title: Participant 30, Stress session, Time 3


title: Participant 29, No-stress session, Time 2

status: Public on Mar 21 2023

type: SRA

city: University Park

first: Idan

last: Shalev

state: PA

address: 219 Biobehavioral Health Building, Penn State University

country: USA

institute: Penn State University

library_source: transcriptomic

data_processing:
Raw reads were preprocessed using BBDuk (version 38.87) for quality trimming (minimum read lengths: 25bp, maximum read lengths: 70bp, quality-trim of Q10 using the Phred algorithm), polyA trimming and read decontamination.
Reads were aligned to the human reference genome (GRCh38) using STAR (version 2.7.9a).
Read counts were generated using featureCounts (version 2.0.1) excluding multimapping reads. “ID” and “gene” were the feature specifications used for –g and –t flags, respectively.
After reads were quantified, edgeR (version 3.38.2) was used to calculate counts per million (CPM) values for each gene. Genes that had a CPM value higher than 1 in 200 or more samples (13,381 genes) were kept, and all other genes were excluded. After filtering out lowly expressed genes, the original count matrices were normalized using the TMM method.
Batch correction was performed using the ComBat function in SVA (version 3.44.0).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes filtered log2-CPM TMM normalized values for all samples.

molecule: total RNA

organism: Homo sapiens

source_name: PBMC

extract_protocol:
Whole blood samples were repeatedly collected via an IV catheter into the antecubital vein. Blood samples collected in 10mL EDTA tubes were immediately centrifuged for 10min at 1500g prior to collection of plasma. Peripheral blood mononuclear cells (PBMCs) were then isolated through density-gradient centrifugation using Ficoll. 1 ug of total RNA per sample was extracted using QIAamp RNA Blood Mini Kit (Qiagen) and samples were delivered to Penn State College of Medicine’s Genomic Facility where RNA quality was verified using the Agilent Bioanalzyer, followed by library construction.
Library preparation was done using the QuantSeq 3’mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen) supplemented with UMI (unique molecular index) as per the manufacturer’s instructions.

tag: cell type

value: PBMC

tag: Sex

value: Female

tag: age

tag: ela status

value: Control

tag: session

value: No-stress

tag: time


title: Participant 29, No-stress session, Time 3


title: Participant 29, No-stress session, Time 1


title: Participant 28, No-stress session, Time 3

value: ELA


title: Participant 28, No-stress session, Time 4


title: Participant 28, No-stress session, Time 1


title: Participant 27, No-stress session, Time 1

value: Male


title: Participant 27, No-stress session, Time 3


title: Participant 28, Stress session, Time 4

value: Stress


title: Participant 27, No-stress session, Time 2


title: Participant 28, Stress session, Time 2


title: Participant 27, Stress session, Time 4


title: Participant 27, Stress session, Time 1


title: Participant 27, Stress session, Time 3


title: Participant 29, No-stress session, Time 4


title: Participant 26, Stress session, Time 2


title: Participant 26, No-stress session, Time 2


title: Participant 26, No-stress session, Time 3


title: Participant 25, Stress session, Time 2


title: Participant 28, No-stress session, Time 2


title: Participant 28, Stress session, Time 3


title: Participant 26, Stress session, Time 1


title: Participant 26, Stress session, Time 4


title: Participant 26, Stress session, Time 3


title: Participant 26, No-stress session, Time 4


title: Participant 26, No-stress session, Time 1


title: Participant 25, Stress session, Time 4


title: Participant 25, Stress session, Time 3


title: Participant 27, Stress session, Time 2


title: Participant 24, No-stress session, Time 4


title: Participant 24, No-stress session, Time 3


title: Participant 24, Stress session, Time 1


title: Participant 24, Stress session, Time 2


title: Participant 25, No-stress session, Time 4


title: Participant 24, No-stress session, Time 2


title: Participant 25, No-stress session, Time 3


title: Participant 25, No-stress session, Time 2


title: Participant 25, Stress session, Time 1


title: Participant 23, No-stress session, Time 1


title: Participant 27, No-stress session, Time 4


title: Participant 28, Stress session, Time 1


title: Participant 23, No-stress session, Time 4


title: Participant 23, Stress session, Time 1


title: Participant 24, Stress session, Time 3


title: Participant 23, Stress session, Time 3


title: Participant 22, Stress session, Time 2


title: Participant 23, Stress session, Time 4


title: Participant 25, No-stress session, Time 1


title: Participant 23, Stress session, Time 2


title: Participant 24, No-stress session, Time 1


title: Participant 24, Stress session, Time 4


title: Participant 22, No-stress session, Time 2


title: Participant 22, No-stress session, Time 3


title: Participant 23, No-stress session, Time 2


title: Participant 23, No-stress session, Time 3


title: Participant 22, Stress session, Time 3


title: Participant 22, Stress session, Time 1


title: Participant 21, No-stress session, Time 2


title: Participant 22, No-stress session, Time 4


title: Participant 22, No-stress session, Time 1


title: Participant 22, Stress session, Time 4


title: Participant 21, Stress session, Time 2


title: Participant 21, No-stress session, Time 1


title: Participant 20, No-stress session, Time 4


title: Participant 21, No-stress session, Time 4


title: Participant 21, Stress session, Time 1


title: Participant 20, No-stress session, Time 3


title: Participant 20, No-stress session, Time 2


title: Participant 21, Stress session, Time 3


title: Participant 21, No-stress session, Time 3


title: Participant 19, Stress session, Time 2


title: Participant 19, Stress session, Time 4


title: Participant 20, No-stress session, Time 1


title: Participant 20, Stress session, Time 1


title: Participant 19, Stress session, Time 1


title: Participant 19, No-stress session, Time 4


title: Participant 19, No-stress session, Time 3


title: Participant 19, No-stress session, Time 2


title: Participant 18, No-stress session, Time 3


title: Participant 18, No-stress session, Time 1


title: Participant 19, No-stress session, Time 1


title: Participant 18, Stress session, Time 4


title: Participant 18, Stress session, Time 3


title: Participant 19, Stress session, Time 3


title: Participant 20, Stress session, Time 3


title: Participant 18, Stress session, Time 1


title: Participant 20, Stress session, Time 2


title: Participant 17, Stress session, Time 3


title: Participant 17, Stress session, Time 4


title: Participant 18, No-stress session, Time 2


title: Participant 17, Stress session, Time 2


title: Participant 17, No-stress session, Time 1


title: Participant 16, Stress session, Time 3


title: Participant 17, No-stress session, Time 3


title: Participant 18, Stress session, Time 2


title: Participant 16, No-stress session, Time 4


title: Participant 16, Stress session, Time 1


title: Participant 15, No-stress session, Time 3


title: Participant 16, No-stress session, Time 2


title: Participant 15, Stress session, Time 2


title: Participant 15, Stress session, Time 4


title: Participant 15, Stress session, Time 1


title: Participant 16, No-stress session, Time 3


title: Participant 15, No-stress session, Time 1


title: Participant 14, Stress session, Time 3


title: Participant 15, No-stress session, Time 4


title: Participant 14, Stress session, Time 4


title: Participant 14, Stress session, Time 1


title: Participant 17, Stress session, Time 1


title: Participant 15, No-stress session, Time 2


title: Participant 17, No-stress session, Time 4


title: Participant 14, Stress session, Time 2


title: Participant 14, No-stress session, Time 4


title: Participant 17, No-stress session, Time 2


title: Participant 14, No-stress session, Time 3


title: Participant 16, Stress session, Time 4


title: Participant 16, No-stress session, Time 1


title: Participant 14, No-stress session, Time 2


title: Participant 15, Stress session, Time 3


title: Participant 13, Stress session, Time 2


title: Participant 14, No-stress session, Time 1


title: Participant 13, Stress session, Time 4


title: Participant 13, Stress session, Time 3


title: Participant 11, No-stress session, Time 4


title: Participant 11, Stress session, Time 1


title: Participant 11, Stress session, Time 2


title: Participant 11, No-stress session, Time 3


title: Participant 9, No-stress session, Time 2


title: Participant 9, Stress session, Time 4


title: Participant 9, No-stress session, Time 3


title: Participant 11, Stress session, Time 4


title: Participant 13, Stress session, Time 1


title: Participant 9, Stress session, Time 2


title: Participant 9, No-stress session, Time 1


title: Participant 9, Stress session, Time 1


title: Participant 11, No-stress session, Time 1


title: Participant 9, Stress session, Time 3


title: Participant 7, Stress session, Time 3


title: Participant 7, Stress session, Time 1


title: Participant 7, Stress session, Time 4


title: Participant 7, No-stress session, Time 4


title: Participant 7, Stress session, Time 2


title: Participant 7, No-stress session, Time 3


title: Participant 7, No-stress session, Time 2


title: Participant 7, No-stress session, Time 1


title: Participant 9, No-stress session, Time 4


title: Participant 11, No-stress session, Time 2


title: Participant 4, Stress session, Time 1


title: Participant 4, Stress session, Time 4


title: Participant 4, Stress session, Time 3


title: Participant 4, Stress session, Time 2


title: Participant 4, No-stress session, Time 4


title: Participant 4, No-stress session, Time 3


title: Participant 4, No-stress session, Time 2


title: Participant 11, Stress session, Time 3


title: Participant 3, No-stress session, Time 2


title: Participant 3, No-stress session, Time 1


title: Participant 3, No-stress session, Time 4


title: Participant 3, No-stress session, Time 3


title: Participant 3, Stress session, Time 4


title: Participant 4, No-stress session, Time 1


title: Participant 3, Stress session, Time 2


title: Participant 2, No-stress session, Time 4


title: Participant 2, No-stress session, Time 3


title: Participant 3, Stress session, Time 3


title: Participant 2, No-stress session, Time 2


title: Participant 2, No-stress session, Time 1


title: Participant 3, Stress session, Time 1


title: WT A549, rSeV-P5T, 8dpi, 1

city: New York

first: Skyler

middle: Andrew

last: Uhl

state: New York

address: 1 Gustave L. levy Pl.

department: Microbiology

institute: Icahn School of Medicine at Mount Sinai

description: TruSeq stranded total RNA, with RiboZero Gold

data_processing:
Base calling and sample deconvolution performed via Illumina BaseSpace
Host reads aligned to Homo sapiens HG19 reference genome assembly and quantified using Salmon as made available in Illumina BaseSpace "RNA-Seq Alignment" application
Viral reads were aligned to viral reference genome via Bowtie 2 using custom app on illumina basespace, Integrative Genomics Viewer (IGV) 2.15.2 was then used to generate a .csv files comparing individual base calls per aligned read to each nucleotide in the reference sequence
Assembly: hg19
Supplementary files format and content: .quant.genes.sf Salmon files (show raw and normalized read counts by gene)
Supplementary files format and content: .csv files show the read count for individual base calls compared to the viral reference sequence

extract_protocol:
Trizol phenol chloroform or Qiagen Rneasy kit
Poly-A enrichment and TruSeq stranded OR TruSeq stranded Total RNA with RiboZero Gold

