title: hippocampus_day_0_replicate_8

description: brain_clean_VST_counts.csv column 118


title: Fibroblasts, EtOH 025%, 12h, K7

status: Public on Aug 01 2023

type: SRA

city: Kraków

first: Artur

last: Gurgul

address: Rędzina 1C

department: Center for Experimental and Innovative Medicine

country: Poland

institute: University of Agriculture in Krakow

library_source: transcriptomic

data_processing:
Quality control, FastQC, v0.11.9
Filtering, Flexbar, 3.5.0
Alignment, STAR, 2.7.5c
Reads counting, Htseq-count, 1.99.2
Reads normalization, DESeq2 3.16
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data files include raw read counts for all samples in tabular format, text files (.txt)

molecule: polyA RNA

organism: Homo sapiens

source_name: skin

extract_protocol:
Standard procedure of TRIzol Reagent
Standard protocol of QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (Lexogen)

tag: tissue

value: skin

tag: cell line

value: fibroblasts

tag: treatment


title: LY1_NAC3

city: Huddinge

first: Martin

last: Bergo

address: MBE Group, Neo bldn. SE-141 83 Huddinge Sweden

department: BioNut

country: Sweden

institute: Karolinska Institutet

data_processing:
Preprocessed reads were aligned to the GRCh38 transcriptome using the STAR Aligner, and genes were quantified with the featureCounts tool. Tests for differential expression of genes identified in RNA-seq analyses were done with DESeq2. Differentially expressed genes with a false-discovery rate < 0.01 were considered statistically significant.
Assembly: GRCh38

molecule: total RNA

growth_protocol: LY1, and Ramos  were cultured in RPMI1640 medium (61870044, ThermoFisher) supplemented with 10% fetal bovine serum (FBS, 26140079, ThermoFisher) and 1% penicillin/streptomycin (15070063, ThermoFisher).

extract_protocol:
Total RNAs were extracted with the RNeasy Plus Mini kit (74136, QIAGEN).
RNA-seq libraries were prepared and sequenced on the Illumina HiSeq 2000 platform at Bioinformatics and Expression Analysis core facility (BEA, Karolinska Institutet, Sweden).

treatment_protocol: Reagents used were N-acetylcysteine (NAC, A7250), and vitamin C (VitC, A5960). Ramos and LY1 were treated with or without NAC, VitC for 24h.

tag: disease state

value: Diffuse large B-cell lymphoma

value: Treatment with N-acetylcysteine (NAC)

tag: genotype

value: High CMYC expression


title: Fibroblasts, EtOH 075%, 12h, K12


title: hippocampus_day_0_replicate_7

city: Gainesville

first: Jake

last: Boles

state: FL

address: LG-152, 1149 Newell Dr

department: Neuroscience

country: USA

institute: University of Florida

description: brain_clean_VST_counts.csv column 117

data_processing:
Reads were filtered to remove adapters, reads with polyA or polyG, reads with more than 5% unknown nucleotides, and reads with more than 20% low-quality bases (Q-value < 20) with Cutadapt.
Reads were mapped to the GRCmm39 genome assembly using STAR (v. 2.7.9)
Reads were counted with Subread (v. 2.0.3) in paired-end mode
Quality control and normalization was performed in R with the WGCNA, DESeq2, and edgeR packages.
Assembly: GRCmm39
Supplementary files format and content: comma-separated file gives raw read counts for each sample
Supplementary files format and content: comma-separated file gives variance-stabilized counts of only high-quality genes and samples

organism: Mus musculus

source_name: hippocampus

extract_protocol:
RNA was extracted using the TRIzol-chloroform based method. Tissue was lysed in TRIzol (ThermoFisher 15596018), and lysate was mixed with phenol:choloroform:isoamyl alcohol (ThermoFisher 15593049) in a 5:1 ratio. Protein and nucleic acids were separated into phases via centrifugation. The top aqueous layer containing the RNA was passed through a QIAshredder column (Qiagen 79656). Eluent was mixed 1:1 with 70% ethanol and applied to an RNease Mini column (Qiagen 74104). After a brief centrifugation, columns were washed once with RW1 buffer and twice with RPE buffer, as per manufacturer's recommendations. RNA was eluted in nuclease-free water. 1µg of total RNA in a concentration of 20ng/µL was shipped to LC Sciences (Houston, TX) for library preparation and RNA sequencing.
Total RNA was enriched for mRNA, fragmented, and reverse transcribed into complementary DNA (cDNA). Second-stranded DNA was synthesized, A-bases were added to the blunt ends of either strand, and DNA was ligated to dual-index adapters. Size selection was performed and DNA was treated with a heat-labile UDG enzyme. Ligated products were amplified with PCR before sequencing.

treatment_protocol: Mice received 2.5% DSS in their drinking water for 7d followed by a recovery period of 14d, and tissue was harvested at the following time points: day 0, 5, 7, 9, 12, 14, 21. Mice were euthanized via rapid decapitation and tissues were flash-frozen in liquid nitrogen immediately upon removal.

value: hippocampus

tag: day

tag: Sex

value: F

tag: strain


title: Fibroblasts, CBD 3uM, 12h, K6


title: MIG1_DMSO_C_S3_RNA-seq

city: SEATTLE

first: Lakshmi

last: Mahendrawada

state: WA

address: 1100 FAIRVIEW AVE N

department: Basic Sciences Division

institute: Fred Hutchinson Cancer Center

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
HTSeq output files are used as input files for differential analysis using DESeq2 (using defaults settings)
Assembly: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Raw output files obtained from DESeq2 analysis

organism: Saccharomyces cerevisiae

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MIG1-3xV5 IAA7::URA3

growth_protocol: 30 degrees in a synthetic complete (SC) medium to mid-log phase.

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

treatment_protocol: After reaching appropriate OD samples were treated with either DMSO or or 3-indolacetic acid (IAA), which was used to induce degradation of TFs. Newly synthesized RNA molecules were labeled for 5 minute with 4TU.For experiments conductions under specific stress conditions,  selected samples were treated with either DMSO or SM, Raffinose or Galactose, no heat shock (30°C) or heat shock (37°C)

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MIG1-3xV5 IAA7::URA3


title: MIG1_DMSO_B_S2_RNA-seq


title: Ramos_VitC3

source_name: Ramos

value: Ramos

value: Burkitt's lymphoma

value: Treatment with Vitamin C (VitC)


title: hippocampus_day_0_replicate_6

description: brain_clean_VST_counts.csv column 116


title: MIG1_DMSO_A_S1_RNA-seq


title: midbrain_day_0_replicate_5

description: brain_clean_VST_counts.csv column 115

source_name: midbrain

value: midbrain


title: Ramos_VitC2


title: Fibroblasts, CBD 3uM, 12h, K4


title: MIG1_3IAA_C_S6_RNA-seq


title: Ramos_VitC1


title: midbrain_day_0_replicate_4

description: brain_clean_VST_counts.csv column 114


title: Fibroblasts, CBD 075uM, 12h, K3


title: MIG1_3IAA_B_S5_RNA-seq


title: Ramos_NAC3


title: midbrain_day_0_replicate_3

description: brain_clean_VST_counts.csv column 113


title: midbrain_day_0_replicate_2

description: brain_clean_VST_counts.csv column 112


title: MGA1_DMSO_C_S33_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MGA1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MGA1-3xV5 IAA7::URA3


