title: Blood sample from individual 193

description: Sample ID: 193


title: wild type input for Red1 rep 4

status: Public on Apr 08 2022

type: SRA

city: New York

first: Andreas

last: Hochwagen

state: NY

address: 1009 Silver Center 100 Washington Square East

country: USA

institute: New York University

description: reanalysis of: GSM1695717

library_source: genomic

data_processing:
Illumina output reads were processed as described in (Paul et al., 2018). The ChIP-seq and MNase-seq reads were mapped to SK1 genome (Yue et al., 2017) using Bowtie (Langmead et al., 2009).  Only reads that mapped to a single position and also matched perfectly to the SK1 genome were retrieved for further analysis. The RNA-seq reads were mapped to the SK1 genome using Tophat2 with first strand library type, no novel junctions, and otherwise default options.
For ChIP-seq, 3' ends of the reads were extended to a final length of 200bp using MACS2 2.1.1 (https://github.com/taoliu/MACS) and probabilistically determined PCR duplicates were removed. For MNase-seq, 3' ends were extended to a final length of 146 and bandwidth was set to 350 using MACS2 2.1.1. For RNA-seq, mapped reads were counted using featureCounts and statistical analysis was performed using a count-based workflow with the edgeR Bioconductor package.
For ChIP-seq, the input and ChIP pileups were SPMR-normalized (signal per million reads) and fold-enrichment of ChIP over input data was used for further analyses. For MNase-seq, the pileup was SPMR-normalized and used for further analyses. For RNA-seq, gene counts were normalized to counts per million and were then gene length-corrected for transcripts per million (tpm).
Axis sites (Red1 summits in wild type conditions) were identified using MACS2 narrow and -log10 qvalue of 20.
Peaks were identified using MACS broad flag.
Genome_build: SK1 (Yue et al., 2017)
Supplementary_files_format_and_content: Bedgraph
Supplementary_files_format_and_content: bed
Supplementary_files_format_and_content: csv (count of mRNAs in tmp)

molecule: genomic DNA

organism: Saccharomyces cerevisiae

source_name: wild type input for Red1 rep 4

growth_protocol: Synchronous meiosis was performed by first innoculating strains at OD600 = 0.3 in BYTA medium and grown for 16.5 hours at 30°C, except for H7606  which was innoculated at OD600 = 0.8 in BYTA medium and grown for 20 hours at room temperature. H7797 was also grown in BYTA medium at room temperature for the 34C experiments. Then cells were washed twice with sterile water and resuspended into SPO medium at OD600 = 1.9 or 2.0 at 30°C (details are described in (Blitzblau et al., 2012)). Rapamycin was added at 0h where indicated.

extract_protocol:
For ChIP-seq samples, 25 ml of the meiotic cells were collected at different time points and fixed for 30 min in 1% formaldehyde. For MNase-seq samples, 50 ml of the meiotic cells were collected at the 3-hr time point and fixed for 30 min in 1% formaldehyde.  The formaldehyde was quenched with 125 mM glycine. ChIP-seq samples were processed as described in (Blitzblau et al., 2012). MNase-seq samples were processed as described in (Pan et al., 2011). A second sonication step was added just before library prep where indicated using a Bioruptor Pico (Diagenode, NJ, USA) with the following settings: 30 secs ON and 30 secs OFF for 5 cycles. For RNA-seq, 1.5 ml meiotic culture was taken at the 3-hr time point and RNA was extracted from mechanically lysed cells using the Qiagen RNeasy RNA isolation Kit and mRNA was extracted using Sera-Mag oligo-dT beads and fragmented.
For MNase-seq and ChIP-seq, libraries were prepared by PCR amplification with TruSeq adaptors (Illumina) as described in (Sun et al., 2015). For RNA-seq, libraries were prepared according to the Illumina TruSeq Stranded mRNA sample preparation kit, and sequencing libraries were prepared by PCR from the cDNA samples after ligation of adapters. Quality of all libraries was checked on 2200 Tapestation or Agilent 2100 Bioanalyzer. Libraries were quantified using qPCR. The libraries were sequenced on Illumina HiSeq 2500 or NextSeq 500 instruments at NYU Biology Genomics core to yield 50 or 51 bp single-end reads or 100 bp single-end reads.

treatment_protocol: For 34C experiments, strains were shaken in SPO medium at room temperature for 1 hour and shifted to 34 degrees Celsius for the remaining time.

tag: strain

tag: meiotic time point

tag: genotype

tag: antibody


title: Blood sample from individual 192

type: genomic

city: Darlinghurst

first: Joseph

middle: E

last: Powell

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: Sample ID: 192

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Genomic DNA extracted from blood was genotyped using the Infinium Global Screening Array-24 v1.0 BeadChip (Illumina).
Primary assessment and SNP call rate quality control of SNP intensity output files were performed using GenomeStudio software (Illumina).
Genotype: AA,AB,BB,or NC (no call)
Processed data file onek1k_genotype_matrix.txt.gz is linked as supplementary file at the foot of the Series record.

label: C-Bio and A-DNP

organism: Homo sapiens

source_name: Blood sample

label_protocol: Standard Illumina label protocol

extract_protocol: DNA was extracted from blood stored in EDTA tubes using the QIAamp Blood Mini kit.

tag: individual id

tag: gender

value: Female

tag: tissue

value: Blood

tag: disease state

value: No active inflammatory disease


title: E47_vpGFP_rep2

city: Utrecht

first: Peter

last: Krijger

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
Reads were mapped and processed using pipe4C (Krijger et al., 2020) (github.com/deLaatLab/pipe4C) with the following parameters: normalization to 1 million reads in cis, non-blind fragments only, window size 21, top 2 read counts removed
Genome_build: Modified versions of hg19 containing the sequences of the integrated regulatory elements at their respective integration site.
Supplementary_files_format_and_content: 4C:  interaction coverage file (wig files generated using pipe4C)

growth_protocol: Human erythroleukemia K562 cells were grown at 37°C at 5% CO2 in RPMI 1640 (Gibco) with 10% FBS (Sigma) and 1% Penicillin-Streptomycin (Gibco). Density was kept between 1x105 and 5x105 cells per ml medium. Cells were routinely tested for mycoplasma. Prior to every experiment, cells were weekly bulk sorted for two consecutive weeks on Becton Dickinson SORP FACSAria FUSION Flow Cytometer. To obtain irreversibly silenced populations of cells, GFP negative cells where weekly sorted GFP-negative for six (E100) or nine (E407) consecutive weeks.

extract_protocol:
4C experiments were performed as described (Krijger et al., 2020).  Eight to ten million cells were cross-linked with formaldehyde. DNA was digested in situ with Csp6I (first cutter) and NlaIII (second cutter).
Indexed Illumina sequencing adapters were introduced to ligation fragments of interest with a two-step PCR strategy as described in Krijger et al., 2020.
OTHER:  4C

treatment_protocol: For differentiation, culture medium was supplemented with porcine hemin (Sigma, 30 µM final concentration) one day after sorting. Hemin and medium were refreshed one day later.

tag: knock down

tag: hemin treatment

tag: facs

tag: viewpoint

value: GFP

tag: barcode

value: GGGGCACAAGCTGGAGTA


title: E47_vpGFP_rep1


title: wild type Red1 chip rep 3

description: reanalysis of: GSM4677902

source_name: wild type Red1 chip rep 3


title: Blood sample from individual 191

description: Sample ID: 191

value: Male


title: wild type (SMC4-PK9) Red1 chip rep 2

description: reanalysis of: GSM4677900

source_name: wild type (SMC4-PK9) Red1 chip rep 2


title: wild type Red1 chip rep1

description: reanalysis of: GSM1695718

source_name: wild type Red1 chip rep1


title: E11_vpGFP_rep2


title: wild type input for Red1 rep1

description: reanalysis of: GSM1695716

source_name: wild type input for Red1 rep1


title: wild type chip for Hop1 rep 4

source_name: wild type chip for Hop1 rep 4


title: E11_vpGFP_rep1


title: wild type input for Rec8 rep 2

description: reanalysis of: GSM1695723

source_name: wild type input for Rec8 rep 2


title: wild type Rec8 chip rep 2

description: reanalysis of: GSM1695725

source_name: wild type Rec8 chip rep 2

value: anti-HA


title: Blood sample from individual 189

description: Sample ID: 189


title: wild type input for Hop1 rep 4

source_name: wild type input for Hop1 rep 4


title: Blood sample from individual 188

description: Sample ID: 188


title: Blood sample from individual 190

description: Sample ID: 190


title: wild type (SMC4-PK9) input for Red1 (rep2) and Hop1 (rep 1)

description: reanalysis of: GSM1695720


title: noE_vpGFP_rep3

value: noE

value: CAGGGGCACAAGCTGGAGTA


title: Blood sample from individual 187

description: Sample ID: 187


title: wild type 3h chip for Top2 3h rep 1

description: reanalysis of: GSM3834061

source_name: wild type 3h chip for Top2 3h rep 1


title: E0_vpGFP_rep2


title: wild type 3h input for Top2 3h rep 1

description: reanalysis of: GSM3834060

source_name: wild type 3h input for Top2 3h rep 1


title: spo11Δ chip for Top2 rep 1

source_name: spo11Δ chip for Top2 rep 1


title: wild type input for Red1 rep 3

description: reanalysis of: GSM4677901

source_name: wild type input for Red1 rep 3


title: wild type (SMC4-PK9) chip for Hop1 rep 1

description: reanalysis of: GSM1695721


title: noE_vpGFP_rep2

value: AGGGGCACAAGCTGGAGTA


title: wild type 0h input for Top2 rep 1

source_name: wild type 0h input for Top2 rep 1


title: wild type 0h chip for Top2 rep 1

source_name: wild type 0h chip for Top2 rep 1


title: Blood sample from individual 185

description: Sample ID: 185


title: noE_vpGFP_rep1


title: Blood sample from individual 184

description: Sample ID: 184


title: noE_vpPos0_rep2

value: TGGCGGCTGCAAGATAC


title: Favorable Wilms Tumor (SJWLM071557_D1)

city: MEMPHIS

first: Andrew

middle: Jackson

last: Murphy

state: TN

address: 262 DANNY THOMAS PLACE, MS 133 DEPARTMENT OF SURGERY

department: Surgery

institute: St. Jude Children's Research Hospital

library_source: transcriptomic

data_processing:
Cell Ranger pipeline was used to generate Fastq files for each sample
Endcounting and matrix files generated using Cell Ranger-10X Genomics Software
Assembly: GRCh38
Supplementary files format and content: tsv.gz, mtx.gz- barcodes, features and matrix

molecule: nuclear RNA

source_name: Kidney

extract_protocol:
Tumor mass was dissociated by using a modified ST based procedure ( Slyper et al., Nat.Med 2020)
Single cell Nucleus was captured and nuclear cDNA and Library was prepared following 3' Single cell Expression V3 from 10X Genomics.
ScRNASeq

value: Kidney

value: Favorable Wilms Tumor

tag: tag

value: Diagnosis

tag: Sex

tag: age

value: 0 Yrs 4 Mos

tag: fraction

value: Single cell Nucleus-PolyA RNA


title: Blood sample from individual 186

description: Sample ID: 186


title: E0_vpGFP_rep1


title: noE_vpPos0_rep1


title: WT_vpPos0_rep2

value: WT


title: spo11Δ input for Top2 rep 1

source_name: spo11Δ input for Top2 rep 1

tag: strain


title: Favorable Wilms Tumor (SJWLM056127_D1)

value: 2 Yrs 1 Mos


title: Blood sample from individual 183

description: Sample ID: 183

source_name: Blood sample

value: Blood


title: Favorable Wilms Tumor (SJWLM071547_D1)

value: Female

value: 1 Yrs 6 Mos


title: Favorable Wilms Tumor (SJWLM043456_D1)

value: 2 Yrs 11 Mos


title: PB01_TREKseq

city: Dublin

first: Marina

last: Ainciburu

state: Dublin

address: Foster Avenue

department: Bioinformatics

country: Ireland

institute: NIBRT

data_processing:
Library strategy: TREK-seq (T-cell Receptor Enrichment to linK clonotypes)
Demultiplexing  and FASTQ generation using CellRanger version 5.0.0
Generate single-cell expression matrix using CellRanger version 5.0.0
Ambient RNA removal using SoupX version 1.5.2
Quality control and filtering using R 4.1.0
Normalization and unsupervised clustering using Seurat 4.0.2
TREK-seq: Demultiplexing with bcl2fastq version 2.20.0
TREK-seq: TCR sequence extraction and scRNAseq pairing using WAT3R
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression matrix (scRNAseq) tab-delimited text file with gene-cell count matrix; metadata (scRNAseq) tab-delimited text file with cell-metadata matrix; WAT3R output (TREK-seq) tab-delimited text file with cell-metadata matrix.