tag: cell line

value: lung carcinoma epithelial cells

tag: genotype

value: WT

tag: treatment

value: rSeV-P5T (MOI=5) --- 8dpi


title: WT A549, rSeV-P5T, 8dpi, 2


title: STAT1 ADAR1 double KO A549, AdV-mcherry-hADAR1,3

value: STAT1 ADAR1 double KO

value: AdV-mcherry-hADAR1 (MOI=100) --- 4dpi


title: STAT1 ADAR1 double KO A549, AdV-mcherry-hADAR1, rSeV-N5T, 8dpi

value: rSeV-N5T (MOI=5) --- 8dpi


title: STAT1 ADAR1 double KO A549, AdV-mcherry-hADAR1,2


title: STAT1 ADAR1 double KO A549, AdV-mcherry-hADAR1,1


title: STAT1 ADAR1 double KO A549, Mock AdV transduction,3

value: Mock --- 4dpi


title: STAT1 ADAR1 double KO A549, Mock AdV transduction,2


title: WT A549, rSeV-P5T, 2dpi,3

value: rSeV-P5T (MOI=5) --- 2dpi


title: WT A549,Mock AdV transduction,3


title: STAT1 ADAR1 double KO A549, Mock AdV transduction,1


title: WT A549,Mock AdV transduction,2


title: WT A549,Mock AdV transduction,1


title: WT A549, rSeV-N5R, 2dpi,2

value: rSeV-N5R (MOI=5) --- 2dpi


title: WT A549, rSeV-P5T, 2dpi,2


title: WT A549, rSeV-N5R, 2dpi,3


title: WT A549, rSeV-N5T, 2dpi,2

value: rSeV-N5T (MOI=5) --- 2dpi


title: WT A549, rSeV-N5T, 2dpi,3


title: WT A549, MOCK, 2dpi,3

value: Mock --- 2 dpi


title: WT A549, rSeV-N5T, 2dpi,1


title: WT A549, MOCK, 2dpi,1


title: WT A549, rSeV-P5T, 1dpi,3

value: rSeV-P5T (MOI=5) --- 1dpi


title: WT A549, rSeV-N5R, 1dpi,1

value: rSeV-N5R (MOI=5) --- 1dpi


title: WT A549, rSeV-N5R, 1dpi,3


title: WT A549, rSeV-P5T, 1dpi,2


title: WT A549, rSeV-P5T, 1dpi,1


title: WT A549, rSeV-N5T, 1dpi,3

value: rSeV-N5T (MOI=5) --- 1dpi


title: WT A549, rSeV-N5T, 1dpi,1


title: WT A549, rSeV-N5R, 1dpi,2


title: WT A549, rSeV-N5T, 1dpi,2


title: Spatial control sample 1

city: Durham

first: Scott

last: Palmer

state: NC

address: 2100 Erwin Road

institute: Duke University

description: 10x Genomics

data_processing:
Cell Ranger v5.0.1 was used to demultiplex raw FASTQ files, align the reads to the 10x GRCh38 reference transcriptome, and generate gene expression matrices for all single cells in each sample. Further downstream analysis was performed using the R package, Seurat v4.1.0.
The top 3,000 genes were selected based on variance using the Seurat implementation FindVariableFeatures. These genes were then centered and scaled using Seurat’s implementation ScaleData and percent mitochondrial genes as a variable to regress out (percent_mt = 0.25).  Scaled data was subsequently used for principal components analysis (npcs = 42), and cell cluster analysis was performed using Seurat’s FindNeighbors (dims = 1:42) and FindClusters (resolution = 1.2) functions. Visualization was performed using uniform manifold approximation and projection.
Fiducial 50µm spots on the H&E image were manually aligned using Loupe browser v5.0.1 (10x Genomics). Space Ranger software (10x Genomics) was used to process raw FASTQ files, align the reads to the 10x GRCh38 reference transcriptome, and generate gene expression matrices for all single cells in each sample. Further downstream analysis of the spot UMI table and reference H&E section was performed in R using Seurat v4.1.0.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited files of single cell dataset include (1) gene expression matrix following sctransform based normalization and (2) cell identities including barcodes, CLAD vs control disease annotation, sample ID, and cell type annotations.
Supplementary files format and content: Loupe files for spatial dataset

source_name: Lung

extract_protocol:
A 2cm x 2cm segment of lung tissue was isolated at least 1cm from the pleura and minced using a razor blade. Tissue was digested at 37C using Miltenyi Multi Tissue Dissociation Kit 1 (Miltenyi Biotech, 130-110-201) for 30 minutes. Mechanical digestion was performed three times using Miltenyi gentleMACS dissociator (Miltenyi, 130-093-235). The cell suspension was spun down at 300g for 10 minutes, and cells were treated with RBC lysis buffer (Sigma, R7757). The cell suspension was filtered using a 70μm filter, spun down at 300g for 10 minutes, and resuspended in PBS with 0.04% BSA. For spatial transcriptomics, 10µm sections were cut from frozen OCT blocks and mounted onto Visium spatial gene expression slides and processed according to the manufacturer’s protocol (10x Genomics). Tissue sections were permeabilized immediately to capture RNA molecules onto barcoded spots on the slide.
Single cells were prepared for cDNA amplification and library preparation using Single Cell 3’ Reagent Kits v2 (10x Genomics) following the manufacturer's protocol

tag: tissue

value: Lung

value: Primary lung tissue

tag: condition

value: Control


title: WT A549, MOCK, 1dpi,1

value: lung carcinoma epithelial cells

value: Mock --- 1 dpi


title: Control sample 3

description:
10x Genomics
Normalized Count Matrix.csv
Cell Identities.csv


title: Spatial CLAD sample 1

description: 10x Genomics

value: CLAD


title: Participant 18, No-stress session, Time 4

value: PBMC

value: Female

value: ELA

value: No-stress


title: Spatial CLAD sample 3

description: 10x Genomics


title: WT A549, MOCK, 1dpi,2

value: WT


title: WT A549, MOCK, 1dpi,3


title: WT A549, rSeV-P5T, 2dpi,1

value: rSeV-P5T (MOI=5) --- 2dpi


title: Spatial CLAD sample 2

description: 10x Genomics


title: Control sample 2


title: WT A549, rSeV-N5R, 2dpi,1

value: rSeV-N5R (MOI=5) --- 2dpi


title: Control sample 1


title: WT A549, MOCK, 2dpi,2

value: Mock --- 2 dpi


title: mtRF1 WT

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

library_source: other

data_processing:
Sequenced reads were adaptor and quality trimmed with Trim Galore! 0.6.7, Cutadapt 4.1 and FastQC 0.11.9 (trim_galore -j 8 --fastqc --small_rna --clip_R1 4 --three_prime_clip_R1 4).
Trimmed reads were initially aligned against the rDNA repeat unit (GenBank: U11369.1) and mitochondrial rDNA sequences from the GRCh38 genome build (with a 3' poly(A) tail of 25 nt to capture any polyadenylated rRNA reads that appear in mitochondria) with Bowtie2 2.4.5 (-L 18 norc).
Unmapped reads were aligned against the GENCODE v41 human protein coding transcript sequences, substituting the mitochondrial transcripts with custom sequences that better reflect the transcripts in vivo. This includes adding 5' or 3' UTRs, representing ATP8/6 and ND4L/4 as single bicistronic transcripts and adding a poly(A) tail of 60 nt to allow reads at the transcript ends to map.
Alignments were filtered to remove those with a MAPQ (as determined by Bowtie2) of < 20.
Coverage depth profiles were made with genomecov from Bedtools 2.30.0, scaled to 1000000 / total reads mapped to mitochondrial mRNAs.
Assembly: GENCODE v41 protein-coding transcripts with substituted custom chrM transcript sequences (bicistronic transcripts, UTRs + polyA added; file provided)
Supplementary files format and content: bedgraph files containing raw and normalised read coverage of mitochondrial mRNAs
Library strategy: Ribo-Seq

molecule: other

growth_protocol: CAL51 cells were cultured at 37C in humidified 95% air/ 5% CO2 in Dulbeccos modified essential medium (DMEM) (Gibco, Life Technologies) containing glucose (4.5 g/L), L-glutamine (2 mM) and fetal bovine serum (FBS) (10%, v/v), 1 mM sodium pyruvate, and 50 g/ml uridine (Sigma).

extract_protocol:
Cells were homogenized using a Potter S pestle (Sartorius) in 5 ml of fresh mitochondrial isolation buffer (MIB) containing 310 mM sucrose, 10 mM Tris-HCl and 0.05 % BSA (w/v) by centrifugation at 4,500 g for 1 min at 4C. The homogenate was centrifuged at 1,000 g for 10 min at 4C and the supernatant was centrifuged at 4,500 g for 15 min at 4C to isolate mitochondria. Crude mitochondrial pellets were suspended in MIB supplemented with 1x Complete EDTA-free protease inhibitor cocktail (Roche). Isolated mitochondria at 10 mg/ml were lysed in 10 mM Tris-HCl, pH 7.5, 260 mM sucrose, 100 mM KCl, 20 mM MgCl2 and 2 % digitonin in the presence of 40 U/ml RNase inhibitor and 1x Complete EDTA-free Protease inhibitor cocktail for 20 min. The lysate was centrifuged at 9,200 g for 45 min at 4 C, the clarified lysate was loaded on a continuous 10-30% sucrose gradient (in 10mM Tris-HCl, pH 7.5, 100 mM KCl, 20 mM MgCl2 in the presence of RNAse and protease inhibitors) and centrifuged at 71,000 g in an Optima Beckman Coulter preparative ultracentrifuge. Fractions were collected and one third of each fraction was precipitated with 0.02% sodium deoxycholate and 12% trichloroacetic acid (final concentration), washed twice with acetone, and the entire precipitate was resolved by SDS-PAGE.
The fraction corresponding to the translating mitoribosome was isolated and digested with RNase T1 (16.7 U/ml, Ambion) for 30 min at 37C and RNA was extracted from the digested fraction using a Direct-zol RNA Microprep Kit  (Zymo Research) incorporating an on-column RNase-free DNase digestion to remove all DNA. The NEXTFLEX Small RNA-seq Kit v3 (Perkin Elmer) was used to prepare the libraries and they were sequenced on an Illumina NovaSeq.

treatment_protocol: CAL51 cells were seeded at 60% confluence and transfected using FuGENE HD (Promega) with 1.5 ug of pD1311-AD mammalian Cas9 expression vector (ATUM) encoding gRNAs targeting MTRF1. To establish stably transfected clones, single-cell sorting was performed 3 days post transfection, where cells were selected based on GFP fluorescence signal using a BD FACSAria II in PBS + 2% FBS (v/v).


title: CLAD sample 3


title: CLAD sample 4


title: CLAD sample 2


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.AU-15530.Donor4.Rep1

city: Boston

first: Cigall

last: Kadoch

state: Massachusetts

address: 450 Brookline Avenue

institute: Broad Institute of MIT and Harvard, Harvard Medical School, Dana-Farber Cancer Institute

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
RNAseq reads were aligned to the mm10 and hg19 transcriptomes with STAR v2.5.2b with default parameters and tracks were generated using the deepTools v2.5.3 bamCoverage function.
Assembly:hg19, mm10
Supplementary files format and content: tab-delimited text files include raw gene count values for each sample

molecule: polyA RNA

source_name: CD8 Positive T-cells

growth_protocol: Human and mouse T cells were maintained in RPMI media supplemented with 10% FBS, 1% Pen/Strep, 1X GlutaMAX, 1X Non-essential Amino Acids, 1X Sodium Pyruvate and 10mM 2-Mercaptoethanol, and 30U/ml human IL2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 100 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Human cells were activated with Human T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat# 11132D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6. Mouse cells were activated with Mouse T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat#11453D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.
Cells were treated with inhibitors (Compound 14 and FHT1015) on Day 3 and Day 6 and taken down for one timepoint at Day9.  Cells were treated with degraders (ACBI1 and AU-15330, 100nM) on Day 3 and Day 6 and taken down for one timepoint at Day9.

value: CD8 Positive T-cells

value: Primary T cells

tag: sample type

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 4 treated with AU-15530 100 nM technical replicate 1

value: Day 9


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.AU-15530.Donor3.Rep2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 3 treated with AU-15530 100 nM technical replicate 2


title: CLAD sample 1

value: Lung

value: Primary lung tissue


title: mtRF1 KO


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.ACBI1.Donor3.Rep1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 3 treated with ACBI1 100 nM technical replicate 1


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.ACBI1.Donor4.Rep1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 4 treated with ACBI1 100 nM technical replicate 1


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.ACBI1.Donor4.Rep2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 4 treated with ACBI1 100 nM technical replicate 2


title: RNAseq.human.CD8.Positive.Tcells.Day9.Chronic.DMSO.Donor4.Rep1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 4 treated with DMSO technical replicate 1

value: DMSO


title: RNAseq.human.CD8.Positive.Tcells.Day9.Chronic.DMSO.Donor4.Rep2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 4 treated with DMSO technical replicate 2


title: RNAseq.human.CD8.Positive.Tcells.Day9.Chronic.DMSO.Donor3.Rep1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 3 treated with DMSO technical replicate 1


