplification was carried out using the following program: 72°C for 5 minutes, 98°C for 30 seconds, 13-14 cycles of 98°C for 10 seconds, 66°C for 30 seconds, 72°C for 30 seconds and a final 72°C for 5 minutes. Final PCR products were pooled and purified by column purification using a Zymo DNA Clean & Concentrator kit (Zymoresearch, D4014) followed by gel extraction using Zymoclean Gel DNA Recovery Kit (Zymoresearch, D4007) to remove adapter dimers. Library concentrations were determined by Qubit and the libraries were visualized by electrophoresis on a 2% E-Gel™ EX Agarose Gels (Invitrogen G402022).

tag: strain

value: eye


title: Patient sample 7, ADT

description:
Library name: P139-ADT
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: anca associated vasculitis

value: ADT


title: mouse intestine

description: Library name: mouse intestine

value: intestine


title: mouse thymus

description: Library name: mouse thymus

source_name: thymus

value: thymus


title: Patient sample 6, TCR

description:
Library name: P138-TCR
10X Genomics scRNA-seq using Chromium Single Cell V(D)J

value: TCR


title: mouse muscle

description: Library name: mouse muscle

source_name: muscle

value: muscle


title: mouse spleen

description: Library name: mouse spleen

source_name: spleen

value: spleen


title: mouse stomach

description: Library name: mouse stomach

source_name: stomach

value: stomach


title: Patient sample 5, TCR

description:
Library name: P137-TCR
10X Genomics scRNA-seq using Chromium Single Cell V(D)J


title: mouse pancreas

description: Library name: mouse pancreas

source_name: pancreas

value: pancreas


title: Patient sample 5, ADT

description:
Library name: P137-ADT
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: Features defined in ANCA_feature_reference.csv


title: Patient sample 5, GEX

description:
Library name: P137-GEX
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: mRNA


title: mouse esophagus

description:
Library name: mouse esophagus
Sequencing instrument: Illumina Nextseq 6000 and NextSeq 1000

source_name: esophagus

value: esophagus


title: Patient sample 4, ADT

description:
Library name: P129-ADT
10X Genomics scRNA-seq using Chromium Single Cell 5'


title: mouse heart

description: Library name: mouse heart

source_name: heart

value: heart


title: Patient sample 4, TCR

description:
Library name: P129-TCR
10X Genomics scRNA-seq using Chromium Single Cell V(D)J


title: Patient sample 4, GEX

description:
Library name: P129-GEX
10X Genomics scRNA-seq using Chromium Single Cell 5'


title: mouse ovary and uterus

description: Library name: mouse ovary and uterus

source_name: ovary and uterus

value: ovary and uterus


title: Patient sample 3, ADT

description:
Library name: P070-ADT
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: kidney


title: Patient sample 3, TCR

description:
Library name: P070-TCR
10X Genomics scRNA-seq using Chromium Single Cell V(D)J

value: T cells


title: control-hfd-r037-5308-as-21

description:
Library name: Control HFD 3
column name is raw-count-all-expressions.txt: Control HFD R037

value: Pancreas

value: Isolated islets

value: Control

value: 15-week HFD


title: mouse cecum

description:
Library name: mouse cecum
Sequencing instrument: Illumina Nextseq 6000 and NextSeq 1000

source_name: cecum

value: cecum


title: mouse bone marrow

description: Library name: mouse bone marrow

source_name: bone marrow

value: bone marrow


title: Patient sample 6, ADT

description:
Library name: P138-ADT
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: anca associated vasculitis

value: ADT


title: Patient sample 2, ADT

description:
Library name: P067-ADT
10X Genomics scRNA-seq using Chromium Single Cell 5'


title: Patient sample 7, GEX

description:
Library name: P139-GEX
10X Genomics scRNA-seq using Chromium Single Cell 5'


title: mouse colon

description: Library name: mouse colon

source_name: colon

value: colon


title: Patient sample 2, TCR

description:
Library name: P067-TCR
10X Genomics scRNA-seq using Chromium Single Cell V(D)J

source_name: kidney

value: TCR


title: mouse mesenteric white adipose tissue

description:
Library name: mouse mesenteric white adipose tissue
Sequencing instrument: Illumina Nextseq 6000 and NextSeq 1000

source_name: mesenteric white adipose tissue

value: mesenteric white adipose tissue


title: Patient sample 6, GEX

description:
Library name: P138-GEX
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: mRNA


title: mouse gonadal white adipose tissue

description:
Library name: mouse gonadal white adipose tissue
Sequencing instrument: Illumina Nextseq 6000 and NextSeq 1000

source_name: gonadal white adipose tissue

value: gonadal white adipose tissue


title: mouse inguinal white adipose tissue

description:
Library name: mouse inguinal white adipose tissue
Sequencing instrument: Illumina Nextseq 6000 and NextSeq 1000

source_name: inguinal white adipose tissue

value: inguinal white adipose tissue


title: Patient sample 1, ADT

description:
Library name: P053-ADT
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: Features defined in ANCA_feature_reference.csv


title: Patient sample 2, GEX

description:
Library name: P067-GEX
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: kidney


title: mouse brown adipose tissue

description: Library name: mouse brown adipose tissue

source_name: brown adipose tissue

value: brown adipose tissue


title: mouse kidney

description: Library name: mouse kidney


title: mouse lung

description: Library name: mouse lung

source_name: lung

value: lung


title: Patient sample 1, TCR

description:
Library name: P053-TCR
10X Genomics scRNA-seq using Chromium Single Cell V(D)J

value: T cells


title: Patient sample 1, GEX

description:
Library name: P053-GEX
10X Genomics scRNA-seq using Chromium Single Cell 5'


title: MM1S_LBH_3

city: Chengdu

first: Qiang

last: Qiu

state: Sichuan

address: No. 17, the Third Part of Renmin South Road

department: SKLB

country: China

institute: Sichuan university

description: Library name: Sample9

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then clean reads for each sample were retained for subsequent analyses. The clean reads were mapped to the reference genome using HISAT2. The read counts of each gene were obtained by HTSeq-count.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

source_name: MM1S cell-derived tumor tissue

extract_protocol:
CDX subcutaneous mice were given a single dose of Vehicle, or PM 10 mg/kg, when tumor size reached around 500 mm3. Tumor tissues were collected for bulk RNA-seq after 24 hours. Total RNA was extracted using the Trizol method.
Total RNA was extracted using the Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: MM1S cell-derived tumor tissue


title: S17_Q_WT_VSB_M

city: Philadelphia

first: Ashley

middle: B

last: Robbins

address: 3501 Civic Center Blvd.

institute: Children's Hospital of Philadephia

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_Q_S17
column name in kallisto_gene_counts_matrix_allsamples.csv: Q_WT_VSB

data_processing:
FASTQ files were generated with bcl2fastq (v2.20)
Kallisto (v0.46.0) was used to pseudoalign samples to the Mus_musculus.GRCm39 transcriptome.
DESeq2 (v1.44.0) via TxImport (v1.32.0), genes with less than 10 counts in at least 5 samples, and differential gene expression analysis was performed between genotypes and treatment groups.
Assembly: GRCm39
Supplementary files format and content: Kalisto output abundance files for each sample as input for Tximport.
Supplementary files format and content: Comma-separated values file containing the kallisto gene counts matrix for all samples used for DESeq2 analysis.

source_name: Lumbar Spinal Cord

extract_protocol:
Total RNA was extracted with Trizol protocol (15596018; Thermo Fisher Scientific, Waltham, MA). Samples were enriched for  PolyA RNA with the NEBNext® Poly(A) mRNA Magnetic Isolation Module(S7590S; New England Biolabs, Ipswitch, MA). 1ug of total RNA was used as input. All samples had RIN values > 8.
Libraries for each sample were prepared following the protocol for the NEBNext Ultra II Directional RNA Library Prep Kit with Sample Purification Beads (E7765; New England Biolabs). cDNA libraries were then indexed using the NEBNext Dual Index Kit (E7600S; New England Biolabs).