molecule: total RNA

source_name: Peripheral blood cells

extract_protocol:
mRNA was extracted by 10x 3' sequencing technology
10x 3' v3 single-cell RNA-sequencing library construction methods were utilized for mRNA libraries. TREK-seq was used to enrich and sequence T-cell receptors.
scRNAseq, TREK-seq

value: peripheral blood

tag: technology

value: TREK-seq


title: Blood sample from individual 181

description: Sample ID: 181

value: No active inflammatory disease


title: Favorable Wilms Tumor (SJWLM030897_D2)

value: Male


title: Favorable Wilms Tumor (SJWLM071558_D1)

value: 0 Yrs 3 Mos


title: WT_vpPos0_rep1

tag: genotype

value: TGGCGGCTGCAAGATAC


title: Blood sample from individual 180

description: Sample ID: 180


title: Favorable Wilms Tumor (SJWLM056485_D1)

value: Kidney

value: 1 Yrs 10 Mos


title: Favorable Wilms Tumor (SJWLM071549_D1)

value: Favorable Wilms Tumor

value: Diagnosis

value: 4 Yrs 10 Mos


title: Favorable Wilms Tumor (SJWLM058497_D1)

value: 5 Yrs 4 Mos

value: Single cell Nucleus-PolyA RNA


title: Blood sample from individual 179

description: Sample ID: 179

value: Blood


title: 1756-bRNA_3

city: Toronto

first: Dakota

last: Gustafson

address: 101 College Street, 3-309

country: Canada

institute: University Health Network

data_processing:
The sequencing data on miRNA expression of target genes were imported into HTG EdgeSeq Parser software.
Post-sequencing QC metrics (QC0, QC1, and QC2) detect three different sample failure modes (1 - Degraded RNA or poor quality of sample, Pos% >- 14% as failure; 2 - Insufficient read depth, Read Deapth <= 500 K as failure; 3 - Minimal expression variability, RSD >= 0.08 as failure).
The HTG EdgeSeq Reveal Application was utilized to quality check and normalize data which utilizes DeSeq.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files including raw counts and processed data; DeSeq Normalized Count Data

source_name: EDTA Platelet Depleted Plasma_Control

growth_protocol: Whole blood was colleced via cubital vein into EDTA tubes and spun down at 2,500xg for 25 minutes according to CLIA protocols for the reduction of platelets. Upon separation plasma was frozen at -80 degrees Celsuis for downstream use. When isolating miRNA, samples were thawed on ice until sample homogeny was verified. Hemoylsis was examed at 414nm using a spectrophotometer to confirm absense of erythrocyte lysis and subsequent contamination.

extract_protocol:
A total of 30uL of thawed plasma was co-incubated with 1:1 volumes of HTG Plasma Lysis buffer (pre-warmed to 50 degrees celsius) and 1/10th v/v proteinase K for three hours at 50 degrees celsius with shaking (200prm).
The lysed sample was transferred to a standard 96-well micro-titer plate, referred to as the sample plate. Target capture was done by the HTG EdgeSeq chemistry. Briefly, the nuclease protection probes (NPPs) were added to the lysed samples in the sample plate in excess amount and hybridized to the target miRNA. Then S1 nuclease was added to digest non-hybridized mRNA and excess NPPs, thus producing a stoichiometric amount of target miRNA NPP duplexes. After the S1 digestion was completed, the processed sample was transferred to a new 96-well micro-titer plate with a v-bottom, referred to as the stop plate, and S1 digestion was terminated by the addition of termination solution followed by heat denaturation of S1 enzyme. Each processed sample from the stop plate was used as   template to set up PCR reactions with specially designed primers, referred to as tags. These tags share common sequences that are complementary to 5’-end and 3’-end “wing” sequences of the probes and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode that is used for sample identification and multiplexing. HTG has developed 12 forward and eight reverse primer tags; therefore, up to 96 samples can be analyzed simultaneously on an Illumina sequencing platform. Clean-up procedures were performed according using AMPure cleanup protocols for Illumina Sequencing Libraries. The library was quantified in accordance with the HTG EdgeSeq KAPA Library Quantification kit for Illumina Sequencing. All samples and controls were quantified in triplicate. No Template Control (NTC) reactions were made for each master mix used (using the same master mix as for samples) during the qPCR process. NTCs serve as a test for qPCR reagent contamination. Molecular-grade water is used in place of test sample in the NTC reactions using the same volume as the template.

tag: grouping

value: Control

tag: tissue/sample type

value: EDTA Platelet Depleted Plasma

tag: molecule subtype

value: microRNA


title: 1756-bRNA_2


title: Favorable Wilms Tumor (SJWLM056407_D1)

tag: tissue

value: 2 Yrs 11 Mos


title: Favorable Wilms Tumor (SJWLM059661_D1)

tag: disease state

value: Female

value: 4 Yrs 0 Mos


title: 1756-bRNA_1


title: Favorable Wilms Tumor (SJWLM030739_D2)

value: Male

value: 7 Yrs 3 Mos


title: 1756-A033674

source_name: EDTA Platelet Depleted Plasma_Severe

value: Severe


title: Anaplastic Wilms Tumor (SJWLM071551_D1)

value: Kidney

value: Anaplastic Wilms Tumor


title: Blood sample from individual 177

description: Sample ID: 177

tag: individual id

tag: gender

value: No active inflammatory disease


title: Blood sample from individual 182

description: Sample ID: 182


title: Favorable Wilms Tumor (SJWLM071559_D1)

value: Favorable Wilms Tumor

value: Diagnosis


title: Anaplastic Wilms Tumor (SJWLM059672_D1)

value: 2 Yrs 6 Mos


title: Anaplastic Wilms Tumor (SJWLM071564_D1)

value: Metastatic

value: 13 Yrs 4 Mos

value: Single cell Nucleus-PolyA RNA


title: Anaplastic Wilms Tumor (SJWLM018918_D1)


title: 1756-A033673

value: EDTA Platelet Depleted Plasma


title: Blood sample from individual 176

description: Sample ID: 176

value: Blood


title: Favorable Wilms Tumor (SJWLM059665_D1)

value: 2 Yrs 10 Mos


title: Anaplastic Wilms Tumor (SJWLM071562_D1)

value: Female

value: 11 Yrs 10 Mos


title: Anaplastic Wilms Tumor (SJWLM051026_D2)

value: 2 Yrs 11 Mos


title: 1756-A033672

value: microRNA


title: Blood sample from individual 175

description: Sample ID: 175


title: Favorable Wilms Tumor (SJWLM071556_D1)

value: 3 Yrs 6 Mos


title: Anaplastic Wilms Tumor (SJWLM051026_D1)

value: Kidney


title: Favorable Wilms Tumor (SJWLM059660_D1)

value: Male

value: 2 Yrs 0 Mos


title: Blood sample from individual 174

description: Sample ID: 174

value: No active inflammatory disease


title: 1756-A033671

value: Severe


title: Blood sample from individual 173

description: Sample ID: 173


title: Favorable Wilms Tumor (SJWLM056073_D1)

value: Favorable Wilms Tumor

value: Diagnosis

value: 0 Yrs 10 Mos


title: Blood sample from individual 178

description: Sample ID: 178


title: Blood sample from individual 172

description: Sample ID: 172


title: Anaplastic Wilms Tumor (SJWLM071554_D1)

value: Anaplastic Wilms Tumor

value: 4 Yrs 7 Mos

value: Single cell Nucleus-PolyA RNA


title: 1756-A033668

value: EDTA Platelet Depleted Plasma


title: Blood sample from individual 171

description: Sample ID: 171

value: Female

value: Blood


title: 1756-A033670


title: Blood sample from individual 170

description: Sample ID: 170


title: 1756-A033669


title: Favorable Wilms Tumor (SJWLM071552_D1)

value: 2 Yrs 6 Mos


title: Anaplastic Wilms Tumor (SJWLM071563_D1)

value: 4 Yrs 4 Mos


title: 1756-A033667

value: microRNA


title: Anaplastic Wilms Tumor (SJWLM030548_D2)

value: Kidney

value: 2 Yrs 3 Mos


title: Blood sample from individual 169

description: Sample ID: 169

value: Male


title: 1756-A033666


title: 212578

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

country: France

institute: CHU Nice

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: The Arrays were then washed using Affymetrix fluidics stations, and scanned using the Gene Chip Scanner 3000.

data_processing:
The array image was acquired using Affymetrix GeneChip® Command Console Software (version 3.2.2). Copy number values for individual SNPs were extracted and converted from CEL files into signal intensities using CHAs (version 4.0). Genomic Smoothing analysis was performed by CHAs
The CNV value is the logarithm base 2 of the sample signal divided by a reference value from the OncoScan_CNV.FFPE.na33.r2.REF_MODEL library. The allelic status is determined accordind the B-Allelic Frequency (BAF = B/(A+B) ; AA : BAF = 0, BB : BAF = 1, AB : BAF = 0,5) or the Allele Difference (Diff = A - B where each A and B allele are 0,5 units. AA : Diff = 1, AB : Diff = 0, BB : Diff = -1)

label: Biotin

source_name: sarcoma

label_protocol: As per manufacturer (Affymetrix)

extract_protocol: DNA was extracted from formol fixed-paraffin embedded fragments using Maxwell FFPE DNA LEV Kit (PROMEGA).

value: sarcoma


title: 214110


title: 1756-A033665

value: Severe


title: Blood sample from individual 168

description: Sample ID: 168

value: No active inflammatory disease


title: Anaplastic Wilms Tumor (SJWLM030043_D1)

value: Diagnosis

value: 5 Yrs 2 Mos


title: 220602-2


title: Anaplastic Wilms Tumor (SJWLM059659_D1)

value: Anaplastic Wilms Tumor

value: 2 Yrs 1 Mos


title: Anaplastic Wilms Tumor (SJWLM059683_D1)

value: 4 Yrs 5 Mos

value: Single cell Nucleus-PolyA RNA


title: 1756-A033664

value: EDTA Platelet Depleted Plasma


title: Blood sample from individual 167

description: Sample ID: 167

value: Female

value: Blood


title: 1756-A033663


title: Favorable Wilms Tumor (SJWLM058490_D1)

value: Favorable Wilms Tumor

value: 0 Yrs 9 Mos


title: Blood sample from individual 166

description: Sample ID: 166


title: 212389


title: Favorable Wilms Tumor (SJWLM030545_D1)

value: Kidney

value: 2 Yrs 5 Mos


title: 1756-A033662

value: microRNA


title: Blood sample from individual 165

description: Sample ID: 165


title: 1756-A033661

source_name: EDTA Platelet Depleted Plasma_Severe Negative

value: Severe Negative


title: Anaplastic Wilms Tumor (SJWLM059679_D1)

value: Male

value: 4 Yrs 2 Mos


title: Blood sample from individual 162

description: Sample ID: 162

value: No active inflammatory disease


title: 1756-A033660


title: Anaplastic Wilms Tumor (SJWLM049191_D2)

value: Diagnosis

value: 3 Yrs 4 Mos


title: Blood sample from individual 161

description: Sample ID: 161


title: Blood sample from individual 160

description: Sample ID: 160


title: 1756-A033657


title: Blood sample from individual 159

description: Sample ID: 159


title: Anaplastic Wilms Tumor (SJWLM051023_D2)

value: Anaplastic Wilms Tumor

value: 5 Yrs 5 Mos


title: Anaplastic Wilms Tumor (SJWLM071560_D1)

value: 3 Yrs 1 Mos

value: Single cell Nucleus-PolyA RNA


title: Blood sample from individual 158

description: Sample ID: 158


title: Favorable Wilms Tumor (SJWLM071550_D1)

value: 1 Yrs 7 Mos


title: Blood sample from individual 163

description: Sample ID: 163

value: Female

value: Blood


title: Pam3 + SA 6h 2

type: RNA

city: Atlanta

first: Manoj

last: Bhasin

state: GA

address: 615 Michael Street, Whitehead Biomedical Research Building

department: Department of Pediatrics

institute: Emory University

description: Samples infected with S. aureus and were given a Pam 3 treatment for 6h.