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.ACBI1.Donor3.Rep2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 3 treated with ACBI1 100 nM technical replicate 2


title: RNAseq.human.CD8.Positive.Tcells.Day9.Chronic.DMSO.Donor3.Rep2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 3 treated with DMSO technical replicate 2


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.AU-15530.Donor3.Rep1

library_source: genomic

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
For the ATACseq data, quality read trimming was performed by Trimmmomatic v0.36, followed by alignment, duplicate read removal, and read quality filtering, using Bowtie2 v2.29, Picard v2.8.0, and SAMtools v0.1.19, respectively.
Output BAM files were converted into BigWig track files using MACS2 and UCSC utilities in order to display coverage throughout the genome (in RPM).
Assembly: hg19, mm10
Supplementary files format and content: bigWig, broadPeak

molecule: genomic DNA

source_name: CD8 Positive T-Cells

extract_protocol:
Regions of tagmented genomic DNA were purified Qiagen's MinElute DNA purification Kit.
Custom PCR primers were used to amplify tagmented DNA for a total of 7 cycles to prevent over amplification.

treatment_protocol:
Human cells were activated with Human T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat# 11132D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.Mouse cells were activated with Mouse T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat#11453D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.
Cells were treated with inhibitors (Compound 14 and FHT1015) on Day 3 and Day 6 and taken down for one timepoint at Day9.  Cells were treated with degraders (ACBI1 and AU-15330, 100nM) on Day 3 and Day 6 and taken down for one timepoint at Day9.

value: CD8 Positive T-Cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 3 treated with AU-15530 100 nM technical replicate 1


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.AU-15530.Donor3.Rep2

value: Primary T cells


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.AU-15530.Donor4.Rep1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 4 treated with AU-15530 100 nM technical replicate 1


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.AU-15530.Donor4.Rep2

value: CD8 Positive T-cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 4 treated with AU-15530 100 nM technical replicate 2

value: Day 9


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.ACBI1.Donor3.Rep2


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.ACBI1.Donor4.Rep2


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.ACBI1.Donor4.Rep1


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.ACBI1.Donor3.Rep1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 3 treated with ACBI1 100 nM  technical replicate 1


title: ATACseq.human.CD8.Positive.Tcells.Day9.Chronic.DMSO.Donor3.Rep1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 3


title: ATACseq.human.CD8.Positive.Tcells.Day9.Chronic.DMSO.Donor4.Rep1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 4


title: ATACseq.human.CD8.Positive.Tcells.Day9.Chronic.DMSO.Donor3.Rep2


title: ATACseq.human.CD8.Positive.Tcells.Day9.Chronic.DMSO.Donor4.Rep2


title: R21017092LR01

city: Shanghai

first: Peng

last: Zhang

address: No. 507 Zhengmin Road

country: China

institute: Department of Thoracic Surgery, Shanghai Pulmonary Hospital

description: Bulk RNAseq

data_processing:
scRNA-seq FASTQ files were processed using the BD Rhapsody Whole Transcriptome Analysis (WTA) Pipeline to get a unique molecular identifier (UMI) matrix for each sample.
Bulk RNAseq FASTQ files were aligned on the hg38 genome reference using the STAR aligner (version 2.7.4a) with default parameters. Salmon (version 1.3.0) was used to quantitate gene expression by transcripts per kilobase million (TPM). The TPM matrix was transformed by log2(TPM+1).
Assembly: GRCh38
Supplementary files format and content: txt

source_name: non-small cell lung cancer (NSCLC)

growth_protocol: Samples from biopsy or surgery were isolated and transported rapidly to the research facility.

extract_protocol:
To capture single-cell transcriptomic information of lung cancer samples, we used the BD Rhapsody Single-Cell Analysis System (BD Biosciences) according to the manufacturer’s protocol. Single-cell capture was achieved by the random distribution of a single cell suspension across ~200,000 microwells. Beads with unique molecular identifiers (UMIs) and cell barcodes were loaded close to saturation, so that each cell was paired with a bead in a microwell. After exposure to cell lysis buffer, polyadenylated RNA molecules hybridized to the beads. Beads were retrieved into a single tube for reverse transcription.
On cDNA synthesis, each cDNA molecule was tagged on the 5’ end (that is, the 3’ end of a messenger RNA transcript) with UMI and cell label indicating its cell of origin. Whole transcriptome libraries were prepared using the BD Resolve single-cell whole transcriptome amplification workflow. Briefly, Rhapsody beads were then subject to second-strand cDNA synthesis, adaptor ligation, and universal amplification. Sequencing libraries were prepared using random priming PCR of the whole-transcriptome amplification products to enrich the 3’end of the transcripts linked with the cell label and UMI. Sequencing libraries were quantified using a High Sensitivity DNA Chip (Agilent) on a Bioanalyzer 2100 and the Qubit High Sensitivity DNA Assay (Thermo Fisher Scientific). The libraries were sequenced on NovaSeq6000 (Illumina) using 2x150 chemistry.

treatment_protocol: Patients received 2 cycles of PD-1 antibody + chemotherapy before surgery

tag: treatment group

value: NSCLC before anti-PD-1 + chemotherapy

value: non-small cell lung cancer (NSCLC)

tag: patient

value: Male

value: IIB

value: Pre-treatment biopsy

value: Squamous

value: NMPR


title: R21025078LR01

description: Bulk RNAseq

value: IB

value: Adeno

value: MPR (pCR)


title: R21017102LR01

description: Bulk RNAseq

value: IIIA


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.AU-15530.Donor3.Rep1

value: CD8 Positive T-cells

value: Primary T cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 3 treated with AU-15530 100 nM technical replicate 1


title: R21008707LR01

description: Bulk RNAseq

value: IIIB

value: MPR


title: R21008694LR01

description: Bulk RNAseq


title: R21008693LR01

description: Bulk RNAseq


title: R20073752LR01

description: Bulk RNAseq

value: NSCLC


title: R20073128LR02

description: Bulk RNAseq

value: NSCLC before anti-PD-1 + chemotherapy


title: ATACseq.human.CD8.Positive.Tcells.Day9.Treatment.AU-15530.Donor4.Rep2

value: CD8 Positive T-Cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 4 treated with AU-15530 100 nM technical replicate 2


title: R20073125LR01

description: Bulk RNAseq

value: non-small cell lung cancer (NSCLC)

value: Female


title: R20073124LR01

description: Bulk RNAseq

value: Male

value: IIB

value: Pre-treatment biopsy


title: R20059511LR01

description: Bulk RNAseq

value: Carcinosarcomatoid

value: NMPR


title: R20059506LR01

description: Bulk RNAseq

value: IIIA

value: Squamous


title: LP1_PANK1_sgrna2_rep2

first: Constantine

last: Mitsiades

state: MA

address: 450 Brookline Avenue Dept. of Medical Oncology

institute: Dana-Farber Cancer Institute, Harvard Medical School

data_processing:
RNA sequencing using Illumina NextSeq 500 Next Gen at the Molecular Biology Core Facility (Dana-Farber Cancer Institute)
Differential gene expression analysis for the RNA-seq data using the bioconductor edgeR package
Raw counts for all samples were generated using STAR (Dobin et al., 29, 1, 15-21, Bioinformatics 2012)
Assembly: gchr38.84
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Multiple Myeloma

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: LP1 cells were stably transduced with a construct for dCas9-Vp64 after lentiviral sgRNA transduction packaged with the pXPR-502 construct (RRID:Addgene_96923). LP1 cells transduced with POU2AF1 sgRNA for CRISPR-based activation of POU2AF1or control OR genes were pelleted down at 0.25MLN cells triplicate and immediately frozen (-80ºC). RNA was extracted by RNeasy plus mini kit (Qiagen 74134) according to instruction. In addition, ERCCRNA spike-in mix(Thermo Fisher 4456740) was added at very first step of extraction (RLT extraction).

value: Multiple Myeloma

value: PANK1 sgRNA 2 AGTTCTCTGGGCTTGCAGAG


title: LP1_PANK1_sgrna2_rep3

value: PANK1 sgRNA 2  AGTTCTCTGGGCTTGCAGAG


title: R20059499LR01

description: Bulk RNAseq


title: LP1_PANK1_sgrna2_rep1


title: R20041445LR01

description: Bulk RNAseq

value: MPR (pCR)


title: R20035974LR01

description: Bulk RNAseq


title: R20052336LR01

description: Bulk RNAseq

value: NSCLC

value: MPR


title: LP1_PANK1_sgrna1_rep2

value: PANK1 sgRNA 1 CACCGACGAGTTTCAACATG


title: LP1_PANK1_sgrna1_rep3

data_processing:
RNA sequencing using Illumina NextSeq 500 Next Gen at the Molecular Biology Core Facility (Dana-Farber Cancer Institute)
Differential gene expression analysis for the RNA-seq data using the bioconductor DEseq2 package
Raw counts for all samples were generated using STAR (Dobin et al., 29, 1, 15-21, Bioinformatics 2012)
Assembly: gchr38.84
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample


title: R20031593LR01

description: Bulk RNAseq

value: NSCLC before anti-PD-1 + chemotherapy


title: WT A549, rSeV-N5T, 10dpi

description: PolyA enriched and prepared using TruSeq Stranded mRNA library prep

value: lung carcinoma epithelial cells

value: WT

value: rSeV-N5T (MOI=5) --- 10dpi


title: R20030544LR01

description: Bulk RNAseq

value: non-small cell lung cancer (NSCLC)

value: Male


title: STAT1 KO A549, rSeV-N5T, 4dpi

value: STAT1 KO

value: rSeV-N5T (MOI=5) --- 4dpi


title: LP1_PANK1_sgrna1_rep1


title: R20073708LR01

description: Bulk RNAseq

value: IIIA

value: Pre-treatment biopsy

value: Adeno

value: NMPR


title: R20028573LR01

description: Bulk RNAseq

value: Squamous


title: WT A549, rSeV-N1T, 6dpi

value: rSeV-N1T (MOI=5) --- 6dpi


title: WT A549, rSeV-N5R, 4dpi

value: rSeV-N5R (MOI=5) --- 4dpi


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.FHT1015.Donor2

value: CD8 Positive T-cells

value: Primary T cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 2 treated with FHT1015 100 nM

value: Day 9


title: R20027161LR01

description: Bulk RNAseq

value: NSCLC before anti-PD-1 + chemotherapy

value: Female


title: R20052328LR01

description: Bulk RNAseq

value: non-small cell lung cancer (NSCLC)


title: R20073704LR03

description: Bulk RNAseq

value: Male

value: IIB


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.FHT1015.Donor1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 1 treated with FHT1015 100 nM