title: Fibroblasts, CBD 075uM, 12h, K2


title: MIG1_3IAA_A_S4_RNA-seq


title: Ramos_NAC1


title: Ramos_NAC2


title: Fibroblasts, CBD 075uM, 12h, K1


title: LY1_Ctrl1

value: Control


title: Fibroblasts, control, 12h, K43


title: MGA1_DMSO_B_S32_RNA-seq


title: midbrain_day_21_replicate_3

description: brain_clean_VST_counts.csv column 109


title: MGA1_DMSO_A_S31_RNA-seq


title: Fibroblasts, control, 12h, K33


title: midbrain_day_21_replicate_1

description: brain_clean_VST_counts.csv column 107


title: Ramos_ctrl3


title: Ramos_ctrl2


title: midbrain_day_21_replicate_2

description: brain_clean_VST_counts.csv column 108


title: Fibroblasts, CBD 3uM, 12h, K5


title: Fibroblasts, control, 12h, K32


title: midbrain_day_21_replicate_7

description: brain_clean_VST_counts.csv column 106

value: M


title: MGA1_3IAA_C_S36_RNA-seq


title: Ramos_ctrl1


title: Fibroblasts, EtOH 075%, 6h, K23


title: MGA1_3IAA_B_S35_RNA-seq


title: midbrain_day_21_replicate_6

description: brain_clean_VST_counts.csv column 105


title: Fibroblasts, EtOH 075%, 6h, K22


title: MGA1_3IAA_A_S34_RNA-seq


title: MET32_DMSO_C_S9_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MET32-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MET32-3xV5 IAA7::URA3


title: midbrain_day_21_replicate_5

description: brain_clean_VST_counts.csv column 104


title: Fibroblasts, EtOH 025%, 6h, K21


title: midbrain_day_5_replicate_10

description: brain_clean_VST_counts.csv column 103


title: Fibroblasts, EtOH 025%, 6h, K20


title: MET32_DMSO_B_S8_RNA-seq


title: midbrain_day_5_replicate_9

description: brain_clean_VST_counts.csv column 102


title: Fibroblasts, CBD 3uM, 6h, K16


title: midbrain_day_5_replicate_4

description: brain_clean_VST_counts.csv column 100


title: Fibroblasts, CBD 3uM, 6h, K17


title: midbrain_day_7_replicate_4

description: brain_clean_VST_counts.csv column 101


title: MET32_3IAA_C_S12_RNA-seq


title: Granulosa cells treated with PD98059 rep2

type: RNA

city: Dummerstorf

first: Vijay simha

last: Baddela

address: Wilhelm-Stahl-Allee 2

department: Reproductive biology

country: Germany

institute: Leibniz institute for farm animal biology

hyb_protocol: The RNA was hybridized overnight (45°C) in the GeneChipR Hybridization Oven (Affymetrix) to the Affymetrix Bovine Gene 1.0 ST arrays. Washing and staining were performed according to the Affymetrix standard protocol.

scan_protocol: The scanning of the microarray was done with the GeneChip Scanner 3000 HR (Affymetrix) and image processing was done with the software AGCC (Affymetrix).

data_processing: Data analysis was performed with the TAC 4.0 software (Affymetrix) and RMA method was used for normalization.

label: Biotin

organism: Bos taurus

source_name: Granulosa cells treated with PD98059

label_protocol: Biotinylated RNA were prepared according to the standard Affymetrix protocol (GeneChip® Expression 3’Amplification One-Cycle Target Labeling and Control Reagents).

growth_protocol: Bovine granulosa cells were cultured serum-free in alpha-MEM supplemented with FSH, IGF-1 and androstenedione for 4 days.

extract_protocol: Total RNA was prepared using RNeasy mini kit (Qiagen, Hilden, Germany).

treatment_protocol: Granulosa cells were subjected to different treatments on day 2 of the culture for 2 hrs follwed by 70% media replacement.

tag: cell type

value: Primary granulosa cells


title: Fibroblasts, CBD 075uM, 6h, K14

value: skin


title: Granulosa cells treated with PD98059 rep3


title: midbrain_day_14_replicate_8

description: brain_clean_VST_counts.csv column 99


title: MET32_3IAA_B_S11_RNA-seq


title: MET32_3IAA_A_S10_RNA-seq


title: midbrain_day_14_replicate_7

description: brain_clean_VST_counts.csv column 98


title: Fibroblasts, CBD 075uM, 6h, K13

value: fibroblasts


title: midbrain_day_12_replicate_8

description: brain_clean_VST_counts.csv column 97


title: Granulosa cells treated with PD98059 rep1


title: Granulosa cells treated with DMSO rep3

source_name: Granulosa cells treated with DMSO

value: DMSO


title: Granulosa cells treated with DMSO rep1


title: Fibroblasts, control, 6h, K35


title: MET31_DMSO_C_S3_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MET31-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MET31-3xV5 IAA7::URA3


title: midbrain_day_7_replicate_3

description: brain_clean_VST_counts.csv column 96


title: MET32_DMSO_A_S7_RNA-seq


title: Fibroblasts, control, 6h, K34


title: MET31_DMSO_A_S1_RNA-seq


title: MET31_DMSO_B_S2_RNA-seq


title: midbrain_day_5_replicate_3

description: brain_clean_VST_counts.csv column 95


title: Human whole cells, CSF, control and MS patients

city: Planegg

first: Anneli

last: Peters

address: Großhaderner Str. 9

institute: Institute for Clinical Neuroimmunology, Biomedical Center, University Hospital of the Ludwig-Maximilians University Munich

library_source: transcriptomic single cell

data_processing:
Sequencing results were demultiplexed and aligned to the human GRCh38 reference genome using Cell ranger (10X Genomics, v.6.1). Gene barcodes with unique molecular identifier (UMI) counts that reached the threshold for cell detection were included in subsequent data analysis, using the R package Seurat (version 4.1.0).
In a first step, data from the different compartments were analysed separately. Data from cells with between 200 and 5000 genes per cell and a percentage of mitochondrial genes below 10 % were included in further analyses. Genes expressed in fewer than three cells were excluded. Data were log-normalized and a batch effect was found in both the CSF and blood compartments. Therefore, established integration methods implemented within the Seurat package (CCA and rPCA) were applied, using the vst algorithm for detection of variable features. Data were then scaled and principal components computed for dimensional reduction. Applying k nearest neighbours, the neighbourhood overlap between cells was computed, followed by clustering the cells with a shared nearest-neighbour-based clustering algorithm. Uniform manifold approximation and projection (UMAP) was applied to visualize data in a two-dimensional space. The information from T cell receptor (TCR) enrichment library sequencing (10x Genomics, v.6.1) was added for each cell, followed by subsetting for cells where a TCR clonotype and only one beta chain had been detected. Small cell clusters with low quality and doublets, as well as a cluster expressing NKT cell signatures, were removed.
For each individual MS or control sample, the amino acid sequence information from the TCR enrichment sequencing was used to match cells with identical TCR expression present in both the blood and CSF compartment of the same patient. If the expression of a TCR was found across compartments, cells were considered as overlapping. For TCRs found more or equal three times in total, cells were labelled as expanded across tissues.
Both data sets were merged, log-normalised, integrated with rPCA, and scaled, before undergoing principal component analysis, neighbourhood computation, clustering and dimensionality reduction using UMAP. The remaining twelve clusters were assigned a number, based on their expression level of CCR7 from high to low. Each of the clusters expressed specific features, making them distinct on a transcriptomic level
GRCh38
Seurat object
meta data from blood csv

source_name: Lymphocytes

extract_protocol:
Human CSF samples (3-6 ml) were processed within 1 h of lumbar puncture. After centrifugation at 300 g for 10 min, the cell pellet was incubated in a 2 ml tube with TotalSeq-C Antibodies: anti-human CD4, CD8A and mouse IgG1 isotype control (Biolegend, 0.5 µg of each) Therefore, we followed the Cell Surface Labelling Protocol from 10x Genomics, but with all centrifugations done at 300 g for 10 min. All cells were loaded on the 10x Chip, with a maximum target cell number of 10,000
Further processing followed the manufacturer's protocol using the Chromium Next GEM Single Cell VDJ v1.1. For CSF samples, the Feature Barcoding technology for Cell Surface Protein steps were also performed. Libraries were sequenced on an Illumina NovaSeq6000 S4 using read lengths of 150 bp read 1, 8 bp i7 index, 150 bp read 3