hyb_protocol: cDNA was hybridized to Affymetrix Mouse Genome 430PM strip arrays.Washing and staining of microarrays was performed using the GeneAtlasplatform (Affymetrix, Santa Clara, CA)

scan_protocol: GeneChips were scanned in a GeneAtlas Imaging Station (Affymetrix, Santa Clara, CA)

data_processing: Expression data were preprocessed using the Robust Multichip Average (RMA) method in R using the Bioconductor and associated package

organism: Mus musculus

source_name: Retina

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: RNA Extraction by Qiagen RNAeasy Min kit as per manufactor's protocol

treatment_protocol: S. aureus infected (3h, 6h, 12h, 24h) and Pam3 treated either left unifected (24h) or infected with SA (6h).

value: Retina

tag: treatment

value: Pam3 + SA 6h


title: Blood sample from individual 157

description: Sample ID: 157


title: Pam3 + SA 6h 1


title: Pam3 alone 3

description: Samples treated with Pam3 alone.

value: Pam3 alone


title: 1756-A033655

value: EDTA Platelet Depleted Plasma

value: microRNA


title: 1756-A033658

value: Severe Negative


title: Veh_1

description: Samples treated with PBS.

value: PBS treated


title: Pam3 + SA 6h 3


title: Pam3 alone 2

description: Samples treated with Pam3 alone.


title: 1756-A033659


title: Pam3 alone 1

description: Samples treated with Pam3 alone.


title: PMBCs for 15 individuals in pool 77

description:
List of pooled individuals: see *GenotypeSamples.txt file
List of individual barcodes: see *Individual_Barcodes.csv

data_processing:
The Cell Ranger Single Cell Software Suite (version 2.2.0) by 10x Genomics was used to process raw sequence data into FASTQ files.
First, raw base calls from multiple flow cells were demultiplexed into separate pools of samples.
Reads from each pool were then mapped to the GRCh37/hg19 genome (release 84) using STAR.
The count data was processed and analyzed in R.
Within each pool, every cell (barcode) was assigned to an individual within that pool using Genotype Data (provided) in demuxlet (version 1.0)
Genome_build: GRCh37/hg19 genome (release 84).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.  Table with list of pooled individuals.  Table with assigned barcodes.

source_name: blood

extract_protocol:
Peripheral blood samples were collected in vacutainer tubes containing either FICOLLTM and sodium heparin (8mL CPTTM; BD Australia, North Ryde, NSW; 362753) or K2EDTA (10mL; BD Australia, North Ryde, NSW; Catalogue: 366643). All CPTTM tubes were processed within 4 hours of collection according to the manufacturer's recommendations.
scRNA-seq libraries were prepared according to 10X Genomics Chromium v2 kit guidelines
Libraries for all samples were multiplexed and sequenced across five 2‚®â150 cycle flow cells on an Illumina NovaSeq 6000.

tag: cell type

value: PBMCs

value: blood

value: untreated

tag: pool id

tag: number of pooled individuals


title: Veh_2

description: Samples treated with PBS.


title: 1756-A033654


title: Favorable Wilms Tumor (SJWLM071553_D1)

value: Kidney

value: Favorable Wilms Tumor

tag: tag

value: Diagnosis

tag: Sex

value: 3 Yrs 5 Mos


title: Anaplastic Wilms Tumor (SJWLM051023_D1)

value: Anaplastic Wilms Tumor

tag: age

value: 5 Yrs 5 Mos

tag: fraction

value: Single cell Nucleus-PolyA RNA


title: 1756-A033656


title: Blood sample from individual 155

description: Sample ID: 155

value: Male

value: Blood

value: No active inflammatory disease


title: Blood sample from individual 156

description: Sample ID: 156

value: Female


title: PMBCs for 15 individuals in pool 76


title: Blood sample from individual 154

description: Sample ID: 154


title: PMBCs for 12 individuals in pool 74


title: SA_24h 3

description: Samples infected with S. aureus for 24h

value: Retina

tag: strain

value: S. aureus infected_24h


title: 1756-A033653

value: Severe Negative

value: EDTA Platelet Depleted Plasma

value: microRNA


title: SA_24h 2

description: Samples infected with S. aureus for 24h


title: SA_12h 3

description: Samples infected with S. aureus for 12h

value: S. aureus infected_12h


title: SA_24h 1

description: Samples infected with S. aureus for 24h


title: 1756-A033652


title: Blood sample from individual 152

description: Sample ID: 152


title: PMBCs for 12 individuals in pool 75

value: PBMCs

value: blood

value: untreated


title: Blood sample from individual 151

description: Sample ID: 151


title: Blood sample from individual 153

description: Sample ID: 153


title: 1756-A033649


title: Blood sample from individual 150

description: Sample ID: 150


title: PMBCs for 9 individuals in pool 70


title: 1756-A033648


title: 1756-A033647


title: PMBCs for 14 individuals in pool 73


title: 1756-A033651


title: PMBCs for 12 individuals in pool 72


title: PMBCs for 12 individuals in pool 71


title: PMBCs for 14 individuals in pool 68


title: SA_12h 1

description: Samples infected with S. aureus for 12h


title: SA_6h 3

description: Samples infected with S. aureus for 6h

value: S. aureus infected_6h


title: Blood sample from individual 149

description: Sample ID: 149


title: SA_6h 4

description: Samples infected with S. aureus for 6h


title: SA_12h 2

description: Samples infected with S. aureus for 12h


title: PMBCs for 13 individuals in pool 69


title: Blood sample from individual 148

description: Sample ID: 148


title: 1756-A033646


title: PMBCs for 14 individuals in pool 64


title: 1756-A033642


title: 1756-A033650


title: 1756-A033645


title: Blood sample from individual 144

description: Sample ID: 144


title: SA_3h 3

description: Samples infected with S. aureus for 3h

value: S. aureus infected_3h


title: SA_6h 1

description: Samples infected with S. aureus for 6h


title: SA_6h 2

description: Samples infected with S. aureus for 6h


title: Blood sample from individual 147

description: Sample ID: 147


title: 1756-A033641


title: SA_3h 1

description: Samples infected with S. aureus for 3h


title: Blood sample from individual 143

description: Sample ID: 143


title: Blood sample from individual 146

description: Sample ID: 146


title: 1756-A033644

value: Severe


title: PMBCs for 15 individuals in pool 65


title: 1756-A033643


title: Blood sample from individual 145

description: Sample ID: 145


title: Blood sample from individual 142

description: Sample ID: 142


title: 1756-A033640


title: PMBCs for 14 individuals in pool 61


title: PMBCs for 14 individuals in pool 63


title: SA_3h 2

description: Samples infected with S. aureus for 3h


title: Blood sample from individual 141

description: Sample ID: 141


title: 1756-A033639


title: PMBCs for 16 individuals in pool 67


title: 1756-A033638


title: PMBCs for 15 individuals in pool 62


title: a251

city: Marburg

first: Veronika

last: Lutz

state: D

country: Germany

institute: Philipps-University of Marburg

data_processing:
Paired-end reads were mapped to the mouse transcriptome (Ensembl 102) using salmon (v1.3.0)
Differential gene expression analysis was performed using DESeq2 (v1.28.1)
Assembly: GRCm38
Supplementary files format and content: txt

source_name: PancOVA

growth_protocol: Lymphnodes and spleen of OT-1 mice were isolated and meshed through 30 µm strainers. Cells were then loaded for 1 hour with 5 µM OVA257-264 peptide (Invivogen) and were cultured for 2 days in RPMI supplemented with 10% FCS and 10 ng/ml recombinant murine IL-12 (Peprotech). After that, cells were cultured for 2 days and again for one more day with 20 ng/ml recombinant murine IL-2 (Peprotech) in order to generate effector CD8+ CTLs.

extract_protocol:
RNA preparation was carried out using the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer’s protocol
Quantity of total RNA was assessed with the Qubit 2.0 and quality was checked using a RNA 6000 Pico chip on Agilent's bioanalyzer. Samples with an RNA integrity number (RIN) of > 8 were used for library preparation. 1 ng of total RNA was used for cDNA synthesis and amplification with Takarabio’s SmartSeqv4 kit. 1 ng of the resulting cDNA was used for library preparation with the Nextera XT DNA Sample Prep Kit according to the manufacturer's instructions (Illumina). Library concentration was determined by Qubit2.0 system and library size distribution was assessed using a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 2100. Barcoded RNA-Seq libraries were sequenced (150 PE) at Novogene (Cambridge, UK) on an Illumina NovaSeq.

treatment_protocol: For the in vivo tumor model 1 × 10^6 Panc02 or PancOVA tumor cells were injected subcutaneously into the right flank of 8-12 week old male mice. 7 days after tumor injection, tumor bearing mice were treated with 1 × 10^6 CTLs i.p.. Three days after adoptive T cell transfer, tumors were isolated and single cell suspensions were generated, which were then FACS sorted for adoptivetransferred T cells..

value: adoptive transferred CD8 CTLs

tag: genotype


title: PMBCs for 14 individuals in pool 59


title: Control 2

description: Samples were not infected with S. aureus or given a PBS or Pam3 treatment.


title: PMBCs for 16 individuals in pool 58


title: Blood sample from individual 139

description: Sample ID: 139


title: PMBCs for 14 individuals in pool 60


title: a250


title: Blood sample from individual 140

description: Sample ID: 140

value: Male


title: 1756-A033636

tag: grouping


title: 1756-A033637

tag: tissue/sample type


title: a249


title: Control 1


title: Blood sample from individual 137

description: Sample ID: 137

value: Blood


title: PMBCs for 14 individuals in pool 55


title: PMBCs for 13 individuals in pool 56


title: PMBCs for 14 individuals in pool 57


title: a245


title: 1756-A033635

tag: molecule subtype


title: 1756-A033634


title: Kidney Wnt4-lineage cells, Wild Type, scRNA-Seq

first: XIANXIAO

last: ZHOU

address: 1470 Madison AVE

department: Department of Genetics and Genomic Sciences

institute: Ichan School of Medicine at Mount Sinai

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data were aligned and quantified using the Cell Ranger Single-Cell Software Suite (version 3.0, 10´Genomics) against the provided mm10 reference genome.
Assembly: mm10
Supplementary files format and content: H5 matrix files

source_name: kidney

extract_protocol:
Individually barcoded scRNA-seq libraries were prepared using the Chromium Platform (10x Genomics) with the 3’ gene expression V3 kit, using an input of approximately 10,000 cells. Briefly, Gel-bead in emulsions (GEM) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs by post-GEM RT-cleanup and amplified for 12 cycles.
Amplified cDNA was fragmented and subjected to endrepair, poly A-tailing, adapter ligation, and 10x-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent Technologies) and QuBit (Thermo Fisher Scientific) analysis.