treatment_protocol: Mice were dosed with PM-AAV9.miAtxn2 or virus buffer by bilateral ICV injection at postnatal day 1. Treatment condition was randomized within each litter and experimenters were blinded prior to data analysis.

value: Lumbar Spinal Cord

value: WT

value: VSB

tag: rna extraction_batch

tag: litter

value: postnatal day 19


title: S16_P_MUT_VSB_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_P_S16
column name in kallisto_gene_counts_matrix_allsamples.csv: P_MUT_VSB


title: MM1S_LBH_2

description: Library name: Sample8


title: mouse skin

description:
Library name: mouse skin
Sequencing instrument: Illumina Nextseq 6000 and NextSeq 1000

source_name: skin

value: skin


title: S15_O_MUT_VSB_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_O_S15
column name in kallisto_gene_counts_matrix_allsamples.csv: O_MUT_VSB


title: MM1S_PM_2

description: Library name: Sample5


title: MM1S_PM_3

description: Library name: Sample6


title: Patient sample 3, GEX

description:
Library name: P070-GEX
10X Genomics scRNA-seq using Chromium Single Cell 5'

value: anca associated vasculitis


title: S14_N_MUT_V1_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_N_S14
column name in kallisto_gene_counts_matrix_allsamples.csv: N_MUT_V1


title: MM1S_PM_1

description: Library name: Sample4


title: S12_L_WT_VSB_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_L_S12
column name in kallisto_gene_counts_matrix_allsamples.csv: L_WT_VSB


title: MM1S_con_2

description: Library name: Sample2


title: MM1S_con_3

description: Library name: Sample3


title: MM1S_con_1

description: Library name: Sample1


title: S10_J_WT_VSB_F

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_J_S10
column name in kallisto_gene_counts_matrix_allsamples.csv: J_WT_VSB


title: S11_K_MUT_V1_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_K_S11
column name in kallisto_gene_counts_matrix_allsamples.csv: K_MUT_V1


title: S8_H_MUT_VSB_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_H_S8
column name in kallisto_gene_counts_matrix_allsamples.csv: H_MUT_VSB


title: pm-3

description: Library name: Sample6

source_name: Patient-derived lymphoma tissue

extract_protocol:
PDX subcutaneous mice were given a single dose of vehicle, or PM 10 mg/kg, when tumor size reached around 500 mm3. Tumor tissues were collected for bulk RNA-seq after 24 hours. Total RNA was extracted using the Trizol method.
Total RNA was extracted using the Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Patient-derived lymphoma tissue


title: S6_F_WT_VSB_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_F_S6
column name in kallisto_gene_counts_matrix_allsamples.csv: F_WT_VSB


title: pm-2

description: Library name: Sample5


title: MM1S_LBH_1

description: Library name: Sample7


title: mouse liver

description: Library name: mouse liver

source_name: liver

value: liver


title: S4_D_WT_VSB_F

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_D_S4
column name in kallisto_gene_counts_matrix_allsamples.csv: D_WT_VSB


title: Vehicle-2

description: Library name: Sample2


title: Vehicle-3

description: Library name: Sample3


title: S5_E_MUT_VSB_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_E_S5
column name in kallisto_gene_counts_matrix_allsamples.csv: E_MUT_VSB


title: S3_C_MUT_VSB_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_C_S3
column name in kallisto_gene_counts_matrix_allsamples.csv: C_MUT_VSB


title: Aged, immune, fractured

city: Farmington

first: Justin

middle: S

last: King

state: Connecticut

address: 263 Farmington Ave

institute: UConn Health

description: 10x Genomics

data_processing:
Demultiplexing barcode processing, gene counting and aggregation were done using the --force-cells argument equal to 6000 using Cell Ranger (v7.0.1) (https://www.10xgenomics.com/support/software/cell-ranger/latest)
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Cell Ranger Output

source_name: Femur periostieum

extract_protocol:
Freshly collected periosteal cells from young and aged mice were FACS sorted gated on Ter119- then CD45+ or CD45- to collect 6000 live cells that were used for 10x Chromium-based single cell seuqecing
Library constructure was perfomred according to manufacter's protocol (SC3Pv3 Chemistry; 10x Genomics).

value: Femur periostieum

value: 18-24 months

value: Immune cell

value: Fractured bone (POD 3)


title: S2_B_MUT_V1_F

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_B_S2
column name in kallisto_gene_counts_matrix_allsamples.csv: B_MUT_V1


title: Vehicle-1

description: Library name: Sample1


title: PBS, donor4

description: Library name: d4.C3_001.filtered

data_processing:
De-multiplexed raw sequencing data were converted into gene counts using QIAGEN Omicsoft Array Studio, which filtered out the sequencing reads with low quality and aligned sequencing reads to the human reference genome GRCh38
genes with low expression in raw count data were filtered out. TMM normalization and log2 transformation were implemented using edgeR
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with normalized counts (log2 and TMM normalized) of each sample

source_name: dorsal root ganglion neurons

extract_protocol:
Total RNA from human DRG neuronal culture was extracted using Qiagen RNeasy Plus Universal mini kit.
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: dorsal root ganglion neurons

value: PBS


title: S1_A_WT_VSB_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_A_S1
column name in kallisto_gene_counts_matrix_allsamples.csv: A_WT_VSB


title: IL4+IL13+dupi, donor2

description: Library name: d2.D5_001.filtered

value: IL-4 + IL-13 + Dupilumab


title: IL4+IL13+Isotype, donor2

description: Library name: d2.D4_001.filtered

value: IL-4 + IL-13 + IgG4k-Isotype


title: IL4+IL13+Isotype, donor4

description: Library name: d4.D4_001.filtered


title: Aged, non-immune, intact

description: 10x Genomics

value: Non-immune cells

value: Intact bone


title: IL4+IL13+dupi, donor3

description: Library name: d3.D5_001.filtered


title: PBS, donor3

description: Library name: d3.C3_001.filtered


title: Young, non-immune, fractured

description: 10x Genomics

value: 3 months


title: IL4+IL13+dupi, donor4

description: Library name: d4.D5_001.filtered


title: Aged, immune, intact

description: 10x Genomics


title: S13_M_MUT_V1_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_M_S13
column name in kallisto_gene_counts_matrix_allsamples.csv: M_MUT_V1

value: Lumbar Spinal Cord


title: Young, immune, fractured

description: 10x Genomics


title: PBS, donor2

description: Library name: d2.C3_001.filtered


title: Young, non-immune, intact

description: 10x Genomics


title: pm-1

description: Library name: Sample4


title: SUM159-1-3, HIF-1α, ChIP

city: Baltimore

first: YONGKANG

last: YANG

state: Maryland

address: Room 673, MRB, 725 North Broadway

department: ICE

institute: Johns Hopkins University

description:
Library name: SUM159-1-3_HIF-1α
Antibody: HIF-1α (Novus, NB100-479)

library_source: genomic

data_processing:
FastQ files were quality checked and adapter trimmed using Trim-Galore (v0.6.6) with the following flags: --paired --fastqc --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 3 --three_prime_clip_R2 3. Trimmed FastQ files were mapped to the hg19 or hg38 human reference genomes using BWA (v0.7.17), and PCR duplicates marked then removed using Biobambam2 (v2.0.87) and Samtools (v1.10), respectively. Coverage tracks were generated using the bamCoverage program in the deepTools (v3.5.1) package. ChIP-seq peaks were called using MACS2 in narrow peak mode with input samples as controls, and peaks were overlaid and subsetted using Bedtools (v2.30.0). Heat maps were generated using the deepTools computeMatrix and plotHeatmap commands. Differentially bound peaks were identified using the DiffBind package (v3.8.4) in R (v4.2). Genes with differential HIF1a binding were identified using Gencode gene annotations.
Assembly: hg19
Supplementary files format and content: bigwig files and excel table containing detailed information on sample comparison, peak metrics and gene annotations.

source_name: breast

growth_protocol: SUM159 cells were maintained in DMEM/Hams F-12 50/50 Mix that were supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1% (vol/vol) penicillin-streptomycin (P/S).