value: Lymphocytes


title: MET31_3IAA_C_S6_RNA-seq


title: Human CD4+ T cells, blood, control and MS patients

source_name: CD4+ T cells

extract_protocol:
After collection of blood into tubes containing EDTA, samples were diluted 1:1 with PBS and added to a SepMate tube containing human Pancoll. During centrifugation (1200 g for 10 min at 4°C) PBMCs were isolated by density gradient. The isolated cells in plasma were transferred to a tube and centrifuged again at 300g 10 min at 4°C. The isolated PBMCs were either used freshly or cryopreserved in liquid nitrogen, using serum-free cryopreservation medium (CTL-Cryo ABC Media Kit, Immunospot). For analysis, samples were thawed quickly, washed twice with 1% BSA/PBS (300g for 10min at 4°C) and labelled using the following procedure: 10min at 4°C with Fc-block (Miltenyi) at 1/50 dilution in FACS buffer (PBS + 2% FBS), followed by the surface antibody mix. The mix comprised: ThermoFisher anti-human CD45RO-FITC (1:40), CCR7-APC (1:40), CD3-AF700 (1:50), Fixable Viability Dye eFluor™ 780 at 1:1000, CD4-Pacific Blue (1:25) and BioLegend: CD8-PerCP (1:25), in a total volume of 100µl FACS buffer and incubated for 30 min at 4°C. Antigen-experienced CD4+ T cells consisting of CD3+CD4+CD8- effector memory (CD45RO+CCR7-), effector (CD45RO-CCR7-) and central memory (CD45RO+CCR7+) cells were collected using a FACS Aria Fusion flow cytometer (BD Biosciences). After, cells were washed in 0.04% BSA/PBS and approximately 16,500 cells per sample were loaded onto the 10x Chip.
Further processing followed the manufacturer's protocol using the Chromium Next GEM Single Cell VDJ v1.1. For CSF samples, the Feature Barcoding technology for Cell Surface Protein steps were also performed. Libraries were sequenced on an Illumina NovaSeq6000 S4 using read lengths of 150 bp read 1, 8 bp i7 index, 150 bp read 2

value: CD4+ T cells


title: midbrain_day_12_replicate_3

description: brain_clean_VST_counts.csv column 94

value: F


title: Crebrf replicate 1

city: San Francisco

first: Phillip

middle: Anthony

last: Dumesic

state: CA

address: 513 Parnassus Ave, HSW1119

department: Diabetes Center

institute: University of California, San Francisco

data_processing:
fastq.bz2C was used for sequencing data quality control and MultiQC was used to aggregate the results.
fastp was used to trim reads
Sequenced reads were aligned to the mm10 reference genome assembly and gene counts were quantified using STAR
Differential gene expression testing was performed by DESeq2
Assembly: mm10
Supplementary files format and content: deseq-normalized-counts

source_name: C2C12 myotube

growth_protocol: C2C12 myoblasts were grown to confluence in 10% FBS in DMEM and then differentiated in 2% HS in DMEM.  Medium was changed every 2 days during differentiation.

extract_protocol:
RNA was harvested at day 7 of differentiation using Trizol reagent and Zymo miniprep spin columns. RNA was treated with Dnase Turbo from Ambion Illumina TruSeq RNA Sample Prep Kit was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Myotubes were transduced at day 4 of differentiation with 250 MOI adenovirus in the presence of 5ug/ml polybrene for 3 hours

tag: agent

value: Treated with adenovirus encoding Crebrf

value: C2C12 myotube


title: Crebrf replicate 2


title: DOHH2.Control.24h.r4

city: Münster

first: Michael

last: Grau

state: Nordrhein-Westfalen

address: Albert-Schweitzer-Campus 1

department: Faculty of Medicine

institute: University of Münster

description: Sequencing performed by Novogene Co., Ltd.

data_processing:
Sequenced reads of mRNA were aligned against the human transcriptome using HISAT2 [D. Kim, B. Langmead and S.L. Salzberg, HISAT: a fast spliced aligner with low memory requirements, Nat. Methods, vol. 12, no. 4, pp. 357–360, 2015.]
Gene and transcript annotations were used from RefSeq (GCF_000001405.38_GRCh38.p12_genomic.fna from ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/reference)
Aligned sequence counts were then aggregated for genes using RSEM [B. Li and C.N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome, BMC Bioinformatics, vol. 12, p. 323, Aug. 2011.]
Assembly: GRCh38.p12
Supplementary files format and content: RSEM aggregation results on gene level are provided as text files with 7 columns: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, and FPKM.

source_name: diffuse large B-cell lymphoma

growth_protocol: RPMI-1640, 10% FCS, Pen/Strep

extract_protocol:
RNeasy Mini (Qiagen)
RNA library was prepared for sequencing on the Illumina platform according to the manufacturers’ protocol

treatment_protocol: DMSO; 0.250 µM JQ-1

value: diffuse large B-cell lymphoma

value: germinal center B-cell-like

value: Solvent

tag: time [hours]

tag: replicate


title: midbrain_day_14_replicate_3

description: brain_clean_VST_counts.csv column 93

value: midbrain


title: Fibroblasts, control, 6h, K36


title: Crebrf replicate 3


title: MET31_3IAA_A_S4_RNA-seq


title: midbrain_day_12_replicate_2

description: brain_clean_VST_counts.csv column 92


title: DOHH2.Control.24h.r3


title: GFP replicate 3

value: Treated with adenovirus encoding Gfp


title: GFP replicate 2


title: midbrain_day_7_replicate_9

description: brain_clean_VST_counts.csv column 90

value: M


title: MET4_DMSO_C_S57_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MET4-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MET4-3xV5 IAA7::URA3


title: DOHH2.Control.24h.r2


title: GFP replicate 1


title: MET4_DMSO_B_S56_RNA-seq


title: midbrain_day_7_replicate_8

description: brain_clean_VST_counts.csv column 89


title: DOHH2.JQ1at250nM.24h.r4

value: JQ1 at 0,25µM


title: VmSC5.OSM#3

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Additional quality control after normalization included removal of biological replicates with a poor Pearson’s correlation (<0.9) and/or poor congregation by principal component analysis of the top 1000 variable genes. Genes with fewer than 15 reads across samples or a high coefficient of variation (>0.30) were removed in Multiplot Studio (GenePattern; Broad Institute).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: VAT

extract_protocol: For freshly-isolated samples, 1000 cells were double-sorted into 5ul TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich). For cultured cells in 96-well plate, 20ul TCL buffer containing 1% 2-mercaptoethanol was used to lyse cells and 5ul of that was submitted to RNA-seq. Floating adipocytes were lysed in QIAzol followed by RNA isolation according to the manufacturer's protocol and 2 ng RNA were resuspended in 5 microliters of TCL buffer containing 1% 2-mercaptoethanol. Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf).