value: Kidney Wnt4-lineage cells

tag: tissue

value: kidney

value: Wild type control


title: Kidney Wnt4-lineage cells, Brg1-deficiency, scRNA-Seq

description: 10x Genomics

value: Brg1cKO/cKO mutant


title: Blood sample from individual 136

description: Sample ID: 136

value: Female

tag: disease state

value: No active inflammatory disease


title: Blood sample from individual 135

description: Sample ID: 135

tag: individual id


title: PMBCs for 14 individuals in pool 54


title: 1756-A033632

value: Severe Negative

value: EDTA Platelet Depleted Plasma

value: microRNA


title: 1756-A033633


title: a243


title: PMBCs for 14 individuals in pool 53

value: PBMCs

value: blood


title: Blood sample from individual 134

description: Sample ID: 134

tag: gender


title: a247

tag: treatment

value: untreated


title: 1756-A033631


title: Blood sample from individual 138

description: Sample ID: 138


title: a241

tag: cell type


title: Blood sample from individual 133

description: Sample ID: 133


title: PMBCs for 14 individuals in pool 52

tag: pool id


title: 1756-A033630


title: Naïve_C5_splicing

city: Farmington

first: Anthony

last: Vella

state: Connecticut

address: 263 Farmington Ave

department: Immunology

institute: UConn Health

description: poly(A) RNA from naïve CD8+ T cells

data_processing:
Base-calling was done using Offline Base Caller (Illumina) v. 1.9.4
alignment was done using HISAT2 v 2.1.0 under default specfications
Fastq files were processed directly through Whippet v 1.6
BAM files were generated and indexed using Samtools v 1.9 under default specifications
Peak-calling was done using Stringtie v 2.1.0 under parameter -B to first generate a usable list of ballgown files to prep for DESeq2 analysis. A separate python script (prepDE.py) was then used to convert the ballgown list (sample_list.txt) to gene and transcript counts as well as FPKM values for each sample as a list of gtf files (using python2.7 - python 3.7.4 does not work).
Analysis of counts was performed using R v 4.0.5, Rstudio v 1.2.1, DESeq2 v 1.30.1 using the filtering parameters of FDR<.05
Assembly: mm10
Supplementary files format and content: tab delimited file of counts on a per gene basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of counts on a transcript basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of FPKM values on a transcript basis (generated from Stringtie)
Supplementary files format and content: PSI_Splicing_AB_Comparison.csv: psi differences

source_name: Purified CD8+ T cells from spleen and lymph nodes

extract_protocol:
QIAGEN miRNEasy Micro Kit
Clonetech SMART-Seq v4 Ultra-low w/Nextera XT, 2x150bp reads

treatment_protocol: CD8+ T cells from OT-I Tg mice were adoptively transferred into C57BL6/J mice. Recipients were stimulated with antigen-only or antigen+costimulatory agonist antibodies (anti-OX40, anti-41BB). Spleen and lymph nodes were collected after 4 days and sorted for pure CD8+ T cells and RNA was extracted. CD8+ T cells from naive OT-I Tg (non transferred) mice were purified as naive control.

value: OT-1 Tg C57BL/6J

value: CD8+ T cell

value: naive


title: Naïve_C4_splicing

description: poly(A) RNA from naïve CD8+ T cells


title: Blood sample from individual 132

description: Sample ID: 132


title: a244

value: adoptive transferred CD8 CTLs


title: PMBCs for 14 individuals in pool 51

tag: number of pooled individuals


title: 1657-bRNA_6

value: Control


title: PMBCs for 14 individuals in pool 50


title: 1657-bRNA_5


title: Blood sample from individual 131

description: Sample ID: 131

value: Blood


title: Blood sample from individual 130

description: Sample ID: 130

value: Male


title: PMBCs for 14 individuals in pool 49


title: Blood sample from individual 129

description: Sample ID: 129


title: Naïve_C2_splicing

description: poly(A) RNA from naïve CD8+ T cells


title: PMBCs for 14 individuals in pool 48


title: Naïve_C3_splicing

description: poly(A) RNA from naïve CD8+ T cells


title: 1657-bRNA_4


title: Costim_B5_splicing

description: poly(A) RNA from CD8+ T cells from mice receiving antigen and costimulatory antibodies


title: PMBCs for 14 individuals in pool 47


title: Naïve_C1_splicing

description: poly(A) RNA from naïve CD8+ T cells


title: 1657-A029969

source_name: EDTA Platelet Depleted Plasma_Severe (Timepoint 5)

value: Severe (Timepoint 5)


title: Blood sample from individual 127

description: Sample ID: 127


title: Blood sample from individual 128

description: Sample ID: 128


title: PMBCs for 14 individuals in pool 46


title: PMBCs for 14 individuals in pool 45


title: Blood sample from individual 126

description: Sample ID: 126


title: Costim_B4_splicing


title: Costim_B3_splicing


title: PMBCs for 14 individuals in pool 44


title: Blood sample from individual 125

description: Sample ID: 125


title: 1657-A029966

source_name: EDTA Platelet Depleted Plasma_Mild

value: Mild


title: 1657-A029964

source_name: EDTA Platelet Depleted Plasma_Moderate

value: Moderate


title: 1657-A029965


title: Costim_B1_splicing


title: Costim_B2_splicing


title: PMBCs for 15 individuals in pool 42


title: 1657-A029960


title: Blood sample from individual 124

description: Sample ID: 124

value: Female

value: No active inflammatory disease


title: 1657-A029958

value: EDTA Platelet Depleted Plasma


title: Blood sample from individual 123

description: Sample ID: 123


title: Blood sample from individual 122

description: Sample ID: 122


title: 1657-A029955

value: microRNA


title: 1657-A029954


title: Antigen_A5_splicing

description: poly(A) RNA from CD8+ T cells from mice receiving antigen-alone

value: antigen-only


title: Antigen_A4_splicing


title: Blood sample from individual 121

description: Sample ID: 121


title: Antigen_A3_splicing


title: PMBCs for 15 individuals in pool 38

value: PBMCs

value: blood


title: PMBCs for 14 individuals in pool 39

value: untreated


title: PMBCs for 14 individuals in pool 43


title: Blood sample from individual 120

description: Sample ID: 120


title: PMBCs for 14 individuals in pool 41


title: 1657-A029951

value: Severe


title: Antigen_A2_splicing

value: OT-1 Tg C57BL/6J

value: CD8+ T cell


title: Blood sample from individual 119

description: Sample ID: 119


title: PMBCs for 14 individuals in pool 37


title: Antigen_A1_splicing


title: PMBCs for 14 individuals in pool 36


title: Blood sample from individual 118

description: Sample ID: 118


title: TardbpKO_T8

data_processing:
alignment was done using HISAT2 v 2.1.0 under default specfications
BAM files were generated and indexed using Samtools v 1.9 under default specifications
Peak-calling was done using Stringtie v 2.1.0 under parameter -B to first generate a usable list of ballgown files to prep for DESeq2 analysis. A separate python script (prepDE.py) was then used to convert the ballgown list (sample_list.txt) to gene and transcript counts as well as FPKM values for each sample as a list of gtf files (using python2.7 - python 3.7.4 does not work).
Analysis of counts was performed using R v 4.0.5, Rstudio v 1.2.1, DESeq2 v 1.30.1 using the filtering parameters of FDR<.05
Fastq files were processed directly through Whippet v 1.6
Assembly: mm10
Supplementary files format and content: tab delimited file of counts on a per gene basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of counts on a transcript basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of splicing changes (generated from Whippet)
Supplementary files format and content: PSI_Splicing_CT_CRISPR_CD8.csv = psi differences

extract_protocol:
QIAGEN miRNEasy Micro Kit
Clonetech SMART-Seq v4 Ultra-low w/Nextera XT, 2x100bp reads

treatment_protocol: CD8+ T cells from OT-I Tg mice were electroporated with Cas9 and Control or Tardbp gRNA and allowed to recover - cells were subsequently adoptively transferred into C57BL6/J mice. Recipients were stimulated with antigen-only or antigen+costimulatory agonist antibodies (anti-OX40, anti-41BB). Spleen and lymph nodes were collected after 4 days and sorted for pure CD8+ T cells and RNA was extracted. CD8+ T cells from naive OT-I Tg (non transferred) mice were purified as naive control.

value: antigen+costimulation (anti-OX40, anti-41BB), Cas9/Tardbp gRNA


title: Blood sample from individual 117

description: Sample ID: 117

value: Blood


title: 1657-A029949


title: PMBCs for 14 individuals in pool 35


title: 1657-A029942


title: PMBCs for 14 individuals in pool 34


title: TardbpKO_T7


title: 1657-A029953


title: TardbpKO_T6


title: 1657-A029941


title: PMBCs for 15 individuals in pool 33


title: TardbpKO_T5


title: Blood sample from individual 115

description: Sample ID: 115

value: Male


title: TardbpKO_T4


title: TardbpKO_T2


title: PMBCs for 14 individuals in pool 31


title: 1657-A029932


title: Blood sample from individual 112

description: Sample ID: 112


title: 1657-A029930

source_name: EDTA Platelet Depleted Plasma_Negative Control

value: Negative Control


title: 1657-A029936


title: 1657-A029950

source_name: EDTA Platelet Depleted Plasma_Severe (Timepoint 3)

value: Severe (Timepoint 3)


title: PMBCs for 14 individuals in pool 32


title: Blood sample from individual 114

description: Sample ID: 114


title: TardbpKO_T1


title: PMBCs for 14 individuals in pool 29


title: 1657-A029928


title: 1657-A029929


title: PMBCs for 13 individuals in pool 30


title: Control_C8

value: antigen+costimulation (anti-OX40, anti-41BB), Cas9/scrambled gRNA


title: Blood sample from individual 116

description: Sample ID: 116

value: Female


title: PMBCs for 14 individuals in pool 28


title: 1657-A029924


title: Blood sample from individual 111

description: Sample ID: 111

value: No active inflammatory disease


title: Blood sample from individual 109

description: Sample ID: 109


title: 1657-A029921

value: EDTA Platelet Depleted Plasma


title: PMBCs for 14 individuals in pool 27


title: Control_C7


title: Blood sample from individual 113

description: Sample ID: 113


title: TardbpKO_T3


title: Blood sample from individual 108

description: Sample ID: 108


title: PMBCs for 15 individuals in pool 26


title: 1657-A029914

value: microRNA


title: Blood sample from individual 107

description: Sample ID: 107


title: Control_C5


title: 1657-A029916


title: 1657-A029920


title: Control_C6


title: PMBCs for 14 individuals in pool 25


title: Blood sample from individual 105

description: Sample ID: 105


title: Blood sample from individual 110

description: Sample ID: 110


title: PMBCs for 14 individuals in pool 24


title: Control_C3


title: Control_C4


title: PMBCs for 14 individuals in pool 23


title: Blood sample from individual 103

description: Sample ID: 103


title: PMBCs for 14 individuals in pool 22


title: PMBCs for 14 individuals in pool 21


title: Blood sample from individual 104

description: Sample ID: 104


title: Control_C2


title: Control_C1


title: 1657-A029912


title: 1657-A029910


title: 1657-A029908


title: PMBCs for 14 individuals in pool 20


title: Repeat_Naïve_C2

description:
poly(A) RNA from naïve CD8+ T cells
L453_40_S23_L002_R1_001.fastq.gz

data_processing:
Base-calling was done using Offline Base Caller (Illumina) v. 1.9.4
alignment was done using HISAT2 v 2.1.0 under default specfications
Fastq files were processed directly through Whippet v 1.6
BAM files were generated and indexed using Samtools v 1.9 under default specifications
Peak-calling was done using Stringtie v 2.1.0 under parameter -B to first generate a usable list of ballgown files to prep for DESeq2 analysis. A separate python script (prepDE.py) was then used to convert the ballgown list (sample_list.txt) to gene and transcript counts as well as FPKM values for each sample as a list of gtf files (using python2.7 - python 3.7.4 does not work).
Analysis of counts was performed using R v 4.0.5, Rstudio v 1.2.1, DESeq2 v 1.30.1 using the filtering parameters of FDR<.05
Assembly: mm10
Supplementary files format and content: tab delimited file of counts on a per gene basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of counts on a transcript basis (generated from Stringtie)
Supplementary files format and content: tab delimited file of splicing differences (generated from Whippet)
Supplementary files format and content: tab delimited file of FPKM values on a transcript basis (generated from Stringtie)