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.Compound14.Donor2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 2 treated with compound 14 100 nM

value: compound 14


title: BD_immune13

description: BD Rhapsody platform

library_source: transcriptomic single cell

value: NSCLC after anti-PD-1 + chemotherapy

value: IIIA

value: Post-treatment surgery


title: BD_immune14

description: BD Rhapsody platform

value: Squamous

value: MPR


title: RNAseq.human.CD8.Positive.Tcells.Day9.Treatment.Compound14.Donor1

value: CD8 Positive T-cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 1 treated with compound 14 100 nM


title: RNAseq.human.CD8.Positive.Tcells.Day9.Transient.Donor2

value: Primary T cells

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from human donor 2


title: R20059498LR01

description: Bulk RNAseq

value: NSCLC before anti-PD-1 + chemotherapy

value: Pre-treatment biopsy

value: NMPR


title: BD_immune12

description: BD Rhapsody platform

value: non-small cell lung cancer (NSCLC)

value: Male

value: Adeno


title: RNAseq.human.CD8.Positive.Tcells.Day9.Transient.Donor1

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from human donor 1

value: Day 9


title: BD_immune11

description: BD Rhapsody platform

value: NSCLC after anti-PD-1 + chemotherapy

value: Female


title: RNAseq.human.CD8.Positive.Tcells.Day6.Donor2

value: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 2

value: Day 6


title: RNAseq.human.CD8.Positive.Tcells.Day9.Chronic.Donor2

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 2


title: RNAseq.human.CD8.Positive.Tcells.Day9.Chronic.Donor1

value: CD8 Positive T-cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 1


title: BD_immune10

description: BD Rhapsody platform

value: IIIA

value: Post-treatment surgery

value: Squamous


title: BD_immune08

description: BD Rhapsody platform

value: NSCLC before anti-PD-1 + chemotherapy

value: Pre-treatment biopsy


title: BD_immune09

description: BD Rhapsody platform

value: non-small cell lung cancer (NSCLC)

value: NMPR


title: BD_immune05

description: BD Rhapsody platform

value: Adeno


title: BD_immune07

description: BD Rhapsody platform

value: Male


title: BD_immune04

description: BD Rhapsody platform


title: BD_immune06

description: BD Rhapsody platform

value: MPR (pCR)


title: BD_immune15

description: BD Rhapsody platform

value: NSCLC after anti-PD-1 + chemotherapy


title: RNAseq.human.CD8.Positive.Tcells.Day6.Donor1

value: Primary T cells

value: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 1


title: BD_immune03

description: BD Rhapsody platform

value: MPR


title: Healthy airway epithelium exposed to pseudomonas aeruginosa 1

first: Hongmei

last: Mou

address: 55 Fruit Street, Jackson 1402

department: The Mucosal Immunology & Biology Research Center

institute: Massachusetts General Hospital

data_processing:
add
Supplementary files format and content: Excel files include Mean and SD values for each Sample

source_name: Airway epithelial cells

growth_protocol: Human airway basal cells were propagated in Small Airway Epithelial Cell Medium (Promocell medium, C-21170) with 5-10 mM ROCKi (Tocris, 1254), 1 mM A-83-01 (Tocris, 2939) and 0.5 mM CHIR99021 (Tocris, 4423) on plates pre-coated with laminin-enriched 804G-conditioned medium. Human airway basal cells were trypsinized and seeded onto 0.4 um transwell membranes pre-coated with 804G-conditioned medium with a density of >6000 cells/mm2. The airway stem cells were 100% confluent after attachment at this density. Following cell attachment for >12 hours, excess cells were removed, and the medium was replaced with complete Pneumacult-ALI medium (StemCell Technology, Cat. 05001) filling both the upper and lower chambers. The next day, ALI medium was added only in the lower chamber to initiate airway-liquid interface. The ALI medium was changed every 2 days until differentiation was well established. We culture ALI for 14-21 days as a standard protocol.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen, 74104).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Human airway epithelial cells were infected with 200 ul pseudomonas aeruginosa (~6 × 107 CFU/ml) or mock-infected (HBSS) on the apical surface for 1 hour.

tag: disease

value: Primary cells from healthy donor

value: Airway epithelial cells

value: pseudomonas aeruginosa

value: 1 h


title: Healthy airway epithelium exposed to HBSS media 4

value: HBSS


title: Healthy airway epithelium exposed to pseudomonas aeruginosa 2


title: BD_immune02

description: BD Rhapsody platform

value: Female

value: IIIA

value: Post-treatment surgery


title: BD_immune01

description: BD Rhapsody platform

value: NSCLC before anti-PD-1 + chemotherapy

value: non-small cell lung cancer (NSCLC)

value: Pre-treatment biopsy

value: Squamous

value: Not available


title: RNAseq.human.CD8.Positive.Tcells.48HR.Donor1

value: CD8 Positive T-cells

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 1

value: 48 hour


title: RNAseq.human.CD8.Positive.Tcells.72HR.Donor1

value: Primary T cells

value: 72 hour CD3/CD28 activated CD8 Positive T cell from human donor 1

value: 72 hour


title: RNAseq.human.CD8.Positive.Tcells.48HR.Donor2

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: TSLP-elicited immature BMBA_01

city: Bunkyo-ku

first: Kensuke

last: Miyake

state: Tokyo

address: 1-5-45, Yushima

department: Institute of Integrated Research

country: Japan

institute: Institute of Science Tokyo

data_processing:
Sequencing data generated by Ion Proton (Thermo) was subjected to adaptor trimming by Cutadapt.
Trimmed reads were aligned against murine reference RNA sequences (GRCm39 RefSeq RNA) by utilizing bowtie2 .
Supplementary files format and content: mm10
Supplementary files format and content: Tab-separated values files

organism: Mus musculus

source_name: bone marrow

extract_protocol:
FcεRIαhiCD49blo immature and FcεRIαloCD49bhi mature basophils isolated from either IL-3- or TSLP-elicited BMBAs by FACS sorting. Total RNA was extracted from isolated cells by using Nucleospin RNA Plus XS Kit (Macherey-Nagel)
Library construction for bulk-RNA sequencing was conducted as described the previous study (Shichino et al. JCI Insight 2019). Sequencing was performed by using an Ion Hi-Q Chef kit, an Ion PI v3 Chip kit, and an Ion Proton Sequencer (Thermo Fisher Scientific) according to the manufacturer’s instructions.

treatment_protocol: Bone marrow cells were cultured in the presence of either 0.3 ng/mL IL-3 or 1 μg/mL TSLP for 7days to obetain bone marrow derived basophils.

value: bone marrow

value: basophil

value: C57BL/6J WT

value: cultured with 1 mg/mL TSLP for 7 days


title: TSLP-elicited immature BMBA_02


title: TSLP-elicited immature BMBA_03


title: Healthy airway epithelium exposed to HBSS media 2

value: Primary cells from healthy donor

value: Airway epithelial cells

value: HBSS

value: 1 h


title: RNAseq.human.CD8.Positive.Tcells.3HR.Donor2

value: 3 hour CD3/CD28 activated CD8 Positive T cell from human donor 2

value: 3 hour


title: Healthy airway epithelium exposed to HBSS media 3


title: TSLP-elicited mature BMBA_03


title: IL-3-elicited immature BMBA_02

value: cultured with 0.3 ng/mLIL-3 for 7 days


title: RNAseq.human.CD8.Positive.Tcells.24HR.Donor2

value: CD8 Positive T-cells

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 2

value: 24 hour


title: RNAseq.human.CD8.Positive.Tcells.3HR.Donor1

value: Primary T cells

value: 3 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: p.Sdel560 STAT3-epithelium (Job Syndrome patient) exposed to pseudomonas aeruginosa 2

value: Primary cells from Job Syndrome patient

value: pseudomonas aeruginosa


title: RNAseq.human.CD8.Positive.Tcells.72HR.Donor2

value: 72 hour CD3/CD28 activated CD8 Positive T cell from human donor 2

value: 72 hour


title: IL-3-elicited immature BMBA_03

value: bone marrow

value: basophil

value: C57BL/6J WT


title: TSLP-elicited mature BMBA_02

value: cultured with 1 mg/mL TSLP for 7 days


title: IL-3-elicited immature BMBA_01


title: RNAseq.human.CD8.Positive.Tcells.0HR.Donor2

value: Naïve CD8 Positive T cells from human donor 2

value: 0 hour


title: RNAseq.human.CD8.Positive.Tcells.24HR.Donor1

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: IL-3-elicited mature BMBA_03

value: cultured with 0.3 ng/mLIL-3 for 7 days


title: p.Sdel560 STAT3-epithelium (Job Syndrome patient) exposed to HBSS media 2

value: Airway epithelial cells

value: HBSS

value: 1 h


title: TSLP-elicited mature BMBA_01


title: p.Sdel560 STAT3-epithelium (Job Syndrome patient) exposed to pseudomonas aeruginosa 1


title: p.Sdel560 STAT3-epithelium (Job Syndrome patient) exposed to HBSS media 1


title: IL-3-elicited mature BMBA_02


title: WT A549, Amplicon Seq, rSeV-N5T, 8dpi

description: Amplicon Sequencing of PCR products

value: lung carcinoma epithelial cells

value: WT

value: rSeV-N5T (MOI=5) --- 8dpi


title: WT A549, Amplicon Seq, rSeV-N5T, 2dpi

description: Amplicon Sequencing of PCR products

value: rSeV-N5T (MOI=5) --- 2dpi


title: IL-3-elicited mature BMBA_01


title: Healthy airway epithelium exposed to HBSS media 1

value: Primary cells from healthy donor


title: AIS3

city: luoyang

first: liyan

last: chen

address: kaiyuan road 263

institute: Henan University of Science and Technology

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Subsequently, unique sequences with length in 18~26 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs.
Length variation at both 3’ and 5’ ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs.
The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3pderived miRNA candidates.
The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations. The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the specific genomes, and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi).
Genome_build: ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: xls include all Normalized data and p values for each Sample

source_name: serum samples

growth_protocol: This research collected serum samples from AIS patients and healthy volunteers and extracted exosome miRNA.

extract_protocol:
Genomic DNA contamination of RNA samples was removed using RNase-free DNase Kit (Promega, Madison, WI, USA). The quantity and purity of total RNA were analyzed by Bioanalyzer 2100 (Agilent, Palo Alto, CA, USA).
Approximately 1 µg total RNA without genomic DNA contamination was used for the sRNA library construction, according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). As a result, nine cucumber fruit sRNA libraries were constructed.

treatment_protocol: Total RNA from all samples was isolated separately using Trizol reagent (Invitrogen, Shanghai, China) following the manufacturer’s instructions.

tag: disease state

value: AIS patients

value: serum samples


title: AIS1


title: WT A549, Amplicon Seq, rSeV-N5T, 4dpi

description: Amplicon Sequencing of PCR products

value: rSeV-N5T (MOI=5) --- 4dpi


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.SS18.Donor1

data_processing:
Illumina NextSeq output data were demultiplexed and converted to FASTQ format using the bcl2fastq software tool.
For Cut and Tag libraries, the CutRunTools pipeline (Zhu et al. 2020) was leveraged to perform read trimming, quality filtering, alignment, peak calling, and track building using default parameters
Assembly: hg19, mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

growth_protocol: Human T cells were maintained in RPMI media supplemented with 10% FBS, 1% Pen/Strep, 1X GlutaMAX, 1X Non-essential Amino Acids, 1X Sodium Pyruvate and 10mM 2-Mercaptoethanol, and 30U/ml human IL2

extract_protocol:
Epicypher's CUT&Tag protocol was used for nuclear extraction and probing chromatin localization.
Epicypher's CUT&Tag protocol was used to ampllify tagmented DNA from isolated genomic DNA with 14 PCR cycles. DNA purification was completed  using AMPure beads (1.3X). Library size distribution was determined using TapeStation D1000.

treatment_protocol: Cells were activated with Human T-Activator CD3/CD28 Dynabeads (Thermo Fisher Scientific, Cat# 11132D) at 1:1 beads-to-cells ratio on Day 0, 3 and 6.