value: VAT

value: Stromal Cell

value: Pparg-Tdt

value: adipogenic differentiation


title: MET4_DMSO_A_S55_RNA-seq


title: MET31_3IAA_B_S5_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MET31-3xV5 IAA7::URA3


title: midbrain_day_7_replicate_7

description: brain_clean_VST_counts.csv column 88


title: MET4_3IAA_C_S60_RNA-seq


title: DOHH2.JQ1at250nM.24h.r3


title: MET4_3IAA_B_S59_RNA-seq


title: VmSC5.OSM#2


title: VmSC5.OSM#1


title: VmSC5.PBS#3


title: midbrain_day_14_replicate_6

description: brain_clean_VST_counts.csv column 87


title: midbrain_day_9_replicate_7

description: brain_clean_VST_counts.csv column 86


title: DOHH2.JQ1at250nM.24h.r2


title: MCM1_DMSO_C_S15_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-MCM1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-MCM1


title: midbrain_day_9_replicate_8

description: brain_clean_VST_counts.csv column 91


title: MET4_3IAA_A_S58_RNA-seq


title: DOHH2.JQ1at250nM.24h.r1


title: VmSC5.PBS#2


title: midbrain_day_5_replicate_8

description: brain_clean_VST_counts.csv column 85


title: DOHH2.Control.24h.r1


title: VmSC5.PBS#1


title: MCM1_DMSO_B_S14_RNA-seq


title: HEK293, DMSO, replicate 2

city: MEMPHIS

first: Andrew

middle: Jackson

last: Murphy

state: TN

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

department: Surgery

institute: St. Jude Children's Research Hospital

data_processing:
Raw RNA-seq FastQ files were input into the Workflow for the Analysis of RNA-seq Differential Expression (WARDEN) program using the St. Jude Cloud-based analysis tool (McLeod C, et. al.  Cancer Discov. 2021;11(5):1082-99). Using WARDEN, log2 counts per million (log2CPM) values were used to quantify gene expression according to mapped RNA-seq reads. WARDEN was used to generate input files for gene set enrichment analysis
Assembly: GRCh37
Supplementary files format and content: Raw count files *.txt

source_name: Embryonic kidney

growth_protocol: The anaplastic WiT49 cell line (RRID: CVCL_0583) was obtained from Dr. Herman Yeger and cultured in DMEM (Corning, 10-017-CV) with 15% fetal bovine serum (FBS). The human embryonic kidney cell line, HEK293 (RRID: CVCL_0045), was obtained from American Type Culture Collection (ATCC, CRL-1573) and cultured in MEM (Corning, 10-010-CV) with 10% FBS.

extract_protocol: Total RNA was isolated using Rneasy Plus Mini kit (Qiagen, 74134)

treatment_protocol: WiT49 and HEK293 cells were treated with 25 nM QC6352 for 72 hours and compared to DMSO vehicle control

value: Embryonic kidney

value: Wild type (unaltered)

value: DMSO vehicle for 72 hrs


title: HEK293, DMSO, replicate 3


title: midbrain_day_14_replicate_4

description: brain_clean_VST_counts.csv column 83


title: VmSC5.with.Treg#3


title: MCM1_DMSO_A_S13_RNA-seq


title: HEK293, DMSO, replicate 1


title: midbrain_day_12_replicate_7

description: brain_clean_VST_counts.csv column 82


title: MCM1_3IAA_C_S18_RNA-seq


title: VmSC5.with.Treg#2


title: HEK293, QC6352, replicate 3

value: 25 nM QC6352 for 72 hrs


title: midbrain_day_9_replicate_4

description: brain_clean_VST_counts.csv column 81

value: F


title: HEK293, QC6352, replicate 2


title: MCM1_3IAA_B_S17_RNA-seq


title: midbrain_day_14_replicate_2

description: brain_clean_VST_counts.csv column 80


title: VmSC5.without.Treg#3


title: MBP1_DMSO_C_S27_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MBP1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MBP1-3xV5 IAA7::URA3


title: VmSC5.without.Treg#2


title: midbrain_day_14_replicate_5

description: brain_clean_VST_counts.csv column 84

value: midbrain


title: midbrain_day_7_replicate_1

description: brain_clean_VST_counts.csv column 78


title: HEK293, QC6352, replicate 1


title: WiT49, DMSO, replicate 3

source_name: Wilms tumor

value: Wilms tumor


title: midbrain_day_12_replicate_6

description: brain_clean_VST_counts.csv column 77

value: M


title: VmSC5.without.Treg#1


title: MBP1_DMSO_B_S26_RNA-seq


title: WiT49, DMSO, replicate 2


title: MCM1_3IAA_A_S16_RNA-seq


title: DTR.adipocyte#3

value: Adipocyte

value: Diphtheria toxin


title: WiT49, DMSO, replicate 1


title: midbrain_day_12_replicate_5

description: brain_clean_VST_counts.csv column 76


title: DTR.adipocyte#2

value: VAT


title: MBP1_DMSO_A_S25_RNA-seq


title: midbrain_day_9_replicate_2

description: brain_clean_VST_counts.csv column 75


title: VmSC5.with.Treg#1

value: Stromal Cell


title: WiT49, QC6352, replicate 3


title: midbrain_day_9_replicate_6

description: brain_clean_VST_counts.csv column 74


title: MBP1_3IAA_B_S29_RNA-seq


title: WiT49, QC6352, replicate 2


title: MBP1_3IAA_A_S28_RNA-seq


title: WiT49, QC6352, replicate 1


title: MAL13_DMSO_C_S3_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MAL13-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MAL13-3xV5 IAA7::URA3


title: midbrain_day_7_replicate_6

description: brain_clean_VST_counts.csv column 73

source_name: midbrain


title: midbrain_day_7_replicate_5

description: brain_clean_VST_counts.csv column 72


title: Transferred.VmSC5-5#2

value: Pparg-Tdt

value: adoptive transfer


title: WT.adipocyte#2


title: midbrain_day_0_replicate_13

description: discarded during WGCNA network construction


title: KYSE450DDP-DTP-6

city: Beijing

first: Yabing Nan

last: Yabing Nan

address: 17 Panjiayuan Nanli, Chaoyang Diistrict

country: China

institute: Cancer Hospital Chinese Academy of Medical Sciences

data_processing:
The paired-end libraries were prepared using a NEBNext UltraTM RNA Library Prep Kit for Illumina
Sequencing was performed using the Illumina NovaSeq 6000 platform.
A fold change of   >2 and P value of <0.05 were set as the criteria for identifying significantly differentially expressed genes
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: Text file for FPKM values of each gene

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

treatment_protocol: No treatment

value: ESCC cell

value: WT

tag: phenotype

value: chemoresistant-DTP


title: MAL13_DMSO_B_S2_RNA-seq


title: midbrain_day_0_replicate_10

description: brain_clean_VST_counts.csv column 71


title: Transferred.VmSC5-5#1


title: Transferred.VmSC4-5#3


title: MAL13_DMSO_A_S1_RNA-seq


title: MBP1_3IAA_C_S30_RNA-seq


title: midbrain_day_0_replicate_9

description: brain_clean_VST_counts.csv column 70


title: Transferred.VmSC4-5#2


title: MAL13_3IAA_C_S6_RNA-seq


title: KYSE450DDP-DTP-3


title: midbrain_day_12_replicate_4


title: MAL13_3IAA_B_S5_RNA-seq


title: Transferred.VmSC4-5#1


title: KYSE450DDP-DTP-2


title: WT.adipocyte#3


title: MAL13_3IAA_A_S4_RNA-seq


title: Transferred.VmSC4-4#2


title: MAC1_DMSO_C_S52_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 MAC1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 MAC1-3xV5 IAA7::URA3


title: KYSE450-DTP-6

value: parental-DTP


title: MAC1_DMSO_B_S51_RNA-seq


title: KYSE450DDP-DTP-4


title: KYSE450DDP-DTP-1


title: KYSE450-DTP-5


title: MAC1_DMSO_A_S50_RNA-seq


title: Transferred.VmSC4-4#1


title: midbrain_day_9_replicate_1

description: brain_clean_VST_counts.csv column 66

value: F


title: VmSC5.8d.ADM#3

value: adipogenic differentiation


title: MAC1_3IAA_C_S55_RNA-seq


title: Transferred.VmSC4-4#3


title: KYSE450DDP-DTP-5


title: VmSC5.8d.ADM#2


title: MAC1_3IAA_B_S54_RNA-seq


title: KYSE450-DTP-2


title: midbrain_day_9_replicate_5

description: brain_clean_VST_counts.csv column 69

value: midbrain


title: VmSC5.8d.ADM#1


title: KYSE450-DTP-3


title: midbrain_day_5_replicate_1

description: brain_clean_VST_counts.csv column 64


title: VmSC4.8d.ADM#3


title: MAC1_3IAA_A_S53_RNA-seq


title: midbrain_day_5_replicate_7

description: brain_clean_VST_counts.csv column 63


title: midbrain_day_14_replicate_1

description: brain_clean_VST_counts.csv column 68


title: midbrain_day_12_replicate_1

description: brain_clean_VST_counts.csv column 67


title: KYSE450-DTP-1


title: LYS14_DMSO_C_S33_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 LYS14-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 LYS14-3xV5 IAA7::URA3