extract_protocol:
QIAGEN miRNEasy Micro Kit
Clonetech SMART-Seq v4 Ultra-low w/Nextera XT, 1x100bp reads

tag: treatmen

value: naive


title: Blood sample from individual 106

description: Sample ID: 106


title: PMBCs for 18 individuals in pool 19

value: PBMCs


title: Blood sample from individual 101

description: Sample ID: 101


title: Blood sample from individual 100

description: Sample ID: 100


title: PMBCs for 14 individuals in pool 18

value: blood


title: Repeat_Costim_B5

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen and costimulatory antibodies
L453_38_S21_L002_R1_001.fastq.gz


title: Blood sample from individual 99

description: Sample ID: 99


title: 1657-A029904


title: Blood sample from individual 102

description: Sample ID: 102


title: PMBCs for 14 individuals in pool 17

value: untreated


title: Repeat_Costim_B4

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen and costimulatory antibodies
L453_37_S20_L002_R1_001.fastq.gz


title: Blood sample from individual 96

description: Sample ID: 96


title: Blood sample from individual 98

description: Sample ID: 98


title: PMBCs for 14 individuals in pool 15


title: PMBCs for 14 individuals in pool 14


title: Repeat_Costim_B3

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen and costimulatory antibodies
L453_36_S19_L002_R1_001.fastq.gz


title: 1657-A029913


title: 1657-A029903


title: 1657-A029907


title: 1657-A029905


title: Repeat_Costim_B1

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen and costimulatory antibodies
L453_34_S17_L002_R1_001.fastq.gz


title: 1657-A029896

value: Mild


title: 1657-A029895


title: PMBCs for 14 individuals in pool 13


title: Blood sample from individual 95

description: Sample ID: 95


title: Repeat_Naïve_C1

description:
poly(A) RNA from naïve CD8+ T cells
L453_39_S22_L002_R1_001.fastq.gz

value: OT-1 Tg C57BL/6J


title: Repeat_Antigen_A5

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen-alone
L453_33_S16_L002_R1_001.fastq.gz

value: CD8+ T cell

value: antigen-only


title: Repeat_Antigen_A4

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen-alone
L453_32_S15_L002_R1_001.fastq.gz


title: PMBCs for 14 individuals in pool 12


title: Blood sample from individual 97

description: Sample ID: 97

value: Blood


title: Blood sample from individual 94

description: Sample ID: 94

value: Male


title: PMBCs for 17 individuals in pool 11


title: 1657-A029897

value: Moderate


title: Blood sample from individual 93

description: Sample ID: 93


title: Repeat_Antigen_A3

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen-alone
L453_31_S14_L002_R1_001.fastq.gz


title: 1657-A029888


title: Repeat_Antigen_A2

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen-alone
L453_30_S13_L002_R1_001.fastq.gz


title: 1657-A029884

value: Severe


title: 1657-A029887


title: PMBCs for 15 individuals in pool 10


title: Blood sample from individual 91

description: Sample ID: 91


title: Repeat_Antigen_A1

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen-alone
L453_29_S12_L002_R1_001.fastq.gz


title: PMBCs for 14 individuals in pool 8


title: PMBCs for 14 individuals in pool 9


title: scRNAseq_islets_ln_TCRseq

city: Pittsburgh

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

institute: University of Pittsburgh

data_processing:
Demultiplexing was performed using bcl2fastq (v2.20.0).
For bulk RNAseq, STAR (v2.5.2a) was used for alignment. Unique mapped reads were normalized using PORT and counts were converted to log2 counts per million. Quantile normalization and precision weighting was performed using limma. For scRNAseq, cellranger (v3.1.0) was used for alignment and to create feature barcode matrices. For scTCRseq, cellranger vdj (v3.1.0) was used to build T cell receptor sequences from single cells. For CITEseq, cite-seq-count (v1.2) was used for alignment and to build feature barcode matrices. For scATACseq, cellranger-arc (v2.0.0) was used for peak calling and counting ATAC molecules and creation of Bigwig files and peak barcode matrices.
Assembly: GRCm38/mm10
Supplementary files format and content: bulk RNAseq: gzipped tar text-delimited file of gene counts per sample; scRNAseq: gzipped tar directory containing filtered feature barcode matrices; CITEseq: gzipped tar directory containing filtered feature barcode matrices; TCRseq: gzipped tar text-dellimited file of TCR reconstruction; multiome_scATACseq: gzipped tar file of bigwig file from cellranger arc; multiome_scRNAseq: gzipped tar directory containing filtered feature barcode matrices

molecule: polyA RNA

source_name: non-draining lymph node, pancreatic islet

growth_protocol: Female mice used for experiments were aged 30 weeks. Different groups of mice were co-housed.

extract_protocol:
CD8+ T cells were FACS sorted from lymph node and islet preparations. Islets were isolated by injecting collagenese solution in the clamped pandcreatic duct. Pancreata were then excised and incubated in collagenase for 30 mins at 37 degrees C and then washed and spun down twice ti distrupt the pancreas. Islets where then picled under a dissecting microscope and incubated for 15 mins at 37 degrees C in dissociation buffer (Life Technologies). CD8+ T cells were then sorted from these single cell suspensions.
For bulk RNAseq, libraries were generated using Smart-seq2. For scRNAseq, 10X Genomics 5' v1 kit was used in conjunction with Total-SeqC antibodies as per the manufacturer's instructions. Libraries were generated from scRNAseq, scATACseq, and CITEseq. For scATACseq, 10X Genomics Multiome ATAC + Gene Expression kit was used as per the manufactuerer's instructions.

value: NOD

value: Lag3L/L-yfp  (WT), Lag3L/L-yfp x E8I-CRE/CRE-gfp (LAG3 KO)

tag: Sex

value: female

value: 8 weeks

value: CD8+ T cells


title: 1657-A029882

value: EDTA Platelet Depleted Plasma

value: microRNA


title: 1657-A029889


title: scRNAseq_islets_ln_CITEseq

tag: age


title: PMBCs for 14 individuals in pool 7

value: PBMCs

value: blood


title: Blood sample from individual 87

description: Sample ID: 87

source_name: Blood sample

value: No active inflammatory disease


title: Blood sample from individual 89

description: Sample ID: 89


title: 1657-A029881


title: Blood sample from individual 88

description: Sample ID: 88


title: PMBCs for 14 individuals in pool 6

value: untreated


title: PMBCs for 14 individuals in pool 5


title: scRNAseq_islets_ln


title: 1657-A029880


title: 1657-A029877


title: Blood sample from individual 86

description: Sample ID: 86


title: Blood sample from individual 92

description: Sample ID: 92


title: Blood sample from individual 90

description: Sample ID: 90

value: Female


title: Tumor-05

city: Chicago

first: Juan

middle: Jose

last: Apiz Saab

state: Illinois

address: 5515 S. Cornell Ave Apt 102

department: Ben May

institute: University of Chicago

description: PDAC Orthotopic Tumor

data_processing:
Concatenate datasets tail-to-head (Galaxy Version 1.0.0)
FastQC Read Quality reports (Galaxy Version 0.72+galaxy1)
Align seq. results to relevant genome with HISAT2  (Galaxy Version 2.2.1+galaxy0)
Measuring total gene counts for differential expression analysis with  featureCounts (Galaxy Version 2.0.1+galaxy1)
Normalizing total gene counts and performing differential expression analysis with limma (Galaxy Version 3.48.0+galaxy1)
Assembly: mm10
Supplementary files format and content: tab-delimited text files include the log2 TMM normalized counts for each sample

source_name: Mouse Pancreatic Ductal Adenocarcinoma

growth_protocol: Cells were seeded at ~60% cionfluency one day prior to RNA extraction. Media was changed 8 hours prior extraction; Tumors were extracted at end-point, dissasociated and cancer cells were flow sorted into RNA extraction buffer. Cells cultured were also flow sorted into RNA extraction buffer.

extract_protocol:
Quiagen RNeasy Micro Kit (74004) was used for RNA extraction of all samples.
RNA libraries were prepared by the University of Chicago Genomics Facility  for sequencing using standard Illumina protocols

treatment_protocol: No treatment

value: KP-/-C

tag: growth conditions

value: PDAC Orthotopic Tumor


title: Tumor-06

description: PDAC Orthotopic Tumor

tag: strain


title: PMBCs for 14 individuals in pool 3


title: Tumor-04

description: PDAC Orthotopic Tumor

tag: genotype


title: 1657-A029875

tag: grouping


title: PMBCs for 14 individuals in pool 2


title: Tumor-03

description: PDAC Orthotopic Tumor


title: Blood sample from individual 83

description: Sample ID: 83

value: Blood


title: Blood sample from individual 84

description: Sample ID: 84

value: Male


title: PMBCs for 12 individuals in pool 1


title: Tumor-02

description: PDAC Orthotopic Tumor


title: 1657-A029874

value: Mild

tag: tissue/sample type


title: 1657-A029873

value: Severe

tag: molecule subtype


title: PMBCs for 14 individuals in pool 4

tag: tissue


title: Blood sample from individual 81

description: Sample ID: 81

tag: disease state


title: Blood sample from individual 85

description: Sample ID: 85

tag: individual id


title: Blood sample from individual 82

description: Sample ID: 82

tag: gender


title: 1657-A029870


title: RNAseq.MSC_NCOA2_rep1

city: Memphis

first: Wojciech

last: Rosikiewicz

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

description:
2003995_MSC_N_1
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore
Paired-end reads were mapped by STAR(v2.7.1a) using parameters "-c -p 4 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outReadsUnmapped None --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM"
Read duplication was marked with MarkDuplicates from GATK (v4.0.4.0)
RSEM was used to quantify read counts per gene
Genome_build: hg38 (GRCh38.p12)
Supplementary_files_format_and_content: gene-based raw counts and FPKM normalized txt files

source_name: MSC

growth_protocol: iPSC MSC grow in Mesenchymal Stem Cell Basal Medium (ATCC PCS-500-030) plus Mesenchymal Stem Cell Growth Kit (ATCC PCS-500-041) in 95% Air, 5% CO2.

extract_protocol:
RNA was extracted using Quick-RNA Mini Prep kit (Zymo research)
Libraries were prepared from total RNA with the TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions (Illumina PN 20020595).