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated and the DNA was sheared to an average length of 300-500 bp with Covaris E220 sonicator.
DNA libraries were prepared using the Takara Bio Low Input ChIP-seq kit according to manufacturer’s instructions. 1 ug of ChIP DNA was used from each sample and amplified with 16 PCR cycles. Libraries were sequenced at an average depth of 50 million reads using an Illumina NovaSeq sequencer (2 × 100 reads)

treatment_protocol: SUM159 cells were exposed in 20% or 1% oxygen condition for 16 hours.

value: breast

value: breast cancer cells

value: wild type

value: 1% oxygen condition for 16 hours


title: Aged, non-immune, fractured

description: 10x Genomics


title: Young, immune, intact

description: 10x Genomics


title: S7_G_MUT_V1_M

description:
Library name: ABR_Atxn2KOTdp43_SC_Mouse_mRNA_G_S7
column name in kallisto_gene_counts_matrix_allsamples.csv: G_MUT_V1

value: postnatal day 19


title: SUM159-1-2, HIF-1α, ChIP

description:
Library name: SUM159-1-2_HIF-1α
Antibody: HIF-1α (Novus, NB100-479)


title: IL4+IL13+Isotype, donor3

description: Library name: d3.D4_001.filtered


title: SUM159-1-1, HIF-1α, ChIP

description:
Library name: SUM159-1-1_HIF-1α
Antibody: HIF-1α (Novus, NB100-479)


title: SUM159-1, Input

description:
Library name: SUM159-1_Input
Antibody: None


title: 63_NR_Tg_2

city: Bethesda

first: Teruhiko

last: Yoshida

address: 10 Center Drive, 9N208

department: NIDDK - KDB

institute: National Institutes of Health

data_processing:
Illumina RTA v3.4.4 software was used fro base calling, Bcl2fastq v2.17 was used for sample demultiplexing
Adapters from the samples were trimmed using Cutadapt 1.18 software
Genome mapping and transcript annotation were using STAR v2.7.0f with reference genome mm10.
The gene expression quantification analysis was performed for all samples using RSEM 1.3.1
Assembly: mm10
Supplementary files format and content: xlsx file contains rawcount matrix from RSEM

source_name: Kidney Cortex

extract_protocol:
Mice were euthanized and collected kidneys in their week of 12 weeks of age. Mouse kidney outer cortex tissues were dissected and homogenized in QIAzol. Total RNA samples were extracted by RNeasy Plus Universal Kit (QIAGEN, Hilden, Germany) following manufacture’s protocol including removal of genomic DNA step.
RNA libraries were prepared for sequencing using standard Illumina TruSeq Stranded mRNA library protocol.

value: Kidney Cortex

value: NR


title: 62_NR_Tg_1


title: 60_NR_WT_2

value: WT


title: SUM159-20-3, HIF-1α, ChIP

description:
Library name: SUM159-20-3_HIF-1α
Antibody: HIF-1α (Novus, NB100-479)

value: 20% oxygen condition for 16 hours


title: 59_NR_WT_1


title: SUM159-20-2, HIF-1α, ChIP

description:
Library name: SUM159-20-2_HIF-1α
Antibody: HIF-1α (Novus, NB100-479)


title: 57_I747_Tg_2


title: MDA231-BrM2 cells, DKD, 1% O2 (biol rep 1)

data_processing:
RNA-seq data were processed and interpreted using Genialis Expressions software (https://www.genialis.com). Sequence quality checks were performed on raw and trimmed reads (FastQC), trimming and quality filtering of reads (BBDuk), mapping to reference human genome Ensembl v.92 (STAR), expression quantification (featureCounts), and expression normalisation (RNA.norm).
Assembly: GRCh38
Supplementary files format and content: Excel tables containing detailed information on TPM values for each Sample

growth_protocol: MDA231-BrM2 cells were maintained in Dulbecco’s modified Eagle medium (DMEM) that were supplemented with 10% (vol/vol) fetal bovine serum (FBS) and 1% (vol/vol) penicillin-streptomycin (P/S).

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and treated with DNase (Qiagen).
Library preparation and sequencing using the NovaSeq 6000 platform (Illumina) were performed by the Johns Hopkins Genetics Resources Core Facility High-Throughput Sequencing Center.

treatment_protocol: HIFs knockdown or control subclones of MDA231-BrM2 cells were exposed in 20% or 1% oxygen condition for 24 hours.

value: MDA231-BrM2 cells

value: HIF-1alpha and HIF-2alpha double knockdown (DKD)

value: 1% O2, 24 hours


title: 61_NR_WT_3


title: 55_I747_WT_3


title: 56_I747_Tg_1


title: 58_I747_Tg_3


title: 54_I747_WT_2


title: MDA231-BrM2 cells, DKD, 20% O2 (biol rep 2)


title: SUM159-20-1, HIF-1α, ChIP

description:
Library name: SUM159-20-1_HIF-1α
Antibody: HIF-1α (Novus, NB100-479)


title: SUM159-20, Input

description:
Library name: SUM159-20_Input
Antibody: None


title: MDA231-BrM2 cells, DKD, 1% O2 (biol rep 2)


title: MDA231-BrM2 cells, DKD, 1% O2 (biol rep 3)


title: MDA231-BrM2 cells, DKD, 20% O2 (biol rep 3)


title: 53_I747_WT_1


title: MDA231-BrM2 cells, NTC, 1% O2 (biol rep 3)


title: MDA231-BrM2 cells, DKD, 20% O2 (biol rep 1)


title: LS Acute naloxone (Nal no mor)

city: Seattle

first: Rhiana

middle: Catherine

last: Simon

state: WA

address: 1959 NE Pacific St

department: Anesthesiology & Pain Medicine

institute: University of Washington

description: 10x Genomics

data_processing:
Demultiplexing, genome alignment, and processing of gene expression matrices were carried out using CellRanger v3.1.0 (samples 1-3) / Cellranger-6.1.2 (samples 4-5)
Assembly: mm10
Library strategy: snRNA-seq