title: KYSE450-DTP-4


title: VmSC4.8d.ADM#2


title: midbrain_day_5_replicate_6

description: brain_clean_VST_counts.csv column 62

value: M


title: midbrain_day_5_replicate_2

description: brain_clean_VST_counts.csv column 65


title: VmSC4.8d.ADM#1


title: KYSE450DDP-6

value: chemoresistant


title: LYS14_DMSO_B_S32_RNA-seq


title: KYSE450DDP-5


title: LYS14_DMSO_A_S31_RNA-seq


title: Granulosa cells treated with DMSO rep2

value: Primary granulosa cells

value: DMSO


title: VmSC5#3

value: VAT

value: Stromal Cell


title: midbrain_day_0_replicate_16

description: brain_clean_VST_counts.csv column 60


title: midbrain_day_0_replicate_15

description: brain_clean_VST_counts.csv column 59


title: VmSC5#2

value: Pparg-Tdt


title: KYSE450DDP-4


title: LYS14_3IAA_C_S36_RNA-seq


title: midbrain_day_0_replicate_14


title: KYSE450DDP-3


title: KYSE450DDP-2


title: midbrain_day_0_replicate_11

description: brain_clean_VST_counts.csv column 58


title: LYS14_3IAA_A_S34_RNA-seq


title: LYS14_3IAA_B_S35_RNA-seq


title: VmSC4#3


title: KYSE450DDP-1


title: midbrain_day_5_replicate_5

description: brain_clean_VST_counts.csv column 61


title: KYSE450-6

value: parental


title: VmSC4#2


title: LEU3_DMSO_C_S39_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 LEU3-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 LEU3-3xV5 IAA7::URA3


title: LEU3_DMSO_B_S38_RNA-seq


title: VmSC4#1


title: midbrain_day_0_replicate_7

description: brain_clean_VST_counts.csv column 56


title: LEU3_DMSO_A_S37_RNA-seq


title: midbrain_day_0_replicate_8

description: brain_clean_VST_counts.csv column 57


title: KYSE450-5

value: ESCC cell

value: WT


title: scRNAseq

city: Augusta

first: Yaoliang

last: Tang

state: GA

address: 1460 Laney Walker Blvd.

department: Medicine

institute: Augusta University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: hearts

extract_protocol:
Cardiac Lin- CDCs were isolated from the hearts of 2- to 3-month-old male C57BL/6 mice. Briefly, in step 1, mouse hearts were perfused with an enzyme solution using the Langendorf Perfusion Isolation System for Adult Mouse Cardiomyocyte Isolation Kit according to the manufacturer's protocol. In step 2, digested cells are filtered through a 40 μM cell strainer to remove the majority of cardiomyocytes and then sorted by magnetically activated cell sorting (MACS) using the Mouse Lineage Cell Depletion Kit. Selected Lin- CDCs were sent to Genome Core for scRNA-seq library preparation.
Library was performed according to the manufacter’s instructions (10x Genomics). Briefly, CDCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: cardiac derived cells

value: hearts

tag: age

value: 6-8 weeks old


title: VmSC5#1


title: midbrain_day_0_replicate_6

description: brain_clean_VST_counts.csv column 55

value: F


title: LEU3_3IAA_C_S42_RNA-seq


title: cortex_day_0_replicate_5

description: brain_clean_VST_counts.csv column 54

source_name: cortex

value: cortex


title: SED_Aged_aIFNg#3

source_name: Muscle

extract_protocol: Muscles were dissected and immediately frozen in liquid nitrogen until all samples were collected. Fresh-frozen muscles were homogenized in TRIzol followed by RNA isolation according to the manufacturer's protocol. 2 ng RNA were resuspended in 5 microliters of TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich). Library construction and sequencing and data processing were performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf).

value: Muscle

value: anti-IFN-gamma


title: cortex_day_0_replicate_4

description: brain_clean_VST_counts.csv column 53


title: LEU3_3IAA_A_S40_RNA-seq


title: cortex_day_0_replicate_3


title: SED_Aged_aIgG#3

value: IgG


title: KYSE450-2


title: LEU3_3IAA_B_S41_RNA-seq


title: SED_Aged_aIFNg#1


title: KYSE450-1


title: KAR4_DMSO_C_S40_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 KAR4-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 KAR4-3xV5 IAA7::URA3


title: cortex_day_0_replicate_2

description: brain_clean_VST_counts.csv column 52


title: SED_Aged_aIgG#1


title: HUWE1-CS, shWRNIP1, DSBseq

city: Tübingen

first: Elias

last: Einig

address: Otfried-Müller Straße 14

department: Medical Oncology and Pulmonology

institute: University Hospital Tübingen

library_source: genomic

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 instrument (1 x 100 bp)
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2).
Reads were aligned to human genome (hg19) with STAR (2.5.4) and tag directories were generated using Homer (version 4.10.3)
Bedgraph files were generated using Homer makeUCSCfile script
Sequencing tag coverage was calculated using Homer annotatePeaks script
Assembly: hg19
Supplementary files format and content: Bedgraph
Library strategy: DSB capture and sequencing

molecule: genomic DNA

source_name: colon

growth_protocol: HCT116 cells were cultured in Dulbecco’s Modified Eagle’s Medium with high glucose (DMEM; Gibco) supplemented with 10% (v/v) fetal bovine serum (FBS; PAN-Biotech), 1% (v/v) penicillin-streptomycin, 1% (v/v) non-essential amino acids and 50 µM 2-mercaptoethanol. Cells were maintained in a humidified atmosphere at 37°C in 7.5% CO2.

extract_protocol:
Double strand break sequencing was performed based on the DSBCapture protocol (Lensing et al., 2016). In brief, 5 million cells were fixed with 90% methanol. Cells were permeabilized in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.1% Triton-X100) for 10 min on ice and bound to Con-A Sepharose (Sigma) in binding buffer (20 mM HEPES, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). DNA ends were repaired using Klenow fragment (NEB) in NEB buffer 2 for 30 min at 25°C followed by A-tailing in dA-tailing buffer (NEB) with Klenow (3'→5' exo-) for 30 min at 37°C. Biotinylated NEB adaptors were ligated to A-tailed DSBs with T4 DNA ligase (NEB) in the corresponding buffer overnight at 16°C. Cells were lysed in 10 mM Tris, pH 8.5, 5 mM EDTA, 0.5% SDS, 250 mM NaCl, 1.2 U Proteinase K (Thermo) at 50°C overnight followed by sonication for 5 min on ice and DNA purification using phenol/chloroform/isoamyl and ethanol. Biotinylated DNA was captured on streptavidin C1 beads (NEB) and washed with 10 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.02 % TritonX100.
Sequencing libraries were prepared using NEB Ultra II DNA library Prep kit according to the manufacturer’s instructions.