value: CD8 Positive T-cells

value: Primary T cells

tag: chip antibody

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from human donor 1


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.SS18.Donor2

tag: cell type

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from human donor 2


title: AIS2


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.SMARCA4.Donor2

value: SMARCA4 (CST, #49360S)


title: iPSC-derived AT2 cells; 30mg/mL aECM hydrogels; Day 4 34C

city: Burlington

first: Korin

last: Eckstrom

state: VT

address: 89 Beaumont Ave

institute: University of Vermont

data_processing:
Illumina bcl2fastq used for basecalling
Sequences were merged by sample when where sequenced acorss multiple lanes, then were trimmed of adaptor sequences, bases <Q25, and length >35bp using Trim Galore! (v.0.6.4)
Reads passing QC were mapped to the human genome using STAR (v 2.7.4a) and duplicates removed using MarkDuplicates from Picard
Mapped reads were counted using HTSeq using default settings
Differential expression was performed using DESeq2. Raw counts were imported, adjusted for library size, and normalized with default methods, and a base filtering of > 0.1 was performed to remove low level or rare gene counts. Differential expression was tested using the interaction of dosage group * treatment day using a Wald test and a significance threshold of <0.05 with Benjamini-Hochberg correction
Assembly: GRCh38, gencode v29 annotation
Supplementary files format and content: comma-separated file with the raw counts

source_name: iPSC-derived

growth_protocol: iAT2s were cultured in CK+DCI directed differentiation medium (3uM CHIR99021; 10ng/mL KGF; 50nM dexamethasone; 0.1mM cAMP; 0.1mM IBMX) in humidified incubator at 37C and 5% CO2

extract_protocol:
iAT2s were extracted from hydrogels using either Liberase DL (hydrogels) or Dispase (Matrigel) and RNA was harvested using Rneasy mini plus kit (Qiagen)
Takara SMARTer Stranded Total RNA-Seq Kit v2

treatment_protocol: iAT2s were 3D cultured in Matrigel, 8mg/mL aECM hydrogels, or 30mg/mL aECM hydrogels under the same conditions and RNA was collected at Day 4 and Day 8 for gene expression analysis

value: iPSC-derived

value: Alveolar type 2 epithelial cell

value: Alveolar type 2 directed differentiation


title: iPSC-derived AT2 cells; 30mg/mL aECM hydrogels; Day 8 38A


title: iPSC-derived AT2 cells; 30mg/mL aECM hydrogels; Day 8 38B


title: iPSC-derived AT2 cells; 30mg/mL aECM hydrogels; Day 8 38C


title: iPSC-derived AT2 cells; 30mg/mL aECM hydrogels; Day 4 34A


title: CON3

value: healthy volunteers


title: CON2


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.PBRM1.Donor2


title: iPSC-derived AT2 cells; 8mg/mL aECM hydrogels; Day 8 88C


title: CON1


title: iPSC-derived AT2 cells; 8mg/mL aECM hydrogels; Day 4 84C


title: iPSC-derived AT2 cells; 8mg/mL aECM hydrogels; Day 8 88A


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.SMARCA4.Donor1


title: iPSC-derived AT2 cells; 8mg/mL aECM hydrogels; Day 8 88B


title: RNAseq.human.CD8.Positive.Tcells.0HR.Donor1

value: Naïve CD8 Positive T cells from human donor 1

value: 0 hour


title: iPSC-derived AT2 cells; Matrigel; Day 8 M8C

value: WT


title: iPSC-derived AT2 cells; 8mg/mL aECM hydrogels; Day 4 84A


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.IgG.Donor2


title: iPSC-derived AT2 cells; Matrigel; Day 4 M4C


title: iPSC-derived AT2 cells; Matrigel; Day 8 M8B


title: Nodose ganglion, 12 week female, biol rep 2

city: Los Angeles

first: Anna

last: Kamitakahara

state: CA

address: 4661 Sunset Blvd, MS 135

institute: Children's Hospital Los Angeles

description:
AK31
week12_Female_Controlvsweek12_Male_Control_all_detectable_genes.csv

data_processing:
Samples were sequenced across four lanes.
Reads were mapped to the UCSC mm10 transcript set using Bowtie2 version 2.1.0.
Gene count was estimated using RSEM v1.2.15.
The trimmed mean of M values (TMM) method was used for gene count normalization to adjust for differences in sequencing depth and library size between samples and differentially expressed genes were identified using the edgeR R program.
Assembly: mm10
Supplementary files format and content: .csv files include TMM values

source_name: Nodose ganglion

extract_protocol:
RNA was isolated from each sample using the QIAGEN RNeasy micro kit. 50ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEB Next Ultra II Directional RNA Library Prep Kit with single indexing following manufacturer's protocols.

value: Nodose ganglion

tag: strain

tag: Sex

value: Female

value: 12 week old


title: Nodose ganglion, 12 week female, biol rep 1

description:
AK30
week12_Female_Controlvsweek12_Male_Control_all_detectable_genes.csv

tag: age


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.H3K27ac.Donor2


title: Nodose ganglion, 12 week female, biol rep 3

description:
AK32
week12_Female_Controlvsweek12_Male_Control_all_detectable_genes.csv


title: iPSC-derived AT2 cells; 30mg/mL aECM hydrogels; Day 4 34B


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.IgG.Donor1


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.H3K27ac.Donor1


title: iPSC-derived AT2 cells; Matrigel; Day 4 M4A


title: Nodose ganglion, 12 week male, biol rep 4

description:
AK25
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv
week12_Female_Controlvsweek12_Male_Control_all_detectable_genes.csv

value: Male


title: 35B-4

type: genomic

description: Stress session Time 4

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium MethylationEPIC Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting.

data_processing:
idat files were preprocessed and detection p-values were calculated using minfi (1.42.0). Beta values were obtained by generating a genomic set ratio object and normalization was performed using the minfi function preprocessNoob.
Noob Normalized Average Beta

label: Cy5 and Cy3

source_name: Participant 35, Stress session, Time 4

label_protocol: Standard Illumina protocol.

extract_protocol: Genomic DNA was extracted and purified from PBMC samples using QIAmp mini kit (Qiagen) according to standard instructions.

value: PBMC

tag: ela status

value: ELA

tag: session

value: Stress


title: iPSC-derived AT2 cells; Matrigel; Day 4 M4B

tag: cell line


title: iPSC-derived AT2 cells; 8mg/mL aECM hydrogels; Day 4 84B

tag: genotype


title: 34B-4

description: Stress session Time 4

source_name: Participant 34, Stress session, Time 4

value: Control

tag: time


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.BRD9.Donor1

value: CD8 Positive T-cells

value: Primary T cells

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from human donor 1


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.ARID1A.Donor2

value: 9 day transient CD3/CD28 activated CD8 Positive T cell from human donor 2


title: Nodose ganglion, 12 week male, biol rep 1

description:
AK22
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv
week12_Female_Controlvsweek12_Male_Control_all_detectable_genes.csv

tag: tissue


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.PBRM1.Donor1


title: 35B-3

description: Stress session Time 3

source_name: Participant 35, Stress session, Time 3


title: 34B-2

description: Stress session Time 2

source_name: Participant 34, Stress session, Time 2


title: Nodose ganglion, 12 week male, biol rep 3

description:
AK24
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv
week12_Female_Controlvsweek12_Male_Control_all_detectable_genes.csv


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.BRD9.Donor2


title: Nodose ganglion, 12 week male, biol rep 2

description:
AK23
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv
week12_Female_Controlvsweek12_Male_Control_all_detectable_genes.csv


title: Nodose ganglion, P9 male, biol rep 10

description:
AK10
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv

value: Postnatal day 9


title: 35B-2

description: Stress session Time 2

source_name: Participant 35, Stress session, Time 2


title: iPSC-derived AT2 cells; Matrigel; Day 8 M8A

value: iPSC-derived

value: Alveolar type 2 epithelial cell

tag: treatment

value: Alveolar type 2 directed differentiation


title: 33B-4

description: Stress session Time 4

source_name: Participant 33, Stress session, Time 4


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.SS18.Donor2

tag: sample type

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 2


title: 33B-1

description: Stress session Time 1

source_name: Participant 33, Stress session, Time 1


title: 32B-3

description: Stress session Time 3

source_name: Participant 32, Stress session, Time 3


title: Nodose ganglion, P9 male, biol rep 8

description:
AK8
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv

value: Nodose ganglion

value: WT


title: 35B-1

description: Stress session Time 1

source_name: Participant 35, Stress session, Time 1

value: Female


title: 33B-3

description: Stress session Time 3

source_name: Participant 33, Stress session, Time 3


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Transient.ARID1A.Donor1

source_name: CD8 Positive T-cells


title: 33B-2

description: Stress session Time 2

source_name: Participant 33, Stress session, Time 2


title: 34B-1

description: Stress session Time 1

source_name: Participant 34, Stress session, Time 1


title: Nodose ganglion, P9 male, biol rep 9

description:
AK9
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv

value: Male


title: 32B-4

description: Stress session Time 4

source_name: Participant 32, Stress session, Time 4

value: PBMC


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.SS18.Donor1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 1


title: Nodose ganglion, P9 male, biol rep 7

description:
AK7
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv


title: 32A-4

description: No-stress session Time 4

source_name: Participant 32, No-stress session, Time 4

value: No-stress


title: 34B-3

description: Stress session Time 3

source_name: Participant 34, Stress session, Time 3

value: Control

value: Stress


title: 32B-1

description: Stress session Time 1

source_name: Participant 32, Stress session, Time 1


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.SMARCA4.Donor2

value: CD8 Positive T-cells

value: Primary T cells

value: SMARCA4 (CST, #49360S)


title: Nodose ganglion, P9 male, biol rep 5

description:
AK5
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv

source_name: Nodose ganglion

value: Postnatal day 9


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.SMARCA4.Donor1


title: 32B-2

description: Stress session Time 2

source_name: Participant 32, Stress session, Time 2


title: 32A-2

description: No-stress session Time 2

source_name: Participant 32, No-stress session, Time 2


title: 32A-1

description: No-stress session Time 1

source_name: Participant 32, No-stress session, Time 1


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.PBRM1.Donor1


title: Nodose ganglion, P9 male, biol rep 3

description:
AK3
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv


title: Nodose ganglion, P9 male, biol rep 6

description:
AK6
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv


title: 31B-4

description: Stress session Time 4

source_name: Participant 31, Stress session, Time 4

value: ELA


title: 31B-3

description: Stress session Time 3

source_name: Participant 31, Stress session, Time 3


title: 31B-2

description: Stress session Time 2

source_name: Participant 31, Stress session, Time 2


title: 31B-1

description: Stress session Time 1

source_name: Participant 31, Stress session, Time 1


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.IgG.Donor1


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.H3K27ac.Donor2


title: Schwann cells_ctrl_Plp_3

city: Pittsburgh

first: Uma

last: Chandran

address: 5607 Baum Blvd.

department: Department of Biomedical Informatics

institute: University of Pittsburgh

data_processing:
Alignment using HISAT2 2.1.0 build of Ensembl GRCm38 of primary assembly with default paired-end unstranded parameters and converting to sorted bam files using Samtools version 1.10.
Counts were generated using HT-Seq 0.11.2 using Ensembl GRCm38 as GTF file and using position sorted order, reverse strandedness, gene_id GFF attribute, union mode, and exon feature type as parameters.
edgeR in Rstudio using R version 4.0 including CPM values for each sample.
Assembly: GRCm38
Supplementary files format and content: Bunimovich_Schwann_rawcounts.csv: Comma-separated text file includes raw counts.

source_name: Schwann cells (skin)

growth_protocol: Freshly isolated by FACS from skin digested to single-cell suspension with collagenase D (1 mg/ml) and DNase (1 mg/mL).

extract_protocol:
RNA from FACS-purified Schwann cells was isolated using RNeasy Micro Kit (Qiagen). RIN 4.0-6.8 were selected, and 20 ng RNA per sample was utilized for RNA-sequencing.
Libraries were constructed using Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus (#20040525) with a read length of 2x75bp.

treatment_protocol: After skin digestion, cell suspension was stained with anti-p75NTR antibodies (EP1039Y, 1:100) for 1 hour at 4C, washed and resuspended in FACS buffer (Miltenyi Biotec, 130-091-221). Cells were purified using 100 micrometer nozzle at 20 psi sheath pressure.