molecule: nuclear RNA

source_name: Septal complex

extract_protocol:
Each day for 3 days prior to tissue collection, all animals were habituated to the procedure room for ~2 hours to control for environmentally-induced immediate early gene activity. On the day of sacrifice, mice were sequentially euthanized with sodium pentobarbital (> 90 mg kg-1 Somnasol) and transcardially perfused with ice-cold NMDG (96 mM NMDG, 2.5 mM KCl, 1.35 mM NaH2PO4, 30 mM NaHCO3, 20 mM HEPES, 25 mM glucose, 2 mM thiourea, 5 mM Na+ ascorbate, 3 mM Na+pyruvate, 0.6 mM glutathione-ethyl-ester, 2 mM N-acetyl-cysteine, 0.5 mM CaCl2, 10 mM MgSO4; pH 7.35–7.40, 300-305 mOsm, continuously oxygenated with 95% O2 and 5% CO2). This NMDG solution was also used for tissue sectioning and for a collection bath. Both the perfusion solution and recovery bath included an inhibitor cocktail containing 500 nM TTX, 10 μM APV, 10 μM DNQX, 5 μM actinomycin, and 37.7 μM anysomycin, as described previously29. 250 μm thick coronal sections containing septum were rapidly harvested using a Leica Vibratome (VT1200). The septal complex was then rapidly microdissected, flash-frozen on powdered dry ice, and stored at -80 °C. We intended to reduce nucleus accumbens contamination as much as possible. To this end, our tissue sections primarily ranged from +1.10 mm through 0.0 mm with respect to Bregma. We also excluded the medial septum and diagonal band level to and ventral to the accumbens. Once tissue from all animals were collected and stored, we proceeded with nuclear isolation. The following steps were all performed on ice. Also note that the PBS used here was Ca2+ and Mg2+ free. For each experimental group, we pooled all mice into the same tube containing a hypertonic lysis buffer (10mM Tris-HCl, 10 mM NaCl, 3 mM MgCl2, 0.1% Igepal, 0.2 U/μl Lucigen NxGen RNase inhibitor). Nuclei were extracted using a glass dounce homogenizer (DWK, #885300-0002) via 5-10 reps of pestle A and 5 reps of pestle B. Nuclei were then incubated in lysis buffer for 5 min. Next, the nuclear extract was moved into a clean tube, diluted to ~5-6 ml using a wash buffer (1X PBS, 1% BSA, 0.2 U/μl RNase inhibitor), and strained into a new 50 ml conical tube using a 40 μm cell strainer (pluriSelect, # 43-50040-51). Strained nuclei were centrifuged for 10 min, 500 x g at 4 °C. The resulting pellet was then retained. To purify our nuclei, we used density gradient centrifugation, where we prepared a two-layer column containing a 25% and 30% iodixanol (OptiPrep, Sigma-Aldrich, #D1556) gradient. Briefly, we suspended the nuclear pellet in a homogenate solution (0.25M Sucrose, 25 mM KCl, 5 mM MgCl2, 20 mM Tris-HCl, pH 7.8-8.0, and 0.2 U/μl RNase inhibitor), and combined the resuspended pellet 1:1 with a 50% iodixanol solution (50% OptiPrep, 25 mM KCl, 5 mM MgCl2, 20 mM Tris-HCl, 1% BSA, 0.2 U/μl RNase inhibitor, pH 7.8-8.0) in a clean 15-ml conical tube. This creates a 25% iodixanol layer. Next, we prepare a 30% iodixanol layer (30% OptiPrep, 25 mM KCl, 5 mM MgCl2, 20 mM Tris-HCl, 1% BSA, 0.2 U/μl RNase inhibitor) and underlaid the 25% iodixanol layer with this 30% layer using a 18G needle. This density gradient column was then centrifuged for 15 min, 3000 x g at 4 °C. The resulting purified and invisible pellet was then resuspended in wash buffer. Nuclei were stained with propidium iodide and assessed for yield and quality using a disposable Neubauer hemocytometer (INCYTO, #DHC-N01) on a fluorescent microscope (Zeiss ApoTome.2). Final nuclear concentration was adjusted to 1,000 nuclei per μl in preparation for single nucleus capture.
Approximately 10,000 nuclei per experimental group were captured and single-nucleus cDNA libraries were constructed using the Chromium Single Cell 3' v3 (samples 1-3) and Chromium NextGEM platform (samples 4-5) according to manufacturer’s instructions. Libraries for samples 1-3 were sequenced using an Illumina 4400 HiSeq platform to a target output of ~ 350,000,000 reads, and libraries 4-5 were sequenced using an Illumina NovaSeq 6000 for a target output of ~350,000,000 reads

treatment_protocol: A total of 30 wildtype mice (~8 weeks) were used for single-nucleus RNA-sequencing. Animals were assigned to one of the following groups: saline (Sal; saline only), chronic morphine (Mor; escalating morphine), naloxone (Nal; escalating morphine plus naloxone), acute morphine (Mor-single; saline 13x, one dose of 10 mg kg-1 morphine) and naloxone only (Nal-no-mor; saline 13x, one dose of 1 mg kg-1 naloxone). Each experimental group included 3 male and 3 female mice that were pooled into the same reaction.

tag: brain region

value: Septal complex

value: 8 weeks

value: Brain

value: Saline 13x, 7 days, 2x day; final dose was 1 mg/kg naloxone; collected 1 hr following naloxone


title: 64_NR_Tg_3

tag: tissue


title: LS Acute morphine (One Mor)

description: 10x Genomics

tag: treatment

value: Saline 13x, 7 days, 2x day; final dose was 10 mg/kg morphine; collected 1 hr following morphine


title: MDA231-BrM2 cells, NTC, 1% O2 (biol rep 2)

value: breast


title: MDA231-BrM2 cells, NTC, 1% O2 (biol rep 1)

value: breast cancer cells


title: MDA231-BrM2 cells, NTC, 20% O2 (biol rep 2)

value: wild type


title: MDA231-BrM2 cells, NTC, 20% O2 (biol rep 1)


title: breast tumor Z022T

type: RNA

city: Prague 10

first: Veronika

last: Boušková

address: Srobarova 48

country: Czech Republic

institute: National Institute of Public Health

hyb_protocol: protocol for miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Version 3.1, Agilent Technologies)

scan_protocol: scanning protocol: AgilentG3_miRNA high-sensitivity

data_processing:
data extraction: Feature Extraction version software (v11.5.1.1, Agilent) with default parameters for miRNA (Grid: 046064_D_F_20141006)
Total gene signal for all miRNA genes on the microarrays was extracted from the Feature extraction reports, quantile normalized, and log2 transformed with the help of AgiMicroRna and Linear Models for Microarray Data (limma) R/Bioconductor software packages (v3.17). The genes detected in less than 75% of samples or having intensities less than 20 percentile were excluded from further analysis.

source_name: breast tumor

extract_protocol: Total RNA was extracted from fresh frozen tumor tissue using the TRIzol reagent (Thermo Fisher Scientific) following the manufacturer’s protocol.

value: primary tumor tissue

tag: gender

value: female


title: MDA231-BrM2-1-2, HIF-1α, ChIP

description: Antibody: HIF-1α (Novus, NB100-479)

treatment_protocol: MDA231-BrM2 cells were exposed in 20% or 1% oxygen condition for 16 hours.

value: 1% oxygen condition for 16 hours


title: MDA231-BrM2-1-1, HIF-1α, ChIP

description: Antibody: HIF-1α (Novus, NB100-479)


title: MDA231-BrM2-1, Input

description: Antibody: None


title: breast tumor M266T

label_protocol: protocol for miRNA Microarray System with miRNA Complete Labeling and Hyb Kit (Version 3.1, Agilent Technologies)


title: MDA231-BrM2-20-3, HIF-1α, ChIP

description: Antibody: HIF-1α (Novus, NB100-479)


title: breast tumor M277T


title: breast tumor M226T


title: primary Large Intestine fibroblasts, IL17, 20 ng/mL

city: Vancouver

first: Lesley

last: Hill

state: BC

address: 2222 Health Sciences Mall

country: Canada

institute: University of British Columbia

description:
Library name: IL17_A
IL17A_LH_LI_A1

data_processing:
Illumina sequencing outputs generated bcl files that were demultiplexed by bcl2fastq2
Demultiplexed read sequences were aligned to the Mouse Genome (mm10) reference sequence using TopHat splice junction mapper with Bowtie 2 or STAR aligners (Illumina Basespace)
Assembly: mm10
Supplementary files format and content: tab-delimited file contains raw counts for each sample
Supplementary files format and content: tab-delimited file contains TPM values for each sample

source_name: cecum and large intestine

growth_protocol: Primary intestinal fibroblasts were maintained in DMEM supplemented with 20% FBS, L-glutamine and pen-strep in humidified atmosphere with 5% CO2

extract_protocol:
RNA was harvested using Rneasy mini kits (Qiagen).
RNA libraries were prepared using TruSeq Stranded mRNA library kit following manufacturer's protocols.