treatment_protocol: 100 ng/ml doxycycline was added for 4 days  to induce shRNA expression

value: colon

value: Colorectal carcinoma cell line

value: HUWE1-CS, shWRNIP1


title: KAR4_DMSO_B_S39_RNA-seq


title: EXT_aIFNg_Foxp3DTRpos_SKM.Qd#3

value: 2 weeks exercise training, DT, anti-IFN-gamma


title: HUWE1-CS, shCtrl, DSBseq

value: HUWE1-CS, shCtrl


title: cortex_day_21_replicate_8

description: brain_clean_VST_counts.csv column 50

value: M


title: KAR4_DMSO_A_S38_RNA-seq


title: KYSE450-4

value: ESCC cell

value: parental


title: EXT_aIFNg_Foxp3DTRpos_SKM.Qd#2


title: HUWE1-WT, shWRNIP1, DSBseq

value: HUWE1-WT, shWRNIP1


title: cortex_day_21_replicate_3

description: brain_clean_VST_counts.csv column 47


title: cortex_day_21_replicate_1

description: brain_clean_VST_counts.csv column 45


title: KYSE450-3

value: WT


title: IXR1_DMSO_B_S56_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 IXR1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 IXR1-3xV5 IAA7::URA3


title: cortex_day_21_replicate_2

description: brain_clean_VST_counts.csv column 46

value: F


title: KAR4_3IAA_B_S42_RNA-seq


title: KAR4_3IAA_A_S41_RNA-seq


title: KAR4_3IAA_C_S43_RNA-seq


title: EXT_IgG_Foxp3DTRpos_SKM.Qd#3

value: 2 weeks exercise training, DT, IgG


title: EXT_IgG_Foxp3DTRpos_SKM.Qd#1

value: Muscle


title: EXT_IgG_Foxp3DTRpos_SKM.Qd#2


title: cortex_day_21_replicate_4

description: brain_clean_VST_counts.csv column 48

value: cortex


title: HUWE1-WT, shWRNIP1, input


title: cortex_day_9_replicate_10

description: brain_clean_VST_counts.csv column 49


title: HUWE1-CS, shWRNIP1, input


title: EXT_aIFNg_Foxp3DTRpos_SKM.Qd#1


title: HUWE1-WT, shCtrl, DSBseq

value: HUWE1-WT, shCtrl


title: EXT_Foxp3DTRpos_SKM.Qd#3

value: 2 weeks exercise training, DT


title: EXT_Foxp3DTRpos_SKM.Qd#2


title: IXR1_3IAA_C_S60_RNA-seq


title: MCF7 noserGTA input

city: palo alto

first: Jiangbin

last: ye

state: California

address: 269 Campus Drive CCSR-South 1245

institute: Stanford university

data_processing:
ChIP-seq reads were mapped to hg38 using bowtie2 v2.3.5.1 with parameters --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700
Potential PCR duplicates were removed by the function "MarkDuplicates" of Picard v2.24.2 with parameter: REMOVE_DUPLICATES=true
Genomic enrichments of ChIP-seq signals were generated using deeptools v3.3.2 with parameters bamCoverage --normalizeUsing CPM --binSize 25 --smoothLength 100 --scaleFactor
The scaling factor was determined by quantifying total H3K27ac by Western blot
Peak calling was done using macs2, and peak comparison was done using bedtools
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a Q500 Sonicator (QSonica).
ChIP-seq libraries were prepared and sequenced by Novogene.

value: ER positive breast cancer

tag: chip antibody

value: -Serine+GTA media for 24h


title: cortex_day_21_replicate_6

description: brain_clean_VST_counts.csv column 43


title: IXR1_DMSO_A_S55_RNA-seq


title: cortex_day_21_replicate_7

description: brain_clean_VST_counts.csv column 44


title: HUWE1-WT, shCtrl, input

value: colon

value: Colorectal carcinoma cell line


title: cortex_day_0_replicate_1

description: brain_clean_VST_counts.csv column 51


title: IXR1_DMSO_C_S57_RNA-seq


title: HUWE1-CS, shCtrl, input

value: HUWE1-CS, shCtrl


title: MCF7 noser input

value: -Serine media for 24h


title: cortex_day_21_replicate_5

description: brain_clean_VST_counts.csv column 42

value: M


title: patient4_B30_TCRbeta

city: Lausanne

first: David

last: Barras

state: Vaud

address: AGORA, Bugnon 25A

department: Oncology

country: Switzerland

institute: Centre hospitalier universitaire vaudois

data_processing:
Deep sequencing of the TCR beta chain was performed on Illumina instrument
The TCR sequences were further processed using ad hoc Perl scripts to: (i) pool all TCR sequences coding for the same protein sequence; (ii) filter out all out-frame sequences; (iii) determine the abundance of each distinct TCR sequence.
TCR with a single read were not considered for the analysis.
Assembly: IMGT data base was used to identifiy TCR
Supplementary files format and content: txt files containing the list of TCR and their frequencies
Library strategy: TCR-seq

source_name: blood

extract_protocol:
mRNA was extracted using the Dynabeads mRNA DIRECT Purification Kit according to the manufacturer instruction and as described in Genolet et al., Cell Report Methods, 2013.
Libraries were prepare using targeted TCR amplification

value: blood

value: peripheral blood mononuclear cell (PBMC)

tag: patient

tag: time

value: post-ACT


title: EXT_Foxp3DTRneg_SKM.Qd#3

tag: tissue


title: IXR1_3IAA_B_S59_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 IXR1-3xV5 IAA7::URA3


title: cortex_day_5_replicate_10

description: brain_clean_VST_counts.csv column 41


title: IXR1_3IAA_A_S58_RNA-seq


title: INO2_DMSO_C_S9_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 INO2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 INO2-3xV5 IAA7::URA3


title: EXT_Foxp3DTRneg_SKM.Qd#1


title: MCF7 ser input

tag: cell line

value: +Serine media for 24h


title: INO2_DMSO_B_S8_RNA-seq


title: MCF7 noserGTA rep1 H3K27ac

value: H3K27ac (Active Motif #39133)

tag: treatment


title: SED_Foxp3DTRpos_SKM.Qd#3

value: Muscle

value: DT


title: INO2_DMSO_A_S7_RNA-seq


title: MCF7 noserGTA rep2 H3K27ac


title: cortex_day_5_replicate_4

description: brain_clean_VST_counts.csv column 40

value: cortex

value: F


title: SED_Foxp3DTRpos_SKM.Qd#2


title: MCF7 noser rep2 H3K27ac

value: ER positive breast cancer


title: INO2_3IAA_C_S12_RNA-seq


title: cortex_day_14_replicate_8


title: EXT_Foxp3DTRneg_SKM.Qd#2

value: 2 weeks exercise training, DT


title: INO2_3IAA_B_S11_RNA-seq


title: cortex_day_14_replicate_7

description: brain_clean_VST_counts.csv column 39


title: SED_Foxp3DTRneg_SKM.Qd#3


title: EXT_Foxp3DTRpos_SKM.Qd#1


title: cortex_day_5_replicate_9


title: cortex_day_7_replicate_4


title: MCF7 ser rep2 H3K27ac


title: MCF7 ser IGG

value: IGG (Diagenode #C15410206)


title: MCF7 noser rep1 H3K27ac


title: MCF7 ser rep1 H3K27ac


title: SED_Foxp3DTRneg_SKM.Qd#2


title: INO2_3IAA_A_S10_RNA-seq


title: IFH1_DMSO_C_S34_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 IFH1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 IFH1-3xV5 IAA7::URA3