value: Tumor free

value: Dorsal skin

value: FACS-purified Schwann cells


title: 32A-3

description: No-stress session Time 3

source_name: Participant 32, No-stress session, Time 3


title: Nodose ganglion, P9 male, biol rep 1

description:
AK1
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv

value: Nodose ganglion


title: Schwann cells_ctrl_Plp_2


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.PBRM1.Donor2

source_name: CD8 Positive T-cells

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 2


title: 31A-2

description: No-stress session Time 2

source_name: Participant 31, No-stress session, Time 2

value: Female


title: 31A-4

description: No-stress session Time 4

source_name: Participant 31, No-stress session, Time 4


title: 30A-4

description: Stress session Time 4

source_name: Participant 30, Stress session, Time 4


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.H3K27ac.Donor1


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.BRD9.Donor2


title: Nodose ganglion, P9 male, biol rep 4

description:
AK4
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv

value: Male

value: WT


title: Schwann cells_ctrl_Plp_1


title: 30A-3

description: Stress session Time 3

source_name: Participant 30, Stress session, Time 3

value: PBMC


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.BRD9.Donor1

value: 9 day chronic CD3/CD28 activated CD8 Positive T cell from human donor 1


title: Schwann cells_PlpB16_3

value: Melanoma


title: Batch1_Soleus_resveratrol_200 mg/kg_mouse5

city: Daejeon

first: Musun

last: Park

address: 1672 Yuseong-daero, Yuseong-gu

country: South Korea

institute: Korean Institute of Oriental Medicine

description: sample S9-5

data_processing:
Quality of RNA-seq raw data was assessed using FastQC (v0.11.9), and the common regions of MGISEQ adapter sequences were removed using TrimGalore (v0.6.5). The trimmed reads were then aligned to the mouse reference genome GRCm38 (mm10) using the STAR (v2.7.3a) with default settings. Transcript abundance per gene including expected read counts and transcripts per million (TPM) were quantified using RSEM (v1.3.3) with gene annotation GRCm38.86.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include Expected counts for each Sample

source_name: Soleus

growth_protocol: Ten weeks-old male C57BL/6N (21 ~ 26g) were supplied by OrientBio (Seongnam, Republic of Korea) and maintained in a polycarbonate cage (~5 mice per cage) in a specific pathogen-free animal laboratory facility under a controlled environment (22 ± 2°C temperature, 45 ± 10% humidity, 12 hr-12 hr dark and light cycle). They had a free access to standard chow and water and were acclimated for at least 1 week before experiments.

extract_protocol:
Total RNA extraction using the TRIzolTM reagent (Thermo Fisher Scientific, #15596018) according to the manufacturer’s guide.
A total RNA (1 microgr) was processed to prepare a mRNA sequencing library using the MGIEasy RNA Directional Library Prep kit (#1000006386, MGI Tech Co., Ltd., China) according to the manufacturer’s instruction. The library was quantified using the QauntiFluor® ssDNA System (E3190, Promega Corporation, WI, USA). The prepared DNA nanoball was sequenced on the MGIseq system (MGI Tech Co., Ltd., China) with 100 bp paired-end reads.

treatment_protocol: The study protocol involving experimental animals was peer-reviewed by the Institutional Animal Care and Use Committee of Korea Institute of Oriental Medicine (Protocol No. 22-048) and all procedures of animal studies were conducted in accordance with the guidelines for the Care and Use of Laboratory Animals by the Ministry of Food and Drug Safety, Republic of Korea. After 1-week acclimation, the mice were randomly allocated to 5 groups (9-10 per group) and subject to behavior tests for baseline correction (D1). Then, mice received intraperitoneal (i.p.) injection of PBS (group 1, normal control) or 25 mg/kg dexamethasone (DEX, group 2 to 5) every day for 10 days. Thirty minutes after PBS or DEX injection, JGT at 100 (group 3) or 400 mg/kg (Group 4) were administered to mice by oral gavage. Group 1 and group 2 (vehicle control) received oral gavage of PBS. A positive control group received oral gavage of resveratrol (RsV, 200 mg/kg) instead of JGT. Water soluble DEX were dissolved in a sterile PBS, and JGT and RsV were resuspended in a sterile 0.5% CMC in PBS on the day of drug administration. One day after final behavioral assessments, mice were deeply anaesthetized by i.p. injection of 2% avertin in PBS (240 mg/kg). The whole bloods were collected from the heart in a 1.5 mL tube using a 23 gauged-1 mL syringe and kept for 1 h at room temperature. Skeletal muscle tissues like gastrocnemius (GA), soleus (SO), and tibialis anterior (TA) muscles were excised from the hindlimbs. The isolated muscle tissues were snap frozen on a dry-ice and stored at -80°C for RNA-seq analysis.

value: Soleus

value: DEX 25 mg/kg, resveratrol 200mg/kg (30min after)

value: 10 days


title: Batch1_Soleus_resveratrol_200 mg/kg_mouse4

description: sample S9-4


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.IgG.Donor2

value: CD8 Positive T-cells

value: Primary T cells


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.ARID1A.Donor2


title: 30A-2

description: Stress session Time 2

source_name: Participant 30, Stress session, Time 2

value: Control

value: Stress


title: Batch1_Soleus_resveratrol_200 mg/kg_mouse2

description: sample S9-2


title: 31A-3

description: No-stress session Time 3

source_name: Participant 31, No-stress session, Time 3

value: ELA

value: No-stress


title: Nodose ganglion, P9 male, biol rep 2

description:
AK2
week12_Male_ControlvsP7_Male_Control_all_detectable_genes.csv

source_name: Nodose ganglion

value: Nodose ganglion

value: Postnatal day 9


title: Schwann cells_PlpB16_2

value: Dorsal skin

value: FACS-purified Schwann cells


title: CutAndTag.human.CD8.Positive.Tcells.Day9.Chronic.ARID1A.Donor1


title: Schwann cells_PlpB16_1


title: 29B-3

description: Stress session Time 3

source_name: Participant 29, Stress session, Time 3

value: Female


title: 31A-1

description: No-stress session Time 1

source_name: Participant 31, No-stress session, Time 1

value: PBMC


title: CutAndTag.human.CD8.Positive.Tcells.Day6.SS18.Donor2

value: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 2


title: Batch1_Soleus_JGT04_400 mg/kg_mouse4

description: sample S8-4

value: DEX 25 mg/kg, JGT04 400mg/kg (30min after)


title: CutAndTag.human.CD8.Positive.Tcells.Day6.SMARCA4.Donor2

value: SMARCA4 (CST, #49360S)


title: 29B-4

description: Stress session Time 4

source_name: Participant 29, Stress session, Time 4


title: 29B-2

description: Stress session Time 2

source_name: Participant 29, Stress session, Time 2


title: CutAndTag.human.CD8.Positive.Tcells.Day6.SS18.Donor1

value: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 1


title: Batch1_Soleus_resveratrol_200 mg/kg_mouse1

description: sample S9-1

value: Soleus

value: DEX 25 mg/kg, resveratrol 200mg/kg (30min after)

value: 10 days


title: CutAndTag.human.CD8.Positive.Tcells.Day6.SMARCA4.Donor1

value: CD8 Positive T-cells

value: Primary T cells


title: Batch1_Soleus_resveratrol_200 mg/kg_mouse3

description: sample S9-3


title: 29B-1

description: Stress session Time 1

source_name: Participant 29, Stress session, Time 1

value: Control

value: Stress


title: Batch1_Soleus_JGT04_400 mg/kg_mouse2

description: sample S8-2


title: 29A-4

description: No-stress session Time 4

source_name: Participant 29, No-stress session, Time 4

value: No-stress


title: 30A-1

description: Stress session Time 1

source_name: Participant 30, Stress session, Time 1


title: Rat cortical tissue, Sham group [T09]

city: Shihezi City

first: Shan

last: Yuan

state: Xinjiang Uygur Autonomous Region

address: North Second Road, Hongshan Street

institute: Shihezi University

description:
Sample 9
total RNA (Remove rRNA)

data_processing:
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 Reverse Transcriptase. 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 insert fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP Beads (Beckman Coulter, Beverly, USA).
Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index(X) Primer.
At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 and qPCR.
The clustering of the index-coded samples was performed on acBot Cluster Generation System using TruSeq PE Cluster Kitv3-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and paired-end reads were generated.
Assembly: Rnor_5.0.Rattus_norvegicus.Rnor_5.0.genome.fa
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample.

organism: Rattus norvegicus

source_name: Brain (cerebral cortex tissue)

growth_protocol: Sprague-Dawley rats (8–9-week-old males weighing 240 ± 20 g).

extract_protocol:
Total RNA was extracted using a TRIzol reagent kit (Invitrogen, Carlsbad, CA, USA), and quality control was performed using an Agilent 2100 instrument. The Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA) were used to remove rRNA from high-quality total RNA.
A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA). Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Sprague-Dawley

value: Brain (cerebral cortex tissue)

value: Male

value: Sham group


title: Rat cortical tissue, Sham group [T07]

description:
Sample 7
total RNA (Remove rRNA)


title: Rat cortical tissue, Sham group [T08]

description:
Sample 8
total RNA (Remove rRNA)


title: Rat cortical tissue, Sham group [T10]

description:
Sample 10
total RNA (Remove rRNA)


title: Batch1_Soleus_JGT04_100 mg/kg_mouse5

description: sample S7-5

value: DEX 25 mg/kg, JGT04 100mg/kg (30min after)


title: Rat cortical tissue, Sham group [T06]

description:
Sample 6
total RNA (Remove rRNA)


title: CutAndTag.human.CD8.Positive.Tcells.Day6.PBRM1.Donor2

source_name: CD8 Positive T-cells

value: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 2


title: 29A-3

description: No-stress session Time 3

source_name: Participant 29, No-stress session, Time 3

value: PBMC

value: Female


title: CutAndTag.human.CD8.Positive.Tcells.Day6.PBRM1.Donor1

value: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 1


title: Rat cortical tissue, MCAO 2 h / R 24 h group [T05]

description:
Sample 5
total RNA (Remove rRNA)

value: MCAO 2 h / R 24 h

tag: condition

value: Cerebral ischemia and hypoxia injury


title: 29A-2

description: No-stress session Time 2

source_name: Participant 29, No-stress session, Time 2


title: Batch1_Soleus_JGT04_400 mg/kg_mouse3

description: sample S8-3

value: Soleus

value: DEX 25 mg/kg, JGT04 400mg/kg (30min after)

value: 10 days


title: Batch1_Soleus_JGT04_100 mg/kg_mouse4

description: sample S7-4


title: CutAndTag.human.CD8.Positive.Tcells.Day6.IgG.Donor2

value: CD8 Positive T-cells

value: Primary T cells


title: Batch1_Soleus_JGT04_100 mg/kg_mouse3

description: sample S7-3


title: 29A-1

description: No-stress session Time 1

source_name: Participant 29, No-stress session, Time 1

value: Control

value: No-stress


title: Rat cortical tissue, MCAO 2 h / R 24 h group [T04]

description:
Sample 4
total RNA (Remove rRNA)

value: Sprague-Dawley

value: Brain (cerebral cortex tissue)


title: Batch1_Soleus_JGT04_400 mg/kg_mouse1

description: sample S8-1


title: Rat cortical tissue, MCAO 2 h / R 24 h group [T03]

description:
Sample 3
total RNA (Remove rRNA)

value: Male


title: CutAndTag.human.CD8.Positive.Tcells.Day6.H3K27ac.Donor2


title: CutAndTag.human.CD8.Positive.Tcells.Day6.IgG.Donor1


title: Batch1_Soleus_JGT04_100 mg/kg_mouse2

description: sample S7-2

value: DEX 25 mg/kg, JGT04 100mg/kg (30min after)


title: Rat cortical tissue, MCAO 2 h / R 24 h group [T02]

description:
Sample 2
total RNA (Remove rRNA)


title: 28A-3

description: Stress session Time 3

source_name: Participant 28, Stress session, Time 3

value: ELA

value: Stress


title: 28A-4

description: Stress session Time 4

source_name: Participant 28, Stress session, Time 4

value: PBMC

value: Female


title: CutAndTag.human.CD8.Positive.Tcells.Day6.H3K27ac.Donor1

value: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 1


title: Rat cortical tissue, MCAO 2 h / R 24 h group [T01]

description:
Sample 1
total RNA (Remove rRNA)

value: MCAO 2 h / R 24 h

value: Cerebral ischemia and hypoxia injury


title: Batch1_Soleus_JGT04_100 mg/kg_mouse1

description: sample S7-1

source_name: Soleus

value: Soleus


title: Batch1_Soleus_JGT03_400 mg/kg_mouse5

description: sample S6-5

value: DEX 25 mg/kg, JGT03 400mg/kg (30min after)