treatment_protocol: Doxycycline (50ng/ml) for 24h

tag: cell full name

value: iPSC-derived Mesenchymal Stem Cells (iPSC-MSCs, ACS-7010)

value: human mesenchymal stem cells

tag: treatment

value: with inducible construct containing NCOA2, with Doxycycline


title: Tumor-01

description: PDAC Orthotopic Tumor


title: RNAseq.MSC_NCOA2_Ctrl_rep2

description:
2003994_MSC_N_C2
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz

tag: cell type

value: with inducible construct containing NCOA2, without Doxycycline


title: TIFM-CO-03

description: murine PDAC Cell culture in TIFM-CO

value: Cell culture in TIFM-CO


title: TIFM-CO-02

description: murine PDAC Cell culture in TIFM-CO


title: 1657-A029868

source_name: EDTA Platelet Depleted Plasma_Severe

value: EDTA Platelet Depleted Plasma

value: microRNA


title: 1657-A029871


title: 1657-A029876


title: Blood sample from individual 80

description: Sample ID: 80


title: RNAseq.MSC_NCOA2_Ctrl_rep1

description:
2003993_MSC_N_C1
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz


title: TIFM-CO-01

description: murine PDAC Cell culture in TIFM-CO


title: Blood sample from individual 78

description: Sample ID: 78


title: 1657-A029867


title: RNAseq.MSC_HEY1_rep2

description:
2003992_MSC_Hey_2
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz

value: with inducible construct containing HEY1, with Doxycycline


title: RNAseq.MSC_HEY1_rep1

description:
2003991_MSC_Hey_1
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz


title: Blood sample from individual 77

description: Sample ID: 77

value: No active inflammatory disease


title: RNAseq.MSC_NCOA2_rep2

description:
2003996_MSC_N_2
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz


title: 1657-A029866


title: 1657-A029864


title: TIFM-02

description: murine PDAC Cell culture in TIFM

value: Cell culture in TIFM


title: RNAseq.MSC_HEY1_Ctrl_rep2

description:
2003990_MSC_Hey_C2
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz

value: with inducible construct containing HEY1, without Doxycycline


title: Blood sample from individual 76

description: Sample ID: 76


title: RNAseq.MSC_HEY1_Ctrl_rep1

description:
2003989_MSC_Hey_C1
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz


title: 1657-A029862


title: Blood sample from individual 79

description: Sample ID: 79

value: Female


title: TIFM-01

description: murine PDAC Cell culture in TIFM

value: KP-/-C


title: 1657-A029861


title: RNAseq.MSC_HEY1-NCOA2_rep2

description:
2004000_MSC_HN_2
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz

value: with inducible construct containing HEY1-NCOA2, with Doxycycline


title: Blood sample from individual 75

description: Sample ID: 75

value: Blood


title: RPMI-02

description: murine PDAC Cell culture in RPMI

value: Cell culture in RPMI


title: RPMI-03

description: murine PDAC Cell culture in RPMI


title: Blood sample from individual 73

description: Sample ID: 73


title: 1656-bRNA_3

source_name: EDTA Platelet Depleted Plasma_Control

value: Control


title: Blood sample from individual 72

description: Sample ID: 72

value: Male


title: RPMI-01

description: murine PDAC Cell culture in RPMI


title: RNAseq.MSC_HEY1-NCOA2_Ctrl_rep2

description:
2003998_MSC_HN_C2
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz

value: iPSC-derived Mesenchymal Stem Cells (iPSC-MSCs, ACS-7010)

value: human mesenchymal stem cells

value: with inducible construct containing HEY1-NCOA2, without Doxycycline


title: 1656-bRNA_2


title: RNAseq.MSC_HEY1-NCOA2_Ctrl_rep1

description:
2003997_MSC_HN_C1
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz


title: TIFM-03

description: murine PDAC Cell culture in TIFM


title: 1656-bRNA_1


title: 1656-A029968

value: Severe (Timepoint 3)


title: Blood sample from individual 70

description: Sample ID: 70


title: LC3-GFP(pos)_in vivo rep4

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

description:
ATAC_invivo_MACS2_Peaks.txt
ATAC_NG_14

data_processing:
Data analysis was performed using Partek Flow. Sequencing adapters were trimmed from raw sequencing reads using Cutadapt. Reads shorter than 25 and those that mapped to mitochondrial genome were discarded. The remaining reads were mapped to the mouse genome (mm10) using BWA. After alignment, duplicate reads, low mapping quality, and more than 2 mismatches were discarded. Reads with the same starting position were treated as duplicate reads. Peaks were then identified using MACS2 with a q-value cut-off of 0.05 and a fold enrichment cut-off of 1. Peaks were then annotated and reads mapping to transcription start sites, transcription termination sites, Intron, Exon, 5’ UTR Exon, 3’ UTR Exon, CDS Exon, and Intergenic regions were quantified. To be considered within a feature, a read was required to have a minimum of 80% overlap with the feature. Reads were then normalized as counts per million mapped reads to be able to compare amongst biological replicates. Differential expression analysis was performed using Gene Specific Analysis (GSA), and the p-value was set at 0.05 to identify statistically significant changes.
Genome_build: mm10
Supplementary_files_format_and_content: combined peak files for in vitro and in vivo experiments

source_name: CD8+ T cells

extract_protocol:
Nuclei from T cells were treated with Tn5 transposase and DNA accessible to Tn5 was extracted
ATAC-seq was performed as described by Corces et al.(PMID: 28846090) with a few modifications. Our modified transposase reaction mix contains, 25 µl 2x TD buffer, 1µl transposase, 16.5 µl PBS, 0.5 µl 1% digitonin, 0.5 µl 10% Tween-20, 6.5 µl H2O. Sequencing was performed at Novogene Corporation Inc (Beijing, China).

treatment_protocol: Purified T cells obtained from Pmel-LC3-GFP-RFP mice were stimulated with αCD3 (2ug/ml)+αCD28 Ab (2ug/ml) for three days in IL2 (100 IU/ml). LC3-GFPpos and LC3-GFPneg Cells were FACS sorted after 24h CO treatment and used for ATAC-seq (in vitro). C57BL/6 mice (n=4 mice/group) were inoculated (s.c) with 0.3×106 B16-F10 melanoma cells for 12 days, after which mice were adoptively transferred with 0.3×106 Pmel LC3-GFPpos or Pmel LC3-GFPneg T cells. After 15 days of T cells transfer, lymphocytes were retrieved from the excised tumor (TILs). Vβ13+CD8+ population was sorted from the individual mouse by FACS and used for ATAC-seq (in vivo).

value: CD8+ T cells

tag: cell population

value: LC3-GFP(pos), in vivo


title: Blood sample from individual 71

description: Sample ID: 71

data_processing:
Genomic DNA extracted from blood was genotyped using the Infinium Global Screening Array-24 v1.0 BeadChip (Illumina).
Primary assessment and SNP call rate quality control of SNP intensity output files were performed using GenomeStudio software (Illumina).
Genotype: AA,AB,BB,or NC (no call)
Processed data file onek1k_genotype_matrix.txt.gz is linked as supplementary file at the foot of the Series record.

extract_protocol: DNA was extracted from blood stored in EDTA tubes using the QIAamp Blood Mini kit.


title: LC3-GFP(neg)_in vivo rep3

description:
ATAC_invivo_MACS2_Peaks.txt
ATAC_NG_15

value: LC3-GFP(neg), in vivo


title: PMBCs for 15 individuals in pool 16

description:
List of pooled individuals: see *GenotypeSamples.txt file
List of individual barcodes: see *Individual_Barcodes.csv

value: PBMCs

value: blood

value: untreated

tag: pool id

tag: number of pooled individuals


title: 1656-A029967

value: Severe

value: EDTA Platelet Depleted Plasma

value: microRNA


title: LC3-GFP(neg)_in vivo rep4

description:
ATAC_invivo_MACS2_Peaks.txt
ATAC_NG_16


title: Blood sample from individual 74

description: Sample ID: 74

value: Blood

value: No active inflammatory disease


title: Blood sample from individual 69

description: Sample ID: 69

value: Female


title: RNAseq.MSC_HEY1-NCOA2_rep1

description:
2003999_MSC_HN_1
RNAseq.RSEM_FPKM.tsv.gz
RNAseq.RSEM_TPM.tsv.gz
RNAseq.RSEM_count.tsv.gz

value: with inducible construct containing HEY1-NCOA2, with Doxycycline


title: LC3-GFP(pos)_in vivo rep3

description:
ATAC_invivo_MACS2_Peaks.txt
ATAC_NG_13


title: Blood sample from individual 68

description: Sample ID: 68

value: Male


title: 1656-A029963


title: ChIPseq.MSC_HEY1_rep2

data_processing:
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4)
Reads were mapped to human reference genome (GRCh38.p12) with bwa aln, followed by bwa samse7 (v0.7.12-r1039) with -K flag set to 10000000
Duplicated reads were marked with bamsormadup tool from biobambam2 (v2.0.87) and Cross-Correlation analysis was conducted with SPP (v1.11)
Genome_build: hg38 (GRCh38.p12)
Supplementary_files_format_and_content: bigwig

extract_protocol:
Common Chip protocol
Libraries were prepared with HyperPrep Library Preparation Kit (Roche PN 07962363001)

value: iPSC-derived Mesenchymal Stem Cells (iPSC-MSCs, ACS-7010)

value: human mesenchymal stem cells

tag: chip antibody

value: anti-Flag M2 antibody (Sigma-Aldrich Co. LLC)

tag: expression

value: inducible construct expressing HEY1


title: ChIPseq.MSC_HEY1_rep1


title: ChIPseq.MSC_Vec-CONTROL_rep2

value: empty vector


title: LC3-GFP(neg)_in vivo rep2

description:
ATAC_invivo_MACS2_Peaks.txt
ATAC_NG_12

value: CD8+ T cells

value: LC3-GFP(neg), in vivo


title: LC3-GFP(neg)_in vivo rep1

description:
ATAC_invivo_MACS2_Peaks.txt
ATAC_NG_11


title: 1656-A029962

value: Severe (Timepoint 5)


title: Blood sample from individual 66

description: Sample ID: 66


title: ChIPseq.MSC_Vec-CONTROL_rep1


title: Blood sample from individual 67

description: Sample ID: 67


title: 1656-A029961


title: LC3-GFP(pos)_in vivo rep2

description:
ATAC_invivo_MACS2_Peaks.txt
ATAC_NG_10

value: LC3-GFP(pos), in vivo


title: ChIPseq.MSC_HEY1-NCOA2_rep1

value: inducible construct expressing HEY1-NCOA2


title: PB01-2_scRNAseq

description:
PB01_scRNAseq_Expression.txt
PB01_scRNAseq_MetaData.txt
barcode.1_2 corresponds to sample PB01-2_scRNAseq

data_processing:
Demultiplexing  and FASTQ generation using CellRanger version 5.0.0
Generate single-cell expression matrix using CellRanger version 5.0.0
Ambient RNA removal using SoupX version 1.5.2
Quality control and filtering using R 4.1.0
Normalization and unsupervised clustering using Seurat 4.0.2
TREK-seq: Demultiplexing with bcl2fastq version 2.20.0
TREK-seq: TCR sequence extraction and scRNAseq pairing using WAT3R
Genome_build: hg38
Supplementary_files_format_and_content: Gene expression matrix (scRNAseq) tab-delimited text file with gene-cell count matrix; metadata (scRNAseq) tab-delimited text file with cell-metadata matrix; WAT3R output (TREK-seq) tab-delimited text file with cell-metadata matrix.

source_name: Peripheral blood cells

value: peripheral blood

tag: technology

value: 10x 3' v3 scRNA-seq


title: Blood sample from individual 65

description: Sample ID: 65

value: Blood


title: 1656-A029956

value: Severe (Timepoint 3)

value: EDTA Platelet Depleted Plasma

value: microRNA


title: LC3-GFP(neg)_in vitro rep2

description:
ATAC_invitro_MACS2_Peaks.txt
ATAC_NG_8

value: LC3-GFP(neg), in vitro


title: LC3-GFP(pos)_in vivo rep1

description:
ATAC_invivo_MACS2_Peaks.txt
ATAC_NG_9


title: ChIPseq.MSC_HEY1-NCOA2_rep2

value: iPSC-derived Mesenchymal Stem Cells (iPSC-MSCs, ACS-7010)


title: Blood sample from individual 63

description: Sample ID: 63

value: Female

value: No active inflammatory disease


title: LC3-GFP(neg)_in vitro rep1

description:
ATAC_invitro_MACS2_Peaks.txt
ATAC_NG_7


title: 1656-A029952


title: 1656-A029957

value: Severe


title: Blood sample from individual 64

description: Sample ID: 64

value: Male


title: Repeat_Costim_B2

description:
poly(A) RNA from CD8+ T cells from mice receiving antigen and costimulatory antibodies
L453_35_S18_L002_R1_001.fastq.gz

tag: strain

value: OT-1 Tg C57BL/6J

value: CD8+ T cell

tag: treatmen


title: 1656-A029959

tag: grouping

tag: tissue/sample type


title: 1656-A029948

tag: molecule subtype


title: LC3-GFP(pos)_in vitro rep1

description:
ATAC_invitro_MACS2_Peaks.txt
ATAC_NG_5

value: CD8+ T cells

value: LC3-GFP(pos), in vitro


title: Blood sample from individual 62

description: Sample ID: 62

tag: tissue

tag: disease state


title: 1656-A029947


title: LC3-GFP(neg) rep2 [SM8]

data_processing:
Data analysis was performed using Partek Flow. Unaligned reads were mapped to mouse genome mm10 using STAR (PMC3530905), and read mapping to each RefSeq transcript was quantified. Differential expression analysis was performed using DESeq2 (PMC4302049), and the p-value was set at 0.05 to identify statistically significant changes.
Genome_build: mm10
Supplementary_files_format_and_content: gene counts

extract_protocol:
RNA was extracted using mirVana™ miRNA Isolation Kit following the manufacturer’s protocol
Samples were then sent to Novogene Corporation Inc (Beijing, China) for sequencing

treatment_protocol: Purified T cells obtained from Pmel-LC3-GFP-RFP mice were stimulated with αCD3 (2ug/ml)+αCD28 Ab (2ug/ml) for three days in IL2 (100 IU/ml). LC3-GFPpos and LC3-GFPneg Cells were FACS sorted after 24h CO treatment.