title: SED_Foxp3DTRneg_SKM.Qd#1


title: cortex_day_7_replicate_3

description: brain_clean_VST_counts.csv column 37


title: ExerD1_Foxp3DTR-_SKM.Qd#3

value: Acute exercise (d1 recovery), DT


title: cortex_day_12_replicate_8

description: brain_clean_VST_counts.csv column 38

value: M


title: ExerD1_Foxp3DTR-_SKM.Qd#2


title: cortex_day_12_replicate_3

description: brain_clean_VST_counts.csv column 35


title: cortex_day_5_replicate_3

description: brain_clean_VST_counts.csv column 36


title: SED_Foxp3DTRpos_SKM.Qd#1


title: IFH1_DMSO_A_S31_RNA-seq


title: IFH1_DMSO_B_S33_RNA-seq


title: MCF7 noser rep1

data_processing:
RNA-seq analysis was performed using the kallisto and sleuth analytical pipeline (Bray et al., 2016; Pimentel et al., 2017).
In brief, a transcript index was generated with reference to Ensembl version 67 for hg19. Paired-end mRNA-seq reads were pseudo-aligned using kallisto (v0.42.4) with respect to this transcript index using 100 bootstraps (-b 100) to estimate the variance of estimated transcript abundances.
Transcript-level estimates were aggregated to transcripts per million (TPM) estimates for each gene, with gene names assigned from Ensembl using biomaRt.
Assembly: hg19
Supplementary files format and content: tab-delimited text files including estimated counts and TPM for each sample
Supplementary files format and content: Matrix table with TPM for every gene and every sample

source_name: MCF7 cancer cell line

extract_protocol:
RNA was harvested from adherent cell cultures using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

value: serine-free media for 24h


title: MCF7 noser rep3


title: cortex_day_14_replicate_3

description: brain_clean_VST_counts.csv column 34


title: MCF7 noser rep2


title: IFH1_3IAA_C_S37_RNA-seq


title: ExerD1_Foxp3DTR-_SKM.Qd#1


title: MCF7 ser rep3

value: serine-containing media for 24h


title: cortex_day_12_replicate_2


title: MCF7 ser rep2


title: IFH1_3IAA_B_S36_RNA-seq


title: ExerD1_Foxp3DTR+_SKM.Qd#3


title: ExerD1_Foxp3DTR+_SKM.Qd#2


title: cortex_day_9_replicate_9

description: brain_clean_VST_counts.csv column 33


title: IFH1_3IAA_A_S35_RNA-seq


title: ExerD1_Foxp3DTR+_SKM.Qd#1


title: MCF7 ser rep1


title: HSF1_DMSO_37_C_S40_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 HSF1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 HSF1-3xV5 IAA7::URA3

value: heat shock


title: cortex_day_9_replicate_8

description: brain_clean_VST_counts.csv column 32


title: HSF1_DMSO_37_B_S39_RNA-seq


title: ExerD7_Foxp3DTR-_SKM.Qd#1

value: Acute exercise (d7 recovery), DT


title: 231 noser rep1

source_name: MDA-MB-231 cancer cell line

value: ER negative breast cancer


title: HSF1_DMSO_30_C_S34_RNA-seq


title: 231 noser rep3


title: HSF1_DMSO_37_A_S38_RNA-seq


title: 231 noser rep2


title: cortex_day_7_replicate_7

description: brain_clean_VST_counts.csv column 29


title: cortex_day_7_replicate_8

description: brain_clean_VST_counts.csv column 30


title: 231 ser rep3


title: ExerD7_Foxp3DTR+_SKM.Qd#3


title: ExerD7_Foxp3DTR+_SKM.Qd#2


title: 231 ser rep2


title: HSF1_DMSO_30_B_S33_RNA-seq


title: HSF1_DMSO_30_A_S32_RNA-seq


title: cortex_day_14_replicate_6


title: Sed_Foxp3DTR-_SKM.Qd#3


title: HSF1_3IAA_37_C_S43_RNA-seq


title: 231 ser rep1


title: Sed_Foxp3DTR-_SKM.Qd#2


title: cortex_day_9_replicate_7

description: brain_clean_VST_counts.csv column 28


title: SC_050322_uG_unstim

city: Novato

first: Fei

last: Wu

address: 8001 Redwood Blvd

institute: Buck Institute for Research on Aging

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

growth_protocol: PBMCs were counted and re-suspended in complete media at 1x10^6 cells/ml (RPMI 1640, 10% Fetal Bovine Serum, 2mM L-Glutamine, 1% penicillin/streptomycin, 0.1mM non-essential Amino acid,1mM sodium pyruvate, 50uM 2-mercaptoethanol,10mM HEPES)

extract_protocol:
De-identified peripheral blood buffy coat samples were obtained from healthy human donors from the Stanford University Blood Center. PBMCs were isolated using a Ficoll gradient method.
1x10^4 PBMCs from each condition were counted and loaded on the 10X Genomics Chromium Controller and the libraries were prepared using Chromium Next GEM Single Cell 5’ Reagent Kit v2 according to the manufacturer’s protocol (10X Genomics, Pleasanton, CA). The quality of libraries was assessed using Agilent TapeStation 4200, and test-sequenced on Illumina NextSeq 550. The full sequencing was performed on an Illumina NovaSeq 6000 by SeqMatic (Fremont, CA).

treatment_protocol:
To generate simulated microgravity, the cell suspension was loaded into 10 ml disposable high aspect ratio vessels (Synthecon, Houston, TX) and rotated at 15 rpm for 25 hours.
For the 1G control, the cell suspension was plated in standard 6-well culture plates

value: Peripheral Blood Mononuclear Cells

value: Blood


title: cortex_day_5_replicate_8

extract_protocol:
RNA was extracted using the TRIzol-chloroform based method. Tissue was lysed in TRIzol (ThermoFisher 15596018), and lysate was mixed with phenol:choloroform:isoamyl alcohol (ThermoFisher 15593049) in a 5:1 ratio. Protein and nucleic acids were separated into phases via centrifugation. The top aqueous layer containing the RNA was passed through a QIAshredder column (Qiagen 79656). Eluent was mixed 1:1 with 70% ethanol and applied to an RNease Mini column (Qiagen 74104). After a brief centrifugation, columns were washed once with RW1 buffer and twice with RPE buffer, as per manufacturer's recommendations. RNA was eluted in nuclease-free water. 1µg of total RNA in a concentration of 20ng/µL was shipped to LC Sciences (Houston, TX) for library preparation and RNA sequencing.
Total RNA was enriched for mRNA, fragmented, and reverse transcribed into complementary DNA (cDNA). Second-stranded DNA was synthesized, A-bases were added to the blunt ends of either strand, and DNA was ligated to dual-index adapters. Size selection was performed and DNA was treated with a heat-labile UDG enzyme. Ligated products were amplified with PCR before sequencing.


title: ExerD7_Foxp3DTR-_SKM.Qd#3

value: Muscle


title: HSF1_3IAA_37_B_S42_RNA-seq

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.


title: cortex_day_14_replicate_5

description: brain_clean_VST_counts.csv column 27

value: cortex


title: cortex_day_7_replicate_9

description: brain_clean_VST_counts.csv column 31


title: SC_050322_1G_unstim

description: 10x Genomics


title: Sed_Foxp3DTR-_SKM.Qd#1

value: DT


title: HSF1_3IAA_37_A_S41_RNA-seq


title: SC_050322_uG_stim

description: 10x Genomics


title: HSF1_3IAA_30_C_S37_RNA-seq


title: HSF1_3IAA_30_B_S36_RNA-seq


title: Sed_Foxp3DTR+_SKM.Qd#2


title: cortex_day_9_replicate_4

description: brain_clean_VST_counts.csv column 24

value: F


title: SC_040522_uG_unstim

description: 10x Genomics


title: HSF1_3IAA_30_A_S35_RNA-seq


title: SC_040522_1G_unstim

description: 10x Genomics


title: cortex_day_12_replicate_7

description: brain_clean_VST_counts.csv column 25


title: HMS2_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 HMS2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 HMS2-3xV5 IAA7::URA3


title: cortex_day_14_replicate_2


title: Sed_Foxp3DTR+_SKM.Qd#3


title: Sed_SKM.TA_ID#06


title: Sed_SKM.TA_ID#07


title: HMS2_DMSO_B_S20_RNA-seq


title: cortex_day_7_replicate_1

description: brain_clean_VST_counts.csv column 22


title: SC_040522_uG_stim

description: 10x Genomics


title: Exer_d1_SKM.TA_ID#19

value: Acute exercise (d1 recovery)


title: cortex_day_12_replicate_6

description: brain_clean_VST_counts.csv column 21


title: SC_040522_1G_stim

description: 10x Genomics


title: Sed_SKM.TA_ID#05


title: cortex_day_7_replicate_2

description: brain_clean_VST_counts.csv column 23


title: SC_050322_1G_stim

description: 10x Genomics


title: Exer_d1_SKM.TA_ID#17


title: cortex_day_14_replicate_4

description: brain_clean_VST_counts.csv column 26


title: Bulk_081022_uG_Q

data_processing:
MTD pipeline
Read count extraction and normalization were performed using DESeq2 R package (version 1.36.0)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw counts, normalized counts for each sample; and Log2FC and p-values for group comparisons.