value: 10 days


title: 28A-2

description: Stress session Time 2

source_name: Participant 28, Stress session, Time 2


title: CutAndTag.human.CD8.Positive.Tcells.Day6.BRD9.Donor2

value: CD8 Positive T-cells

value: Primary T cells

value: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 2


title: Batch1_Soleus_JGT03_400 mg/kg_mouse4

description: sample S6-4


title: 27B-4

description: No-stress session Time 4

source_name: Participant 27, No-stress session, Time 4

value: No-stress


title: 27B-3

description: No-stress session Time 3

source_name: Participant 27, No-stress session, Time 3


title: CutAndTag.human.CD8.Positive.Tcells.Day6.BRD9.Donor1


title: Batch1_Soleus_JGT03_400 mg/kg_mouse3

description: sample S6-3


title: Batch1_Soleus_JGT03_400 mg/kg_mouse2

description: sample S6-2


title: POA_P22_DES 6_5

city: Liège

first: Arnaud

last: Lavergne

state: Liège

address: Avenue de l'hôpital 11

department: GIGA

country: Belgium

institute: University of Liège

data_processing:
Basecalling performed using Illumina bcl2fastq v2.20
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Reads were processed for mapping and quantification using nf-core rnaseq pipeline v1.4.2 (https://nf-co.re/rnaseq/1.4.2/usage) and using Gene set from Ensembl.org release 102.
Assembly: Rnor_6.0
Supplementary files format and content: tab-delimited text file include raw counts for annotations for all Sample

source_name: pre-optic area

extract_protocol:
At PND22, PND42 and PND90,  the pre-optic area (POA) and the mediobasal hypothalamus (MBH) were dissected and frozen. Total RNA was extracted from the MBH and POA using Universal RNA mini kit (Qiagen,Venlo, Netherlands) following the manufacturer’s instructions.
Libraries were prepared using Truseq® stranded mRNA Sample Preparation Kits (Illumina, CA, USA) following manufacturer’s instructions. Libraries were validated using QIAxcel Advanced System and quantified by qPCR using the KAPA library quantification kit. Libraries were multiplexed and sequenced on an Illumina NovaSeq6000 sequencer to generate more than ~25,000,000 paired-end reads (2 × 150 bases) per library.

treatment_protocol: Dams were exposed by oral gavage with either chemical or vehicle (corn oil) once daily from GD 7 until birth and from the day after birth until postnatal (PND) 22. Doses for DES were 0; 3; 6; 12 µg/kg bw/day and doses for KTZ were 0; 3; 6; 12 mg/kg bw/day.

value: Sprague-Dawley

value: female

value: pre-optic area

value: DES 6 ug/kg bw/day


title: POA_P22_DES 6_4


title: 27B-2

description: No-stress session Time 2

source_name: Participant 27, No-stress session, Time 2

value: Male

value: ELA


title: POA_P22_DES 3_5

value: DES 3 ug/kg bw/day


title: CutAndTag.human.CD8.Positive.Tcells.Day6.ARID1A.Donor2


title: 27B-1

description: No-stress session Time 1

source_name: Participant 27, No-stress session, Time 1

value: PBMC


title: POA_P22_DES 3_4


title: CutAndTag.human.CD8.Positive.Tcells.Day6.ARID1A.Donor1

value: 6 day CD3/CD28 activated CD8 Positive T cell from human donor 1


title: Batch1_Soleus_JGT03_400 mg/kg_mouse1

description: sample S6-1


title: CutAndTag.human.CD8.Positive.Tcells.72HR.SS18.Donor2

value: 72 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: Batch1_Soleus_JGT03_100 mg/kg_mouse5

description: sample S5-5

value: Soleus

value: DEX 25 mg/kg, JGT03 100mg/kg (30min after)


title: POA_P22_control_5

value: vehicle


title: 27A-4

description: Stress session Time 4

source_name: Participant 27, Stress session, Time 4

value: Stress


title: 27A-3

description: Stress session Time 3

source_name: Participant 27, Stress session, Time 3


title: CutAndTag.human.CD8.Positive.Tcells.72HR.SS18.Donor1

value: CD8 Positive T-cells

value: Primary T cells

value: 72 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: POA_P22_control_4

value: Sprague-Dawley


title: Batch1_Soleus_JGT03_100 mg/kg_mouse3

description: sample S5-3

value: 10 days


title: CutAndTag.human.CD8.Positive.Tcells.72HR.SMARCA4.Donor1

value: SMARCA4 (CST, #49360S)


title: POA_P22_control_3

value: female

value: pre-optic area


title: CutAndTag.human.CD8.Positive.Tcells.72HR.SMARCA4.Donor2


title: 27A-2

description: Stress session Time 2

source_name: Participant 27, Stress session, Time 2

value: Male

value: ELA


title: 27A-1

description: Stress session Time 1

source_name: Participant 27, Stress session, Time 1

value: PBMC


title: Batch1_Soleus_JGT03_100 mg/kg_mouse2

description: sample S5-2


title: CutAndTag.human.CD8.Positive.Tcells.72HR.PBRM1.Donor2

source_name: CD8 Positive T-cells


title: POA_P22_KTZ 3_5

value: KTZ 3 mg/kg bw/day


title: 26B-4

description: Stress session Time 4

source_name: Participant 26, Stress session, Time 4

value: Female

value: Control


title: CutAndTag.human.CD8.Positive.Tcells.72HR.PBRM1.Donor1


title: POA_P22_KTZ 3_4


title: Batch1_Soleus_JGT02_400 mg/kg_mouse5

description: sample S4-5

value: Soleus

value: DEX 25 mg/kg, JGT02 400mg/kg (30min after)


title: 26B-3

description: Stress session Time 3

source_name: Participant 26, Stress session, Time 3

value: Stress


title: Batch1_Soleus_JGT02_400 mg/kg_mouse4

description: sample S4-4


title: CutAndTag.human.CD8.Positive.Tcells.72HR.IgG.Donor2

value: CD8 Positive T-cells

value: 72 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: 26B-2

description: Stress session Time 2

source_name: Participant 26, Stress session, Time 2


title: POA_P22_DES 12_5

value: DES 12 ug/kg bw/day


title: Batch1_Soleus_JGT02_400 mg/kg_mouse3

description: sample S4-3


title: POA_P22_DES 12_4

value: Sprague-Dawley


title: 26B-1

description: Stress session Time 1

source_name: Participant 26, Stress session, Time 1


title: CutAndTag.human.CD8.Positive.Tcells.72HR.IgG.Donor1

value: Primary T cells

value: 72 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: Batch1_Soleus_JGT03_100 mg/kg_mouse4

description: sample S5-4

value: DEX 25 mg/kg, JGT03 100mg/kg (30min after)

value: 10 days


title: CutAndTag.human.CD8.Positive.Tcells.72HR.H3K27ac.Donor2


title: 25B-4

description: Stress session Time 4

source_name: Participant 25, Stress session, Time 4


title: Batch1_Soleus_JGT02_400 mg/kg_mouse2

description: sample S4-2

source_name: Soleus


title: POA_P22_control_2

value: female

value: pre-optic area

value: vehicle


title: CutAndTag.human.CD8.Positive.Tcells.72HR.H3K27ac.Donor1


title: POA_P22_DES 3_3

value: DES 3 ug/kg bw/day


title: Batch1_Soleus_JGT02_400 mg/kg_mouse1

description: sample S4-1


title: Batch1_Soleus_JGT03_100 mg/kg_mouse1

description: sample S5-1


title: POA_P22_DES 6_3

value: DES 6 ug/kg bw/day


title: Batch1_Soleus_JGT02_100 mg/kg_mouse5

description: sample S3-5

value: DEX 25 mg/kg, JGT02 100mg/kg (30min after)


title: 25B-2

description: Stress session Time 2

source_name: Participant 25, Stress session, Time 2

value: PBMC

value: Female

value: ELA


title: CutAndTag.human.CD8.Positive.Tcells.72HR.BRD9.Donor1

value: CD8 Positive T-cells


title: CutAndTag.human.CD8.Positive.Tcells.72HR.BRD9.Donor2

value: 72 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: Batch1_Soleus_JGT02_100 mg/kg_mouse4

description: sample S3-4

value: Soleus


title: POA_P22_DES 3_2

value: Sprague-Dawley


title: Batch1_Soleus_JGT02_100 mg/kg_mouse3

description: sample S3-3


title: POA_P22_DES 3_1


title: 24B-4

description: Stress session Time 4

source_name: Participant 24, Stress session, Time 4

value: Control

value: Stress


title: CutAndTag.human.CD8.Positive.Tcells.72HR.ARID1A.Donor2

value: Primary T cells


title: 24B-3

description: Stress session Time 3

source_name: Participant 24, Stress session, Time 3


title: Batch1_Soleus_JGT02_100 mg/kg_mouse2

description: sample S3-2

value: 10 days


title: POA_P22_KTZ 12_5

source_name: pre-optic area

value: female

value: KTZ 12 mg/kg bw/day


title: CutAndTag.human.CD8.Positive.Tcells.48HR.SS18.Donor2

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: Batch1_Soleus_JGT02_100 mg/kg_mouse1

description: sample S3-1


title: CutAndTag.human.CD8.Positive.Tcells.72HR.ARID1A.Donor1

value: 72 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: POA_P22_control_1

value: pre-optic area

value: vehicle


title: Batch1_Soleus_vehicle(DEX)_mouse4

description: sample S2-4

value: DEX 25 mg/kg


title: 24B-1

description: Stress session Time 1

source_name: Participant 24, Stress session, Time 1

value: PBMC

value: Female


title: POA_P22_DES 12_3

value: DES 12 ug/kg bw/day


title: POA_P22_DES 6_2

value: DES 6 ug/kg bw/day


title: 25B-3

description: Stress session Time 3

source_name: Participant 25, Stress session, Time 3

value: ELA


title: 24A-3

description: No-stress session Time 3

source_name: Participant 24, No-stress session, Time 3

value: No-stress


title: CutAndTag.human.CD8.Positive.Tcells.48HR.SMARCA4.Donor2

value: CD8 Positive T-cells

value: SMARCA4 (CST, #49360S)


title: POA_P90_DES 12_5

value: Sprague-Dawley


title: Batch1_Soleus_vehicle(DEX)_mouse3

description: sample S2-3

value: Soleus

value: 10 days


title: CutAndTag.human.CD8.Positive.Tcells.48HR.SMARCA4.Donor1

value: Primary T cells

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: POA_P90_DES 3_5

value: female

value: DES 3 ug/kg bw/day


title: 25B-1

description: Stress session Time 1

source_name: Participant 25, Stress session, Time 1

value: Stress


title: 24A-2

description: No-stress session Time 2

source_name: Participant 24, No-stress session, Time 2

value: Control


title: Batch1_Soleus_vehicle(DEX)_mouse2

description: sample S2-2

value: DEX 25 mg/kg


title: Batch1_Soleus_vehicle(DEX)_mouse1

description: sample S2-1


title: POA_P90_control_5

value: pre-optic area

value: vehicle


title: 24A-4

description: No-stress session Time 4

source_name: Participant 24, No-stress session, Time 4

value: PBMC

value: Female


title: POA_P42_control_5


title: CutAndTag.human.CD8.Positive.Tcells.48HR.PBRM1.Donor1

source_name: CD8 Positive T-cells


title: POA_P42_control_4


title: CutAndTag.human.CD8.Positive.Tcells.48HR.SS18.Donor1


title: CutAndTag.human.CD8.Positive.Tcells.48HR.IgG.Donor2

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: 24A-1

description: No-stress session Time 1

source_name: Participant 24, No-stress session, Time 1

value: No-stress


title: Batch1_Soleus_non-treat_mouse4

description: sample S1-4

value: non-treat


title: Batch1_Soleus_non-treat_mouse5

description: sample S1-5


title: 23A-2

description: Stress session Time 2

source_name: Participant 23, Stress session, Time 2


title: Batch1_Soleus_non-treat_mouse3

description: sample S1-3


title: 23A-1

description: Stress session Time 1

source_name: Participant 23, Stress session, Time 1


title: CutAndTag.human.CD8.Positive.Tcells.48HR.IgG.Donor1

value: CD8 Positive T-cells


title: Batch1_Soleus_non-treat_mouse2

description: sample S1-2

value: Soleus


title: 22B-4

description: Stress session Time 4

source_name: Participant 22, Stress session, Time 4

value: ELA


title: CutAndTag.human.CD8.Positive.Tcells.48HR.PBRM1.Donor2

value: Primary T cells


title: CutAndTag.human.CD8.Positive.Tcells.48HR.H3K27ac.Donor2


title: Batch1_Soleus_non-treat_mouse1

description: sample S1-1

value: 10 days


title: POA_P42_KTZ 6_4

value: Sprague-Dawley

value: female

value: KTZ 6 mg/kg bw/day


title: POA_P42_DES 12_5

value: DES 12 ug/kg bw/day


title: 22B-3

description: Stress session Time 3

source_name: Participant 22, Stress session, Time 3

value: Stress


title: POA_P42_DES 3_5

value: pre-optic area

value: DES 3 ug/kg bw/day


title: CutAndTag.human.CD8.Positive.Tcells.48HR.H3K27ac.Donor1

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: Batch1_Gastrocnemius_resveratrol_200 mg/kg_mouse5