title: T2

city: Shanghai

first: Xu

last: Chen

address: Zhizaoju Road No.639

country: China

institute: Shanghai Jiao Tong University School of Medicine

data_processing:
Single-cell suspensions were loaded onto a Chromium single cell controller instrument (10×Genomics) to generate single-cell gel beads inemulsions (GEMs).
After cDNA clean-up, cDNA was amplified by PCR for appropriate cycles. Next, these amplified cDNA was fragmented, end-repaired, A-tailed, and ligated to an index adaptor, and then the library was amplified.
Every library was sequenced on a Hiseq X Ten platform (Illumina), and 150-bp paired-end reads were generated.
The Cell Ranger software pipeline (version 3.1.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner, and down-sample reads as required to generate normalized aggregate data across samples, producing a matrix of gene counts versus cells.
Genome_build: GRCH38
Supplementary_files_format_and_content: cell barcode files, gene files, and gen-barcode counts

source_name: oral

extract_protocol:
Samples from the tumor and adjacent non-malignant oral cancer tissue from the same resection specimen were isolated and saved in storage buffer. Each sample was subsequently minced on ice to less than 1 mm cubic pieces, followed by enzymatic digestion using type 2 collagenase (Sigma) with manual shaking every 5 min. Samples were then centrifuged at 300 relative centrifugal force (RCF) for 30 s at room temperature and removed the supernatant without disturbing the cell pellet. Next, 1× PBS (calcium and magnesium free) containing 0.04% BSA (400 µg/ml) was added and then centrifugation at 300 RCF for 5 min. The cell pellet was re-suspended in 1 ml red blood cell lysis buffer and incubated for 10 min at 4℃. After lysis of red blood cells, samples were re-suspended in 1 ml PBS containing 0.04% BSA. Next, samples were filtered over 40-µm cell strainers (VWR) to obtain single-cell suspension. After tumor dissociation, cell concentration and cell viability were determined by hemocytometer and trypan blue staining.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: type

value: oral cancer


title: Blood sample from individual 60

description: Sample ID: 60

tag: individual id

tag: gender


title: Blood sample from individual 61

description: Sample ID: 61


title: PB01-1_scRNAseq

description:
PB01_scRNAseq_Expression.txt
PB01_scRNAseq_MetaData.txt
barcode.1_1 corresponds to sample PB01-1_scRNAseq

extract_protocol:
mRNA was extracted by 10x 3' sequencing technology
10x 3' v3 single-cell RNA-sequencing library construction methods were utilized for mRNA libraries. TREK-seq was used to enrich and sequence T-cell receptors.
scRNAseq, TREK-seq

value: peripheral blood


title: N1

value: adjacent normal tissues


title: 1656-A029945

data_processing:
The sequencing data on miRNA expression of target genes were imported into HTG EdgeSeq Parser software.
Post-sequencing QC metrics (QC0, QC1, and QC2) detect three different sample failure modes (1 - Degraded RNA or poor quality of sample, Pos% >- 14% as failure; 2 - Insufficient read depth, Read Deapth <= 500 K as failure; 3 - Minimal expression variability, RSD >= 0.08 as failure).
The HTG EdgeSeq Reveal Application was utilized to quality check and normalize data which utilizes DeSeq.
Genome_build: hg38
Supplementary_files_format_and_content: Excel files including raw counts and processed data; DeSeq Normalized Count Data

extract_protocol:
A total of 30uL of thawed plasma was co-incubated with 1:1 volumes of HTG Plasma Lysis buffer (pre-warmed to 50 degrees celsius) and 1/10th v/v proteinase K for three hours at 50 degrees celsius with shaking (200prm).
The lysed sample was transferred to a standard 96-well micro-titer plate, referred to as the sample plate. Target capture was done by the HTG EdgeSeq chemistry. Briefly, the nuclease protection probes (NPPs) were added to the lysed samples in the sample plate in excess amount and hybridized to the target miRNA. Then S1 nuclease was added to digest non-hybridized mRNA and excess NPPs, thus producing a stoichiometric amount of target miRNA NPP duplexes. After the S1 digestion was completed, the processed sample was transferred to a new 96-well micro-titer plate with a v-bottom, referred to as the stop plate, and S1 digestion was terminated by the addition of termination solution followed by heat denaturation of S1 enzyme. Each processed sample from the stop plate was used as   template to set up PCR reactions with specially designed primers, referred to as tags. These tags share common sequences that are complementary to 5’-end and 3’-end “wing” sequences of the probes and common adaptors required for cluster generation on an Illumina sequencing platform. In addition, each tag contains a unique barcode that is used for sample identification and multiplexing. HTG has developed 12 forward and eight reverse primer tags; therefore, up to 96 samples can be analyzed simultaneously on an Illumina sequencing platform. Clean-up procedures were performed according using AMPure cleanup protocols for Illumina Sequencing Libraries. The library was quantified in accordance with the HTG EdgeSeq KAPA Library Quantification kit for Illumina Sequencing. All samples and controls were quantified in triplicate. No Template Control (NTC) reactions were made for each master mix used (using the same master mix as for samples) during the qPCR process. NTCs serve as a test for qPCR reagent contamination. Molecular-grade water is used in place of test sample in the NTC reactions using the same volume as the template.


title: Blood sample from individual 59

description: Sample ID: 59

value: Blood


title: LC3-GFP(pos)_in vitro rep2

description:
ATAC_invitro_MACS2_Peaks.txt
ATAC_NG_6

tag: cell type


title: LC3-GFP(pos) rep2 [SM7]

tag: cell population


title: T1


title: N2


title: 1656-A029943

value: Severe (Timepoint 5)


title: P10_Relapse_area_2

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

institute: LMU University Hospital

description: Relapse

data_processing:
Sequencing adapters were removed from raw reads using Trimmomatic (v0.36).
Trimmed reads were mapped with STAR aligner (v2.5.3a) to GRCh38_r77.
Quantification was performed with Salmon v0.9.1 in alignment-based mode.
Counts were processed and imported into R via package tximport and differential gene expression was performed with DESeq2.
The gene log-scale expression matrix was generated by variance-stabilized transformation (vst).
Genome_build: GRCh38
Supplementary_files_format_and_content: Tab-delimited text file with Variance-stabilized log-expression per gene.
Supplementary_files_format_and_content: read counts

source_name: head and neck squamous cell carcinoma

growth_protocol: 19 tumor areas of primary and recurrent tumors were collected as FFPE specimens from surgically resected tumor tissues or pan-endoscopic biopsies from n=3 HNSCC patients.

extract_protocol:
Simultaneous DNA and total RNA extraction using the AllPrep DNA/RNA FFPE Kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol.
Prior to sequencing, RNA integrity was assessed using the Agilent Bioanalyzer RNA 6000 Nano Kit (Agilent Technologies, Waldbronn, Germany) by calculating the percentage of fragments > 200 nucleotides (DV200). Sequencing libraries were prepared with 100 ng total RNA using the QuantSeq 3'-RNA-Seq Library Prep Kit FWD for Illumina with i5 6 nt Dual Indexing(Lexogen GmbH, Vienna, Austria) according to the manufacturer's instructions for dual-indexing and low quantity samples. For library amplification, PCR cycles were determined using the PCR Add-on Kit for Illumina (Lexogen). Quantity and quality of sequencing libraries were assessed using the Quanti-iT PicoGreen dsDNA Assay Kit (ThermoScientific) and the Bioanalyzer High Sensitivity DNA Analysis Kit (Agilent Technologies). Libraries were sequenced in 150bp paired-end mode on a HiSeq4000 sequencer (Illumina, Berlin, Germany). The pool of individually barcoded libraries was distributed across the lanes of the same flow-cell aiming for approximately ten million paired-end reads per sample.
150bp paired-end

treatment_protocol: Serial sections of FFPE tumor blocks were macrodissected for the enrichment of tumor cells.

value: tumor cell

value: cancer


title: P10_Relapse_area_1

description: Relapse


title: Blood sample from individual 57

description: Sample ID: 57


title: P10_Relapse_area_3

description: Relapse


title: 1656-A029944

value: Severe (Timepoint 3)

value: EDTA Platelet Depleted Plasma

value: microRNA


title: Blood sample from individual 56

description: Sample ID: 56

value: Female

value: No active inflammatory disease


title: 1656-A029940


title: P10_Primary_area_2

description: Primary


title: P10_Primary_area_3

description: Primary


title: 1656-A029939


title: Blood sample from individual 53

description: Sample ID: 53


title: 1656-A029938

value: Severe


title: LC3-GFP(neg) rep1 [SM2]


title: Blood sample from individual 55

description: Sample ID: 55


title: Control - 4

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

description: H

data_processing:
Files were demutiplexed using Casava
Reads were checked for quality with FastQC and trimmed using TrimGalore!
Trimed reads were alligned to the mm10 genome with Hisat2 and counted usign Feature Counts from Rsubread
Genome_build: mm10
Supplementary_files_format_and_content: Normalised counts, csv, Counts normalised for library size with DESeq2
Supplementary_files_format_and_content: Raw count table, csv, raw counts post featurecount

source_name: Tumor

growth_protocol: 2.5 x 10^5 MC38 tumour cells were injected into 9-week old female B6 Kaede.

extract_protocol:
RNA was extracted using a QiaCube
Illumina SMARTER stranded total RNA, as per manufactuers instructions

treatment_protocol: 10 days post inoculation when tumour sizes were about 5 mm in diametre, 4 tumours (sample 1-4) were exposed to Violet light 405 for 3 minutes while the rest 4 tumours (sample 5-8) were not exposed and used as non-photoconversion controls. 5 hours post photoconversion, all tumours were collected in RNAlater and kept in 4oC fridge until further processing.

tag: group

value: Control


title: Control - 1

description: E


title: Control - 2

description: F


title: Blood sample from individual 52

last: Powell

institute: Garvan Institute of Medical Research

description: Sample ID: 52


title: Blood sample from individual 58

description: Sample ID: 58

value: Male


title: P10_Primary_area_1

description: Primary


title: Blood sample from individual 54

description: Sample ID: 54


title: Photoconverted - 4

description: D

value: Photoconverted


title: P08_Relapse_area_3

description: Relapse


title: LC3-GFP(pos) rep1 [SM1]

value: CD8+ T cells


title: Blood sample from individual 51

description: Sample ID: 51


title: 1656-A029934


title: 1656-A029935

value: Mild


title: 1656-A029937


title: Control - 3

description: G


title: Blood sample from individual 50

description: Sample ID: 50


title: P08_Relapse_area_2

description: Relapse


title: P08_Relapse_area_1

description: Relapse


title: 1656-A029946


title: Photoconverted - 2

description: B


title: Photoconverted - 3

description: C


title: Blood sample from individual 49

description: Sample ID: 49


title: Photoconverted - 1

description: A


title: Blood sample from individual 48

description: Sample ID: 48


title: P08_Primary_area_3

description: Primary


title: 1656-A029931

value: Negative Control


title: 1656-A029926


title: P08_Primary_area_2

description: Primary


title: P08_Primary_area_1

description: Primary


title: 1656-A029927


title: S-RhoBTB1.AngII_rep12

city: Wauwatosa

first: Shi

last: Fang

state: Wisconsin

address: 8701 W Watertown Plank Rd.