treatment_protocol: Cells were treated with media supplemented with IL-17A at 20 ng/mL or 200 ng/mL. Control cells received 1% BSA. Cells were treated ~24 hours after plating and cells were lysed 24 hours after treatment.

value: cecum and large intestine

value: primary

value: fibroblasts

value: IL-17A, 20 ng/mL


title: primary Large Intestine fibroblasts, control

description:
Library name: Control
Control_LH_LI_C2

value: control


title: primary Large Intestine fibroblasts, IL17, 200 ng/mL

description:
Library name: IL17_B
IL17B_LH_LI_B1


title: MDA231-BrM2-20-2, HIF-1α, ChIP

description: Antibody: HIF-1α (Novus, NB100-479)

value: 20% oxygen condition for 16 hours


title: breast tumor M202T


title: breast tumor M199T


title: MDA231-BrM2 cells, NTC, 20% O2 (biol rep 3)

value: MDA231-BrM2 cells


title: scRNA-Seq-BLM rep3

city: New Orleans

first: Victor

middle: J

last: Thannickal

state: LA

address: 333 South Liberty Street

department: Medicine

institute: Tulane University

description: 10 X genomics

data_processing:
10x Cellranger V.7.0.0 were used to generate Fastq files, perform alignment, filtering, barcode counting, UMI counting and aggregation.
Assembly: mm10
Supplementary files format and content: Tab separated values files and matrix files

source_name: Lung

extract_protocol:
mRNA was extracted from mouse single cell suspension using the 10X Genomics Chromium™ Single Cell G Chip Kit
Library construction was performed according to 10x Genomics Chromium™ Single Cell 3' Reagent Kit v3.1 protocol.

value: Lung

value: Lung cells

tag: disease state

value: mouse model of bleomycin-induced lung fibrosis


title: scRNA-Seq-BLM rep2

description: 10 X genomics


title: MDA231-BrM2-20-1, HIF-1α, ChIP

description: Antibody: HIF-1α (Novus, NB100-479)


title: scRNA-Seq-BLM rep1

description: 10 X genomics


title: Normal human plasma 1

city: Guangzhou

first: kai

last: lei

address: 107 Yan Jiang West Road

department: Department of Thoracic Surgery

institute: Sun Yat-sen Memorial Hospital, Sun Yat-sen University

description: Biological replicate 1 of 3.Normal human plasma

hyb_protocol: 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: Normal human plasma

label_protocol: The enriched circular RNAs were amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen). The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

growth_protocol: Three pairs of plasma were collected from patients with ESCC and normal individuals

extract_protocol: Total RNA from each sample was quantified using the NanoDrop ND-1000. The sample preparation and microarray hybridization were performed based on the Arraystar’s standard protocols. Briefly, total RNAs were digested with Rnase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs.

treatment_protocol: Fresh plasma from ESCC patients and normal individuals was used for subsequent microarray analysis

value: plasma


title: MDA231-BrM2-20, Input

description: Antibody: None

value: breast


title: Plasma of ESCC patients 3

description: Biological replicate 3 of 3.Plasma of ESCC patients

source_name: Plasma of ESCC patients


title: Plasma of ESCC patients 1

description: Biological replicate 1 of 3.Plasma of ESCC patients


title: Plasma of ESCC patients 2

description: Biological replicate 2 of 3.Plasma of ESCC patients


title: scRNA-Seq-BLM anti CLTA4 rep3

description: 10 X genomics

value: anti-CLTA4 mAb


title: MDA231-BrM2-1-3, HIF-1α, ChIP

description: Antibody: HIF-1α (Novus, NB100-479)

value: breast cancer cells

value: wild type


title: breast tumor M169T

value: primary tumor tissue

value: female


title: scRNA-Seq-BLM anti CLTA4 rep2

description: 10 X genomics


title: Normal human plasma 3

description: Biological replicate 3 of 3.Normal human plasma


title: Normal human plasma 2

description: Biological replicate 2 of 3.Normal human plasma


title: breast tumor M152T


title: scRNA-Seq-BLM anti CLTA4 rep1

description: 10 X genomics


title: whole blood, sample 14

city: Shanghai

first: Zhen

last: Yang

address: 131 Dongan Road

institute: Fudan University

data_processing:
QuickMiRseq
Raw reads were subjected to exhaustive adapter trimming using cutadapt v2.8, the miRDeep2 was used to generate count tables of aligned reads for mature miRNA quantification
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPM values for each Sample

source_name: Whole blood

extract_protocol:
Total RNA was isolated from each sample using the miRNA kit (Qiagen, Germany). RNA quality was examined by gel electrophoresis and with Qubit (Thermo, Waltham, MA, USA)
Sequencing libraries were generated using VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina

value: Whole blood

tag: wbc

tag: cd4 t_cell

tag: cd8 t_cell

tag: b cell

tag: nk cell

tag: monocyte

tag: neutrophil

tag: eosnophils

tag: basophil


title: HEK293T DamN126A Nanopore-DamID

city: St Lucia

first: Seth

last: Cheetham

state: Queensland

address: Australian Institute of Bioengineering and Nanotechnology

country: Australia

institute: University of Queensland

data_processing:
Nanopore reads were aligned to the mouse genome (mm10) or human genome (hg38) using Minimap2  with the options -a --MD --cs=long -x map-ont. Mapped reads were filtered for map quality using SAMtools view -q 10 and converted to bigwig format using deepTools bamCoverage. Short-read DamID was mapped using minimap2 44 and filtered for alignment quality using samtools view -q 10.
Lamin-associated domains were identified by binning reads from LaminB1-DamID samples into 20 kb bins using bedtools coverage. Ratios of LaminB1-Dam/(Dam+1) were calculated using awk and Lamin-associated domains called using HMMt27. Consensus LADs (between the Nanopore-DamID undiluted and 1:1/10 dilution and between the two Illumina replicates) were determined using intersectBed.
CTCF Nanopore-DamID peaks were called by first binning reads from both replicates separately into GATC fragment bins using BEDtools53 coverage. To remove bias from amplified regions of the HEK293T genome, we normalised the Nanopore DamID coverage by readcount and HEK293T Nanopore WGS coverage. The two replicates were then quantile normalised and averaged. Peaks were called on the average coverage using the DamID peak caller47 (https://github.com/owenjm/find_peaks). Peaks were only considered if they were present in both WGS-normalised and unnormalised peak sets.
Assembly: mm10 or hg38
Supplementary files format and content: Bed files containing Lamin associated domains or CTCF binding sites
Supplementary files format and content: Bigwig files containing genomic coverage
Supplementary files format and content: Bedgraph files containing CTCF average genomic coverage normalised to WGS coverage

extract_protocol:
Dam fusion protein expression was induced with 2μg/mL doxycycline and genomic DNA (gDNA) was extracted from one million cells cultured in Nunc™ T75 flasks using an NEB Monarch® gDNA extraction kit according to manufacturer's instructions, with the exception of using inversion rather than vortexing for mixing.
For Nanopore-DamID 2.5μg of gDNA was dephosphorylated by the addition of 5μl of 10X NEB Cutsmart® buffer and 1μl of QuickCIP (NEB) in a total volume of 48μL. The reaction was mixed by gentle flicking and incubated at 37°C for 30 minutes. The QuickCIP was then heat inactivated at 80°C for 5 min. 2μl of DpnI (NEB) was added to the reaction, mixed by gently flicking and incubated at 37°C overnight. DNA was A-tailed by addition of 1μL 10mM dATPs and 1μL of Klenow exo- (NEB) and incubation at 37°C for 1hr. The digested DNA was purified using the Qiagen QiaQuick™ PCR Purification kit (which purifies fragments <10kb) and eluted in 60μL of H2O. The DNA was prepared for ONT sequencing with the DNA Ligation Sequencing Kit (LSK110), starting from the adaptor ligation step and using the Short Fragment Buffer. For Illumina-DamID libraries were prepared according to the protocol in Marshall et al., 2016, Nature Protocols) using the NEBnext UltraII kit for Illumina library construction.
Nanopore DamID or Illumina-DamID