description: sample G9-5

source_name: Gastrocnemius

value: Gastrocnemius

value: DEX 25 mg/kg, resveratrol 200mg/kg (30min after)


title: Batch1_Gastrocnemius_resveratrol_200 mg/kg_mouse4

description: sample G9-4


title: POA_P42_control_3

value: vehicle


title: 22B-2

description: Stress session Time 2

source_name: Participant 22, Stress session, Time 2

value: PBMC

value: Female


title: 23A-4

description: Stress session Time 4

source_name: Participant 23, Stress session, Time 4

value: Control


title: 22B-1

description: Stress session Time 1

source_name: Participant 22, Stress session, Time 1

value: ELA


title: CutAndTag.human.CD8.Positive.Tcells.48HR.ARID1A.Donor2

value: CD8 Positive T-cells

value: Primary T cells

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: POA_P42_KTZ 12_5

source_name: pre-optic area

value: Sprague-Dawley

value: female

value: KTZ 12 mg/kg bw/day


title: Batch1_Gastrocnemius_resveratrol_200 mg/kg_mouse3

description: sample G9-3

value: 10 days


title: 21A-4

description: Stress session Time 4

source_name: Participant 21, Stress session, Time 4

value: Stress


title: 21A-3

description: Stress session Time 3

source_name: Participant 21, Stress session, Time 3


title: Batch1_Gastrocnemius_resveratrol_200 mg/kg_mouse2

description: sample G9-2


title: CutAndTag.human.CD8.Positive.Tcells.48HR.ARID1A.Donor1


title: POA_P42_KTZ 6_5

value: pre-optic area

value: KTZ 6 mg/kg bw/day


title: CutAndTag.human.CD8.Positive.Tcells.3HR.SS18.Donor2

value: 3 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: POA_P42_KTZ 3_5

value: KTZ 3 mg/kg bw/day


title: Batch1_Gastrocnemius_resveratrol_200 mg/kg_mouse1

description: sample G9-1

value: Gastrocnemius

value: DEX 25 mg/kg, resveratrol 200mg/kg (30min after)


title: 21A-1

description: Stress session Time 1

source_name: Participant 21, Stress session, Time 1

value: PBMC

value: Female


title: POA_P42_DES 12_4

value: DES 12 ug/kg bw/day


title: Batch1_Gastrocnemius_JGT04_400 mg/kg_mouse4

description: sample G8-4

value: DEX 25 mg/kg, JGT04 400mg/kg (30min after)


title: CutAndTag.human.CD8.Positive.Tcells.3HR.SS18.Donor1

value: CD8 Positive T-cells

value: Primary T cells

value: 3 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: POA_P42_DES 6_5

value: Sprague-Dawley

value: female

value: DES 6 ug/kg bw/day


title: Batch1_Gastrocnemius_JGT04_400 mg/kg_mouse3

description: sample G8-3

value: 10 days


title: CutAndTag.human.CD8.Positive.Tcells.3HR.SMARCA4.Donor2

value: SMARCA4 (CST, #49360S)


title: CutAndTag.human.CD8.Positive.Tcells.48HR.BRD9.Donor2

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: Batch1_Gastrocnemius_JGT04_400 mg/kg_mouse2

description: sample G8-2


title: POA_P22_KTZ 12_4

value: pre-optic area

value: KTZ 12 mg/kg bw/day


title: 21A-2

description: Stress session Time 2

source_name: Participant 21, Stress session, Time 2

value: Control

value: Stress


title: CutAndTag.human.CD8.Positive.Tcells.48HR.BRD9.Donor1

value: 48 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: POA_P42_KTZ 3_4

value: KTZ 3 mg/kg bw/day


title: 20B-2

description: No-stress session Time 2

source_name: Participant 20, No-stress session, Time 2

value: PBMC

value: Female

value: ELA

value: No-stress


title: 20B-3

description: No-stress session Time 3

source_name: Participant 20, No-stress session, Time 3


title: CutAndTag.human.CD8.Positive.Tcells.3HR.PBRM1.Donor2

source_name: CD8 Positive T-cells

value: CD8 Positive T-cells

value: Primary T cells

value: 3 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: Batch1_Gastrocnemius_JGT04_400 mg/kg_mouse1

description: sample G8-1

value: Gastrocnemius

value: DEX 25 mg/kg, JGT04 400mg/kg (30min after)


title: POA_P42_DES 6_4

value: Sprague-Dawley

value: female

value: DES 6 ug/kg bw/day


title: 20B-1

description: No-stress session Time 1

source_name: Participant 20, No-stress session, Time 1


title: Batch1_Gastrocnemius_JGT04_100 mg/kg_mouse5

description: sample G7-5

value: DEX 25 mg/kg, JGT04 100mg/kg (30min after)

value: 10 days


title: CutAndTag.human.CD8.Positive.Tcells.3HR.PBRM1.Donor1

value: 3 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: POA_P22_KTZ 12_3

value: pre-optic area

value: KTZ 12 mg/kg bw/day


title: Batch1_Gastrocnemius_JGT04_100 mg/kg_mouse4

description: sample G7-4


title: POA_P42_KTZ 12_4


title: CutAndTag.human.CD8.Positive.Tcells.3HR.IgG.Donor2


title: 20A-3

description: Stress session Time 3

source_name: Participant 20, Stress session, Time 3

value: PBMC

value: Stress


title: 20A-2

description: Stress session Time 2

source_name: Participant 20, Stress session, Time 2

value: Female

value: ELA


title: CutAndTag.human.CD8.Positive.Tcells.3HR.IgG.Donor1

value: CD8 Positive T-cells


title: Batch1_Gastrocnemius_JGT04_100 mg/kg_mouse3

description: sample G7-3


title: POA_P42_DES 3_4

value: DES 3 ug/kg bw/day


title: CutAndTag.human.CD8.Positive.Tcells.3HR.H3K27ac.Donor2

value: Primary T cells

value: 3 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: 20A-1

description: Stress session Time 1

source_name: Participant 20, Stress session, Time 1


title: 19B-4

description: Stress session Time 4

source_name: Participant 19, Stress session, Time 4

value: Control


title: Batch1_Gastrocnemius_JGT04_100 mg/kg_mouse2

description: sample G7-2

source_name: Gastrocnemius

value: Gastrocnemius


title: CutAndTag.human.CD8.Positive.Tcells.3HR.SMARCA4.Donor1

value: SMARCA4 (CST, #49360S)


title: CutAndTag.human.CD8.Positive.Tcells.3HR.H3K27ac.Donor1


title: Batch1_Gastrocnemius_JGT04_100 mg/kg_mouse1

description: sample G7-1


title: 19B-2

description: Stress session Time 2

source_name: Participant 19, Stress session, Time 2


title: 19B-3

description: Stress session Time 3

source_name: Participant 19, Stress session, Time 3


title: CutAndTag.human.CD8.Positive.Tcells.3HR.BRD9.Donor2


title: Batch1_Gastrocnemius_JGT03_400 mg/kg_mouse4

description: sample G6-4

value: DEX 25 mg/kg, JGT03 400mg/kg (30min after)


title: POA_P22_KTZ 12_2

value: Sprague-Dawley

value: female


title: POA_P42_KTZ 6_3

value: KTZ 6 mg/kg bw/day


title: Batch1_Gastrocnemius_JGT03_400 mg/kg_mouse5

description: sample G6-5

value: 10 days


title: CutAndTag.human.CD8.Positive.Tcells.3HR.BRD9.Donor1

value: 3 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: 19B-1

description: Stress session Time 1

source_name: Participant 19, Stress session, Time 1

value: PBMC


title: CutAndTag.human.CD8.Positive.Tcells.3HR.ARID1A.Donor2


title: Batch1_Gastrocnemius_JGT03_400 mg/kg_mouse3

description: sample G6-3


title: POA_P42_KTZ 6_2

source_name: pre-optic area

value: pre-optic area


title: 19A-4

description: No-stress session Time 4

source_name: Participant 19, No-stress session, Time 4

value: Female

value: No-stress


title: POA_P42_DES 6_3

value: DES 6 ug/kg bw/day


title: Batch1_Gastrocnemius_JGT03_400 mg/kg_mouse2

description: sample G6-2


title: POA_P42_DES 6_2


title: CutAndTag.human.CD8.Positive.Tcells.24HR.SS18.Donor2

value: CD8 Positive T-cells

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: POA_P42_DES 3_3

value: DES 3 ug/kg bw/day


title: Batch1_Gastrocnemius_JGT03_400 mg/kg_mouse1

description: sample G6-1


title: POA_P42_KTZ 12_3

value: KTZ 12 mg/kg bw/day


title: 19A-3

description: No-stress session Time 3

source_name: Participant 19, No-stress session, Time 3

value: Control


title: CutAndTag.human.CD8.Positive.Tcells.24HR.SS18.Donor1

value: Primary T cells

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: 19A-1

description: No-stress session Time 1

source_name: Participant 19, No-stress session, Time 1


title: POA_P22_KTZ 6_5

value: Sprague-Dawley


title: POA_P42_KTZ 12_2

value: female


title: Batch1_Gastrocnemius_JGT03_100 mg/kg_mouse4

description: sample G5-4

value: Gastrocnemius

value: DEX 25 mg/kg, JGT03 100mg/kg (30min after)


title: 18A-4

description: Stress session Time 4

source_name: Participant 18, Stress session, Time 4

value: ELA

value: Stress


title: Batch1_Gastrocnemius_JGT03_100 mg/kg_mouse3

description: sample G5-3

value: 10 days


title: CutAndTag.human.CD8.Positive.Tcells.24HR.SMARCA4.Donor1

value: SMARCA4 (CST, #49360S)


title: POA_P42_KTZ 12_1

value: pre-optic area


title: Batch1_Gastrocnemius_JGT03_100 mg/kg_mouse2

description: sample G5-2


title: POA_P42_KTZ 6_1

value: KTZ 6 mg/kg bw/day


title: CutAndTag.human.CD8.Positive.Tcells.24HR.SMARCA4.Donor2

value: CD8 Positive T-cells


title: 18A-2

description: Stress session Time 2

source_name: Participant 18, Stress session, Time 2

value: PBMC

value: Female


title: CutAndTag.human.CD8.Positive.Tcells.24HR.PBRM1.Donor1


title: CutAndTag.human.CD8.Positive.Tcells.3HR.ARID1A.Donor1

value: 3 hour CD3/CD28 activated CD8 Positive T cell from human donor 1


title: 18A-1

description: Stress session Time 1

source_name: Participant 18, Stress session, Time 1


title: CutAndTag.human.CD8.Positive.Tcells.24HR.IgG.Donor2

source_name: CD8 Positive T-cells

value: 24 hour CD3/CD28 activated CD8 Positive T cell from human donor 2


title: Batch1_Gastrocnemius_JGT02_400 mg/kg_mouse5

description: sample G4-5

value: DEX 25 mg/kg, JGT02 400mg/kg (30min after)


title: CutAndTag.human.CD8.Positive.Tcells.24HR.PBRM1.Donor2

value: Primary T cells


title: 17B-4

description: Stress session Time 4

source_name: Participant 17, Stress session, Time 4

value: Male

value: Control