department: Physiology

institute: The Medical College of Wisconsin

data_processing:
Data was trimmed and quality assessed with FastQC and RSeQC
Reads were aligned to the mouse reference Gencode vM23 (based on Ensembl v98) using the STAR aligner and MAPR-Seq workflow v3.0
Differential gene expression was processed through EdgeR utilizing both the pairwise and generalized linear model statistics with the cutoffs set at an FDR <0.05 and log 2 fold change ≥1 or ≤-1.
Genome_build: Gencode vM23 (GRCm38.p6)
Supplementary_files_format_and_content: GeneCount,RPKM

source_name: aorta

extract_protocol:
Aortae were disscted, cleaned and snap frozen in liquid nitrogen. Tissue were lysed in Trizol using a bead mill homogenizer. Total RNA were extracted following the instructions provided by the Invitrogen Purelink kit.
RNA was quantifed by fluorimetirc methods (Qubit, Invitrogen) and quality assessed by Fragment Analysis (Agilent).  Library preparation was initiated with 500ng of RNA and completed following manufacture's recommendations for the TruSeq stranded mRNA kit (Illumina).  Final libraries were quantified by qPCR (Kapa Library Quantification Kit, Kapa Biosystems) and fragment size observed with high sensitivity DNA fragment analysis (Agilent).  Paired end sequencing was completed on the NovaSeq 6000 at 2x100bp reads, targeting 50 million reads per sample.

treatment_protocol: Mice were first implanted with osmotic mini pumps that releases either vehicle or Ang-II continously for 6 weeks. Two weeks after the implantation, five daily tamoxifen injections were used to activate the transgene. Tissue were collected two weeks after the completion of the tamoxifen injections.

tag: genotype

value: smooth muscle-specific, tamoxifen inducible RhoBTB1 transgene

tag: treatment

value: angiotensin II


title: Blood sample from individual 47

city: Darlinghurst

first: Joseph

address: 384 Victoria Street

description: Sample ID: 47

value: Blood


title: Blood sample from individual 46

description: Sample ID: 46


title: S-RhoBTB1.AngII_rep10


title: P03_Relapse_area_4

description: Relapse

value: tumor cell


title: 1656-A029933


title: 1656-A029925


title: P03_Relapse_area_3

description: Relapse

value: cancer


title: S-RhoBTB1.AngII_rep9


title: Blood sample from individual 45

description: Sample ID: 45


title: S-RhoBTB1.AngII_rep8


title: P03_Relapse_area_2

description: Relapse


title: Blood sample from individual 44

description: Sample ID: 44


title: 1656-A029923


title: P03_Relapse_area_1

description: Relapse


title: 1656-A029919


title: Blood sample from individual 42

description: Sample ID: 42


title: S-RhoBTB1.AngII_rep7


title: Blood sample from individual 43

description: Sample ID: 43


title: S-RhoBTB1.AngII_rep5


title: 1656-A029918


title: P03_Primary_area_3

description: Primary


title: Blood sample from individual 40

description: Sample ID: 40


title: Blood sample from individual 41

description: Sample ID: 41


title: S-RhoBTB1.AngII_rep4


title: S-RhoBTB1.AngII_rep2


title: P03_Primary_area_1

description: Primary


title: P03_Primary_area_2

description: Primary


title: pHUVEC - Severe_5

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
ICU_5

data_processing:
Sequencing quality was examined using fastqc (v0.11.2), and adaptors were subsequently trimmed with trimmomatic (v0.36).
One sample was removed on the basis of abnormal read duplication rates (n=1 ambulatory disease, sample Mild_4). Gene quantification was performed using salmon (v1.3.0) using adaptor-trimmed reads.
Salmon index was built using the entire hg38 genome (obtained from UCSC) as the decoy sequence with Gencode transcript annotation (V31).
Genes were quantified by Salmon with command "salmon quant" with the following parameters: "-l A --gcBias --validateMappings". Read counts were imported into R using R package tximport (v 1.18.0) with argument (countsFromAbundance="lengthScaledTPM").
Read counts were first normalized by DESeq2 (v 1.26.0), with the svaseq() function (from "sva" package, v 3.34.0) being used to subsequently estimate hidden batch effects with n.sv=4.
Sva-normalized read counts were obtained by regressing out covariates using the cleaning function. Differential gene expression analysis was performed with DESeq2 with sva-estimated surrogate variables added to the design matrix.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include Salmon quantification results for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Pooled human umbilical vein endothelial cells (pHUVEC)

growth_protocol: Pool human umbilical vein endothelial cells (pHUVEC, Lonza, Basel, Switzerland) were cultured in Endothelial Cell Growth Basal Medium-2 (Lonza, Basel, Switzerland) containing the complete Endothelial Cell Growth Medium BulletKitTM (Lonza, Basel, Switzerland) at 37°C in a 5% CO2 humidified incubator. Cells were maintained on 10 cm tissue culture plates (Corning, Costar, New York, NY, USA) coated with 0.1% (v/v) gelatin attachment factor (ThermoFisher, Waltham, MA, USA) and passaged every 2-4 days at 70%-80% confluency. For experimentation, pHUVECs at passages 3-7 were used. Source cell vials were monitored and subsequently tested negative for the presence of mycoplasma contamination (ThermoFisher, Waltham, MA, USA).

extract_protocol:
Isolation of RNA was facilitated using a Qiagen RNeasy Plus Micro Kit (Cat#: 74004) only after washing twice with ice-cold Dulbecco's Phosphate Buffered Saline (PBS) without magnesium and calcium.
RNA quantities and quality were assessed using the Agilent 2100 Bioanalyzer with all samples passing a quality control threshold (RIN ≥ 7.0) to proceed to library preparations and RNA-seq. A total amount of 20 ng RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μL USER Enzyme was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 minutes followed by five minutes at 95 °C before PCR. PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. The resulting PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. Sequencing was carried out on an Illumina NovaSeq® 6000 (Illumina, San Diego, California, United States), using paired end 2×150 bp chemistry at a depth of 20 million reads per sample.

treatment_protocol: Once the cells reached the peak of log phase, 20% v/v plasma (differing severties) or PBS was added, and the cells co-incubated at 37°C in a 5% CO2 atmosphere for six hours.

tag: passage

value: HUVEC

value: SARS-CoV-2 Postitive Plasma (Severe)


title: 1656-A029922

value: EDTA Platelet Depleted Plasma

value: microRNA


title: Blood sample from individual 39

description: Sample ID: 39

value: Female

value: No active inflammatory disease


title: 1656-A029917


title: 1656-A029915


title: 1656-A029909


title: S-RhoBTB1.AngII_rep1


title: pHUVEC - Severe_3

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
ICU_3


title: Blood sample from individual 37

description: Sample ID: 37


title: S-RhoBTB1.Vehicle_rep11

value: vehicle


title: Blood sample from individual 36

description: Sample ID: 36

value: Male


title: 1656-A029906


title: S-RhoBTB1.Vehicle_rep10


title: S-RhoBTB1.AngII_rep3


title: pHUVEC - Severe_4

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
ICU_4


title: pHUVEC - Severe_2

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
ICU_2


title: Blood sample from individual 35

description: Sample ID: 35


title: 1656-A029911


title: 1656-A029902


title: pHUVEC - Severe_1

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
ICU_1


title: 1656-A029901

value: Severe


title: Blood sample from individual 34

description: Sample ID: 34


title: pHUVEC - Moderate_5

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Ward_7

value: SARS-CoV-2 Postitive Plasma (Moderate)


title: Blood sample from individual 38

description: Sample ID: 38


title: S-RhoBTB1.Vehicle_rep8


title: 1656-A029899


title: S-RhoBTB1.Vehicle_rep6


title: Blood sample from individual 33

description: Sample ID: 33


title: 1656-A029900

value: Moderate


title: 1656-A029898


title: S-RhoBTB1.Vehicle_rep4


title: S-RhoBTB1.Vehicle_rep5


title: pHUVEC - Moderate_3

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Ward_4


title: pHUVEC - Moderate_2

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Ward_3


title: S-RhoBTB1.Vehicle_rep9


title: Blood sample from individual 31

description: Sample ID: 31


title: pHUVEC - Moderate_1

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Ward_2


title: S-RhoBTB1.Vehicle_rep3


title: Blood sample from individual 32

description: Sample ID: 32


title: 1656-A029894


title: Blood sample from individual 30

description: Sample ID: 30


title: S-RhoBTB1.Vehicle_rep2


title: 1656-A029893


title: S-RhoBTB1.Vehicle_rep1


title: Blood sample from individual 29

description: Sample ID: 29


title: pHUVEC - Mild_5

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
ER_6

value: SARS-CoV-2 Postitive Plasma (Mild)


title: pHUVEC - Mild_4

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
ER_5


title: ISM-Cre.AngII_rep10

value: smooth muscle-specific, tamoxifen inducible Cre


title: pHUVEC - Moderate_4

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Ward_5


title: 1656-A029891

source_name: EDTA Platelet Depleted Plasma_Mild

value: Mild


title: pHUVEC - Mild_3

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
ER_4


title: Blood sample from individual 27

description: Sample ID: 27

value: Blood


title: ISM-Cre.AngII_rep9

value: angiotensin II


title: Blood sample from individual 26

description: Sample ID: 26

value: Giant Cell Arteritis


title: pHUVEC - Mild_2

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
ER_3

value: HUVEC


title: 1656-A029890


title: ISM-Cre.AngII_rep8


title: pHUVEC - Mild_1

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
ER_2


title: 1656-A029886

source_name: EDTA Platelet Depleted Plasma_Moderate


title: ISM-Cre.AngII_rep7


title: Blood sample from individual 24

description: Sample ID: 24


title: pHUVEC - Negative_5

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Negative_7

value: SARS-CoV-2 Negative Plasma


title: pHUVEC - Negative_4

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Negative_4


title: Blood sample from individual 25

description: Sample ID: 25


title: 1656-A029885

value: EDTA Platelet Depleted Plasma


title: ISM-Cre.AngII_rep6


title: 1656-A029883

value: microRNA


title: ISM-Cre.AngII_rep5


title: Blood sample from individual 22

description: Sample ID: 22

value: Female


title: pHUVEC - Negative_3

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Negative_3


title: 1656-A029879


title: 1656-A029892


title: Blood sample from individual 28

description: Sample ID: 28

value: No active inflammatory disease


title: ISM-Cre.AngII_rep4


title: pHUVEC - Negative_2

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Negative_2


title: Blood sample from individual 21

description: Sample ID: 21


title: ISM-Cre.AngII_rep3


title: 1656-A029872


title: Blood sample from individual 20

description: Sample ID: 20


title: ISM-Cre.AngII_rep2


title: pHUVEC - PBS_5

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Control_6

value: PBS


title: Blood sample from individual 23

description: Sample ID: 23

value: Male


title: Blood sample from individual 19

description: Sample ID: 19


title: ISM-Cre.AngII_rep1


title: Blood sample from individual 18

description: Sample ID: 18


title: ISM-Cre.Vehicle_rep10

value: vehicle


title: 1656-A029865


title: 1656-A029863

value: Severe


title: ISM-Cre.Vehicle_rep9


title: pHUVEC - PBS_2

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Control_3


title: 1656-A029878

value: Moderate


title: pHUVEC - PBS_4

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Control_5


title: Blood sample from individual 15

description: Sample ID: 15


title: pHUVEC - PBS_3

description:
RNeasy Plus Micro kit (Qiagen, Germantown, MD, USA
Control_4


title: ISM-Cre.Vehicle_rep7


title: 1656-A029860