tag: cell line


title: HEK293T CTCF-DamN126A Nanopore-DamID2


title: whole blood, sample 13


title: breast tumor M218T


title: whole blood, sample 12


title: breast tumor M330T


title: HEK293T CTCF-DamN126A  Nanopore-DamID1


title: CUT&RUN using anti-LSD1 antibody with CD34 cells Donor4028 at Day14

first: Kaiwen

last: Deng

state: Michigan

address: 3305 NCRC Building 520

data_processing:
The LSD1 CNR datasets were processed using the nf-core CUT&RUN pipeline version 3.2.1 (https://nf-co.re/cutandrun/3.2.1/)
We specify these arguments: --genome GRCh38, --normalisation_mode RPKM, --macs2_pvalue 0.05
And keep the other arguments as their default
Assembly: GRCh38
Supplementary files format and content: bigWig files (.bigWig) storing the RPKM normalized pile-ups of the reads
Supplementary files format and content: bed files (.bed) storing the peaks called by MACS2
Library strategy: CUT&RUN

source_name: Human CD34 cells

extract_protocol:
DNA purification was performed using phenol chloroform extraction. DNA were evaluated by Qubit ﬂuorometer and bioanalyzer for quality control followed by library preparation.
Library preparation was performed following the modified protocol for TF-targeted short fragments using NEBNext Ultra II DNA Library Prep Kit

value: Human CD34 cells


title: whole blood, sample 11


title: CUT&RUN using anti-IgG antibody with CD34 cells Donor4028 at Day14


title: whole blood, sample 10


title: CUT&RUN using anti-IgG antibody with CD34 cells Donor4010 at Day14


title: breast tumor M111T


title: CUT&RUN using anti-LSD1 antibody with CD34 cells Donor4010 at Day14


title: CUT&RUN using anti-IgG antibody with CD34 cells Donor4011 at Day14


title: CUT&RUN using anti-LSD1 antibody with CD34 cells Donor4011 at Day14


title: CUT&RUN using anti-IgG antibody with CD34 cells Donor4028 at Day11


title: CUT&RUN using anti-LSD1 antibody with CD34 cells Donor4028 at Day11


title: breast tumor P061T


title: CUT&RUN using anti-IgG antibody with CD34 cells Donor4011 at Day11


title: breast tumor P054T


title: CUT&RUN using anti-LSD1 antibody with CD34 cells Donor4011 at Day11


title: whole blood, sample 7


title: CUT&RUN using anti-LSD1 antibody with CD34 cells Donor4010 at Day11


title: breast tumor Z107T


title: whole blood, sample 8


title: CUT&RUN using anti-IgG antibody with CD34 cells Donor4010 at Day11


title: whole blood, sample 6


title: breast tumor P125T


title: Calu3 cells - Silymarin - 48hrs - rep 2 (Drug study)

first: ARJIT VIJEY

last: JEYACHANDRAN

address: Tiverton Ave

description:
Library name: Sample 22
Drug treatment only / Mock (48 hrs)

data_processing:
Raw FASTQ files were quality-checked using FastQC.
Reads were aligned to the human genome (GRCh38) using STAR aligner v2.7.11b.
Gene-level quantification was performed using featureCounts v2.0.6.
Normalization and differential expression analysis were done using DESeq2 v1.40.1 in R v4.3.0.
Assembly: Homo sapiens genome GRCh38, Ensembl release 112
Supplementary files format and content: Tab-delimited gene count matrix; rows = Ensembl gene IDs, columns = sample names. Values represent raw read counts.

growth_protocol: Primary pulmonary endothelial cells were cultured in Vascular Cell Basal Medium supplemented with Endothelial Cell Growth Kit-VEGF and Pen/Strep. Calu-3 cells were maintained in EMEM with 20% FBS, NEAA, L-glutamine, and Pen/Strep at 37°C with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) for 5–10 minutes, followed by storage at -80°C. RNA was purified using the Bio-Rad RNA Mini Kit and quantified using NanoDrop 2000.
Libraries were prepared using the KAPA Stranded mRNA-Seq Kit. mRNA was selected, followed by cDNA synthesis, end repair, adaptor ligation, and PCR amplification. Libraries were multiplexed and sequenced using Illumina NovaSeq 6000 with 2×50 bp paired-end reads.

treatment_protocol: Calu-3 cells were treated with 6-Azauridine, Silymarin, Urolithin B, or Favipiravir at specified doses for 48 hrs. Endothelial cells were infected with ANDV, SNV, or HTNV at MOI 0.1 for 48 hrs.

tag: cell type

value: Lung epithelial cells

tag: genotype

value: WT

value: Mock, Urolithin B, 6AZA, Favipiravir, Silymarin

tag: batch


title: Calu3 cells - Favipiravir - 48hrs - rep 2 (Drug study)

description:
Library name: Sample 20
Drug treatment only / Mock (48 hrs)


title: whole blood, sample 9

tag: tissue


title: breast tumor Z103T


title: Calu3 cells - Favipiravir - 48hrs - rep 1 (Drug study)

description:
Library name: Sample 19
Drug treatment only / Mock (48 hrs)

tag: treatment


title: whole blood, sample 5


title: Calu3 cells - 6AZA - 48hrs - rep 2 (Drug study)

description:
Library name: Sample 18
Drug treatment only / Mock (48 hrs)


title: breast tumor P115T

tag: gender


title: whole blood, sample 4


title: breast tumor Z078T


title: Calu3 cells - 6AZA - 48hrs - rep 1 (Drug study)

description:
Library name: Sample 17
Drug treatment only / Mock (48 hrs)


title: Calu3 cells - Urolithin B - 48hrs - rep 2 (Drug study)

description:
Library name: Sample 16
Drug treatment only / Mock (48 hrs)


title: whole blood, sample 3


title: breast tumor Z076T


title: Calu3 cells - Urolithin B - 48hrs - rep 1 (Drug study)

description:
Library name: Sample 15
Drug treatment only / Mock (48 hrs)


title: Calu3 cells - Mock - 48hrs - rep 2 (Drug study)

description:
Library name: Sample 14
Drug treatment only / Mock (48 hrs)


title: breast tumor Z074T


title: Calu3 cells - Mock - 48hrs - rep 1 (Drug study)

description:
Library name: Sample 13
Drug treatment only / Mock (48 hrs)


title: whole blood, sample 2


title: Calu3 cells - Silymarin - 48hrs - rep 1 (Drug study)

description:
Library name: Sample 21
Drug treatment only / Mock (48 hrs)


title: Pulmonary endothelial cells - Hantaan virus - 48hrs - rep 3

description:
Library name: Sample 12
Virus infection only / Mock (48 hrs)

source_name: Primary Pulmonary Artery Endothelial Cells; Normal, Human (HPAEC)

value: Pulmonary endothelial cells

value: Mock, ANDV, SNV, HTNV


title: whole blood, sample 1


title: Pulmonary endothelial cells - Hantaan virus - 48hrs - rep 2

description:
Library name: Sample 11
Virus infection only / Mock (48 hrs)

value: Primary Pulmonary Artery Endothelial Cells; Normal, Human (HPAEC)


title: breast tumor Z065T


title: breast tumor Z039T


title: Pulmonary endothelial cells - Andes virus - 48hrs - rep 3

description:
Library name: Sample 09
Virus infection only / Mock (48 hrs)


title: PEO4, H3K27M3, ChIP

first: Laura

last: Elnitski

address: 49 Convent Dr

institute: NIH

data_processing:
Basecalls were performed using bcl2fastq v(GET VERSION) for Novaseq output in fastq format.
Raw fastq files were uploaded to Basepairtech (https://www.basepairtech.com).
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.1.0. using the Basepairtech bowtie alignment pipeline and fiiiltering out and trimming low quality reads or reads too short.
Bigwig files were generated in basepairtech pipeline by extending fragments by 400bp.
Peaks were called using MACS v2.1.0.  and the Basepairtech peak calling pipeline. narrowPeak files were generated using MACS v2 with default settings and broad peak parameters were used for histone markers.
Assembly: hg38
Supplementary files format and content: bigwig, peak files in txt format (except for input)

growth_protocol: Cell line was cultured in RPMI 1640 (Gibco #61870-036) media supplemented with 10% FBS (Gibco #16140-071) at 370C in 5% CO2 humidified incubator.

extract_protocol:
Cells were fixed following Active motif’s ChIP Cell Fixation Protocol (https://www.activemotif.com/documents/1848.pdf).Chromatin was prepared using RIPA buffer containing 10 mM Tris-HCl, pH 7.6, 1 mM EDTA, 0.1% SDS, 0.1% Na-Deoxycholate, 1% Triton X-100 and 100 μL of protease inhibitor cocktail (Millipore Sigma #11836170001 Roche) and sonicated using QSonica apparatus for optimal fragmentation. Pulldown was set up using respective antibodies for overnight. DNA was extracted from pulled down chromatin.
Libraries were prepared using 5 ng of DNA using Ovation® Ultralow System V2 (TECAN #0344-32) following manufacturer’s protocol.

treatment_protocol: 24hours after seeding the cells, old media was replaced with the fresh media containing indicated drugs 17-beta-estradiol, CI 182780 and  JQ1 and incubated for 24 hours in the CO2 incubator.

value: human ovary

tag: antibody


title: Pulmonary endothelial cells - Hantaan virus - 48hrs - rep 1

description:
Library name: Sample 10
Virus infection only / Mock (48 hrs)


title: Pulmonary endothelial cells - Andes virus - 48hrs - rep 2

description:
Library name: Sample 08
Virus infection only / Mock (48 hrs)


title: breast tumor Z007T


title: PEO4, BRD4 100E2, ChIP

value: 100nM Estradiol


title: breast tumor P188T


title: Pulmonary endothelial cells - Sin Nombre virus - 48hrs - rep 2

description:
Library name: Sample 05
Virus infection only / Mock (48 hrs)


title: Pulmonary endothelial cells - Sin Nombre virus - 48hrs - rep 1

description:
Library name: Sample 04
Virus infection only / Mock (48 hrs)


title: Pulmonary endothelial cells - Sin Nombre virus - 48hrs - rep 3

description:
Library name: Sample 06
Virus infection only / Mock (48 hrs)


title: Pulmonary endothelial cells - Mock - 48hrs - rep 3

description:
Library name: Sample 03
Virus infection only / Mock (48 hrs)


title: PEO4, BRD4 500IJ, ChIP


title: Pulmonary endothelial cells - Mock - 48hrs - rep 2

description:
Library name: Sample 02
Virus infection only / Mock (48 hrs)


title: PEO4, BRD4 500I, ChIP


title: breast tumor P176T


title: N2A Wildtype


title: breast tumor P174T


title: PEO4, BRD4, 500J, ChIP

value: 500nM JQ1


title: N2A 10% LaminB1-Dam  Nanopore-DamID


title: N2A Dam Nanopore-DamID


title: N2A LaminB1-Dam Nanopore-DamID


title: PEO4, BRD4, VEH, ChIP

value: DMSO


title: Cisplatin+3%HET, Muscle, 15

city: Inashiki-gun

first: Hitomi

last: Sekine

state: Ibaraki

address: 3586, Yoshiwara, Ami-machi

department: TSUMURA Kampo Research Laboratories Kampo Research & Development Division

country: Japan

institute: TSUMURA & CO.

description:
Library name: Sample 40
HET_H.40

data_processing:
miRNA-seq libraries were sequenced using single reads on a NextSeq 500 system (Illumina).
Raw sequencing reads were trimmed and quality-filtered using cutadapt (version 3.7).
The trimmed reads were aligned to the mouse reference genome GRCm39 (mm39) using STAR (version 2.7.9a), and the resulting BAM files were processed using Samtools (version 1.12).
Gene-level counts were obtained by assigning reads to annotated genes using featureCounts (version 2.0.1).
FPKM values were calculated from mapped reads by normalizing to total counts and transcript.
Assembly: GRCm39 (mm39)
Supplementary files format and content: The tab-delimited text file contains either read count or FPKM data for each sample.

source_name: the red regions of the gastrocnemius muscle

extract_protocol:
The miRNeasy Mini Kit (217004; Qiagen, Valencia, CA, United States) was used for miRNA extraction from red muscle of gastrocnemius muslce.
RNA sequence library preparation, sequencing, mapping, gene expression, and gene ontology enrichment analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). Qualities of total RNA were assessed by Bioanalyzer (Agilent) to ensure that RIN (RNA integrity number) is over 7.0. For library preparation, the QIAseq miRNA Library Kit (QIAGEN, 331502) was used according to the manufacturer’s instructions.

tag: strain

tag: Sex

value: male

value: Cisplatin + 3% HET


title: breast tumor P151T


title: Cisplatin+3%HET, Muscle, 14

description:
Library name: Sample 39
HET_H.39

value: the red regions of the gastrocnemius muscle


title: Pulmonary endothelial cells - Andes virus - 48hrs - rep 1

institute: UCLA

description:
Library name: Sample 07
Virus infection only / Mock (48 hrs)


title: PEO4, H3K27Ac, ChIP


title: Cisplatin+3%HET, Muscle, 13

description:
Library name: Sample 38
HET_H.38


title: breast tumor P026T

value: primary tumor tissue


title: PEO4, ESR1 500IJ, ChIP


title: Cisplatin+3%HET, Muscle, 12

description:
Library name: Sample 37
HET_H.37


title: PEO4, ESR1 500I, ChIP


title: breast tumor P217T

value: female


title: Cisplatin+3%HET, Muscle, 11

description:
Library name: Sample 36
HET_H.36


title: PEO4, ESR1 500J, ChIP


title: Cisplatin+3%HET, Muscle, 10

description:
Library name: Sample 35
HET_H.35


title: Pulmonary endothelial cells - Mock - 48hrs - rep 1

description:
Library name: Sample 01
Virus infection only / Mock (48 hrs)


title: breast tumor P179T


title: breast tumor P215T


title: PEO4, ESR1 VEH, ChIP


title: 30 T1D Teplizumab

city: Seattle,

first: Stephanie

last: Osmond

address: 1201 9th Ave

institute: Benaroya Research Institute

description: Library name: Library group 18

data_processing:
The FASTQs were aligned to the human GRCh38 release 91 reference genome, using STAR v.2.4.2a.
Gene counts were generated using htseq-count (v0.4.1).
Quality control and metrics analysis was performed using the Picard family of tools (v1.134).
To identify TCR chains, the Trinity assembler was used to generate contigs. TCR sequences were identified and annotated from these contigs using MiXCR (v2.1.3).
Assembly: GRCh38 release 91 reference genome
Supplementary files format and content: P338countsForGEO.csv. Gene count matrix, libid by gene, csv
Supplementary files format and content: P338TCRs.csv, assembled TCR sequences, csv

source_name: Blood

growth_protocol: PBMCs stained with HLA A02 or HLA A01 B08 Class 1 beta cell NIH Tetramers conjugated with PE, EBV tetramers labeled with APC. Enriched with Miltenyi Anti-PE/APC beads and columns prior to sorting

extract_protocol:
Sequencing libraries were prepared using Nextera XT DNA kits
scRNA-Seq

treatment_protocol: Cells individual sorted into 96 well PCR plates with Takara Lysis buffer(Smart Seq V4)

value: Blood

value: PMBC

tag: time

tag: specificity

value: Teplizumab

tag: ebv serostatus

value: see sample_metadata.xlsx


title: 30 EBV Teplizumab

description: Library name: Library group 17

value: EBV


title: Cisplatin+3%HET, Muscle, 08

description:
Library name: Sample 33
HET_H.33


title: breast tumor P158T


title: Cisplatin+3%HET, Muscle, 07

description:
Library name: Sample 32
HET_H.20


title: 18 T1D Teplizumab

description: Library name: Library group 16


title: breast tumor P207T


title: PEO4, ESR1 100E2, ChIP


title: Cisplatin+3%HET, Muscle, 06

description:
Library name: Sample 31
HET_H.19


title: breast tumor P210T


title: PEO4, FOXA1, ChIP


title: 18 T1D Placbo

description: Library name: Library grpup 15

value: Placebo


title: Cisplatin+3%HET, Muscle, 05

description:
Library name: Sample 30
HET_H.18


title: breast tumor P195T


title: breast tumor P196T


title: Cisplatin+3%HET, Muscle, 04

description:
Library name: Sample 29
HET_H.17


title: PEO4, PITX1, ChIP


title: PEO4, ESR1, ChIP


title: Cisplatin+3%HET, Muscle, 09

description:
Library name: Sample 34
HET_H.34


title: breast tumor P190T


title: breast tumor P189T


title: 6 T1D Teplizumab

description: Library name: Library group 12


title: isolated_MSCs, biol rep 4

city: Tokyo

first: Daisuke

last: Hisamatsu

address: 2-1-1 Hongo, Bunkyo-ku

institute: Juntendo University Graduate School of Medicine

data_processing:
To generate a sequence alignment, quality control and preprocessing of FASTQ data were performed using fastp v.0.20.1 (https://github.com/OpenGene/fastp).
Transcript was quantified using Salmon (https://combine-lab.github.io/salmon/).
Read count normalization were performed using edgeR.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: subcutaneous white adipose tissue

growth_protocol: MSCs were maintained in DMEM supplemented with 20% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted from these cells using an RNeasy Mini kit (Qiagen, Hilden, Germany).
Sequencing library was prepared using the SMART-Seq v4 Ultra Low Input RNA kit (Takara, Kusatsu, Japan).

value: subcutaneous white adipose tissue

value: mesenchymal stem/stromal cells

tag: cell subtype

value: isolated MSCs

value: untreated

tag: disease state

value: healthy


title: Cisplatin+3%HET, Muscle, 02

description:
Library name: Sample 27
HET_H.15


title: 6 T1D Placebo

description: Library name: Library group 11


title: isolated_MSCs, biol rep 3


title: PEO4, MED1, ChIP

value: human ovary


title: breast tumor P370T


title: isolated_MSCs, biol rep 2


title: Cisplatin+3%HET, Muscle, 01

description:
Library name: Sample 26
HET_H.14

value: male


title: breast tumor P368T


title: 6 EBV Teplizumab

description: Library name: Library group 10


title: Cisplatin, Muscle, 15

description:
Library name: Sample 25
cisplatin_C.32

value: Cisplatin


title: breast tumor P332T


title: isolated_MSCs, biol rep 1


title: Cisplatin, Muscle, 14

description:
Library name: Sample 24
cisplatin_C.31

value: the red regions of the gastrocnemius muscle


title: 18 EBV Teplizumab

description: Library name: Library group 14


title: 6 EBV Placebo

description: Library name: Library group 9


title: adhered_MSCs, biol rep 4

value: adhered MSCs


title: breast tumor P290T

value: primary tumor tissue

value: female


title: 3 T1D Teplizumab

description: Library name: Library group 8

value: Blood

value: PMBC


title: Cisplatin, Muscle, 13

description:
Library name: Sample 23
cisplatin_C.30


title: adhered_MSCs, biol rep 3


title: 18 EBV Placebo

description: Library name: Library group 13

value: see sample_metadata.xlsx


title: Cisplatin, Muscle, 12

description:
Library name: Sample 22
cisplatin_C.29


title: 3 T1D Placebo

description: Library name: Library group 7


title: breast tumor P287T


title: Cisplatin+3%HET, Muscle, 03

description:
Library name: Sample 28
HET_H.16

value: Cisplatin + 3% HET


title: 3 EBV Teplizumab

description: Library name: Library group 6

value: EBV

value: Teplizumab


title: breast tumor P272T


title: adhered_MSCs, biol rep 2

value: subcutaneous white adipose tissue

value: mesenchymal stem/stromal cells


title: 3 EBV Placebo

description: Library name: Library group 5

value: Placebo


title: breast tumor P227T


title: adhered_MSCs, biol rep 1

value: untreated

value: healthy


title: breast tumor P220T


title: breast tumor P477T


title: 0 T1D Teplizumab

description: Library name: Library group 4


title: Cisplatin, Muscle, 09

description:
Library name: Sample 19
cisplatin_C.26

value: male


title: Cisplatin, Muscle, 10

description:
Library name: Sample 20
cisplatin_C.27

value: Cisplatin


title: PCON_PB_6

city: Providence

first: Patrycja

middle: M

last: Dubielecka

state: RI

address: 1 Hoppin St., Coro West, 5th Fl., Suite 5.36

department: Division of Hematology/Oncology, Department of Medicine

institute: Warren Alpert Medical School of Brown University and Rhode Island Hospital

data_processing:
Adapter and quality read trimming was performed using Skewer (version 0.2.1) and alignments were performed using SALMON (version 1.3.0) against the human primary assembly transcriptome (GRCh38 v42).
Assembly: GRCh38 v42
Supplementary files format and content: Tab-delimited text file includes raw counts.
Supplementary files format and content: Tab-delimited text file includes abundance (TPM).

source_name: Whole Blood

extract_protocol:
QIAamp® RNA Blood kit (Qiagen #52304) and RNase-Free DNase Sets (Qiagen catalog 79254) were used for RNA extraction from peripheral blood samples.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries were pooled and sequenced on Illumina NovaSeq6000 at PE150. Each library was sequenced to 6G (20 million paired-end reads).

value: Whole Blood

value: Male

tag: age

tag: group

value: PCON

tag: disease

value: Healthy

tag: scd

value: Normal


title: PCON_PB_4

value: Female


title: breast tumor P424T

value: primary tumor tissue

value: female


title: 0 T1D Placebo

description: Library name: library grpup 3

value: Blood

tag: cell line

value: PMBC

tag: cell type

value: see sample_metadata.xlsx


title: Cisplatin, Muscle, 07

description:
Library name: Sample 17
cisplatin_C.12

tag: tissue

value: the red regions of the gastrocnemius muscle


title: 0 EBV Teplizumab

description: Library name: Library group 2

value: EBV

tag: treatment

value: Teplizumab


title: breast tumor P422T

tag: gender


title: PCON_PB_2


title: Cisplatin, Muscle, 08

description:
Library name: Sample 18
cisplatin_C.13


title: 0 EBV Placebo

description: Library name: Library group 1

value: Placebo


title: Cisplatin, Muscle, 06

description:
Library name: Sample 16
cisplatin_C.11

value: male


title: Cisplatin, Muscle, 05

description:
Library name: Sample 15
cisplatin_C.10

value: Cisplatin