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Cat# 74134, Qiagen) as per the manufacturer's instruction.
RNA quantity check, preparation of RNA library, and mRNA sequencing were conducted by Novogene Co., LTD (CA, US). About 20 million paired-end 150 bp reads per sample were generated from Illumina NovaSeq 6000 Sequencing System.

value: simulated microgravity with quercetin treatment

value: 25 hours


title: HMS2_3IAA_C_S24_RNA-seq


title: cortex_day_12_replicate_5

description: brain_clean_VST_counts.csv column 20

value: M


title: HMS2_DMSO_A_S19_RNA-seq


title: HMS2_3IAA_B_S23_RNA-seq


title: Exer_d1_SKM.TA_ID#16


title: cortex_day_9_replicate_3

description: brain_clean_VST_counts.csv column 19


title: cortex_day_9_replicate_2


title: Bulk_081022_1G

value: normal gravity


title: HMS2_3IAA_A_S22_RNA-seq


title: Exer_d2_SKM.TA_ID#14

value: Acute exercise (d2 recovery)


title: cortex_day_9_replicate_6

description: brain_clean_VST_counts.csv column 18


title: Exer_d2_SKM.TA_ID#15


title: HCM1_DMSO_C_S27_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-HCM1

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 mini-N-deg-3xV5-HCM1


title: Exer_d2_SKM.TA_ID#13


title: HCM1_DMSO_B_S26_RNA-seq


title: Bulk_080722_uG_Q


title: Bulk_080722_1G_Q

value: normal gravity with quercetin treatment


title: Exer_d7_SKM.TA_ID#10

value: Acute exercise (d7 recovery)


title: Exer_d7_SKM.TA_ID#09


title: HCM1_DMSO_A_S25_RNA-seq


title: cortex_day_7_replicate_5

description: brain_clean_VST_counts.csv column 16


title: Bulk_080722_uG

value: simulated microgravity


title: HCM1_3IAA_C_S30_RNA-seq


title: Bulk_080722_1G

value: Peripheral Blood Mononuclear Cells


title: Bulk_081022_1G_Q


title: Exer_d7_SKM.TA_ID#08


title: HCM1_3IAA_B_S29_RNA-seq


title: Bulk_072022_uG_Q


title: Sed_SKM.Qd_ID#07


title: HCM1_3IAA_A_S28_RNA-seq


title: Bulk_081022_uG


title: Sed_SKM.Qd_ID#06


title: Bulk_072022_1G_Q


title: Sed_SKM.Qd_ID#05


title: HAP5_DMSO_B_S14_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 HAP5-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 HAP5-3xV5 IAA7::URA3


title: HAP5_DMSO_C_S15_RNA-seq


title: Bulk_072022_uG


title: Exer_d1_SKM.Qd_ID#19

value: Muscle


title: cortex_day_0_replicate_13

description: brain_clean_VST_counts.csv column 15

value: cortex


title: cortex_day_12_replicate_4

description: brain_clean_VST_counts.csv column 11


title: cortex_day_0_replicate_12

description: brain_clean_VST_counts.csv column 14


title: cortex_day_0_replicate_10

description: brain_clean_VST_counts.csv column 13


title: Bulk_072022_1G


title: cortex_day_7_replicate_6

description: brain_clean_VST_counts.csv column 17


title: HAP5_DMSO_A_S13_RNA-seq


title: cortex_day_9_replicate_5

description: brain_clean_VST_counts.csv column 10


title: Exer_d1_SKM.Qd_ID#17


title: cortex_day_14_replicate_1

description: brain_clean_VST_counts.csv column 9


title: HCT116, HU+Cdk9i, DSBseq

extract_protocol:
Double strand break sequencing was performed based on the DSBCapture protocol (Lensing et al., 2016). In brief, 5 million cells were fixed with 0.2% PFA for 4 min and the reaction was quenched by addition of 200 mM glycine for 4 min. Scraped cells were permeabilized in wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.1% Triton-X100) for 10 min on ice and bound to Con-A Sepharose (Sigma) in binding buffer (20 mM HEPES, 10 mM KCl, 1 mM CaCl2, 1 mM MnCl2). DNA ends were repaired using Klenow fragment (NEB) in NEB buffer 2 for 30 min at 25°C followed by A-tailing in dA-tailing buffer (NEB) with Klenow (3'→5' exo-) for 30 min at 37°C. Biotinylated NEB adaptors were ligated to A-tailed DSBs with T4 DNA ligase (NEB) in the corresponding buffer overnight at 16°C. Cells were lysed in 10 mM Tris, pH 8.5, 5 mM EDTA, 0.5% SDS, 250 mM NaCl, 1.2 U Proteinase K (Thermo) at 50°C overnight followed by sonication for 5 min on ice and DNA purification using phenol/chloroform/isoamyl and ethanol. Biotinylated DNA was captured on streptavidin C1 beads (NEB) and washed with 10 mM Tris-HCl pH 8.0, 0.5 mM EDTA, 1 M NaCl, 0.02 % TritonX100.
Sequencing libraries were prepared using NEB Ultra II DNA library Prep kit according to the manufacturer’s instructions.

treatment_protocol: Hydroxyurea at 1 mM for 24 hours with or without pre-treatment with Cdk9i AZD4573 20 nM for 6 h

value: colon

value: Colorectal carcinoma cell line

value: Hydroxyurea + Cdk9 inhibitor AZD4573


title: HAP5_3IAA_C_S18_RNA-seq


title: HCT116, Cdk9i, DSBseq

value: Cdk9 inhibitor AZD4573


title: Exer_d1_SKM.Qd_ID#16

value: Acute exercise (d1 recovery)


title: HAP5_3IAA_B_S17_RNA-seq


title: cortex_day_12_replicate_1

value: F


title: cortex_day_0_replicate_9

description: brain_clean_VST_counts.csv column 12

value: M


title: HAP5_3IAA_A_S16_RNA-seq


title: HCT116, HU, DSBseq

value: Hydroxyurea


title: cortex_day_9_replicate_1

description: brain_clean_VST_counts.csv column 8


title: HCT116, Ctrl, DSBseq

value: DMSO


title: Exer_d2_SKM.Qd_ID#14

value: Acute exercise (d2 recovery)


title: Exer_d2_SKM.Qd_ID#13


title: cortex_day_5_replicate_2


title: HAP3_DMSO_B_S8_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 HAP3-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 HAP3-3xV5 IAA7::URA3


title: HCT116, HU+Cdk9i, input


title: HAP3_DMSO_C_S9_RNA-seq


title: cortex_day_5_replicate_1

description: brain_clean_VST_counts.csv column 7

source_name: cortex


title: HCT116, Cdk9i, input


title: cortex_day_5_replicate_7

description: brain_clean_VST_counts.csv column 6


title: HAP3_3IAA_C_S12_RNA-seq


title: Exer_d7_SKM.Qd_ID#10

source_name: Muscle

value: Acute exercise (d7 recovery)


title: Exer_d7_SKM.Qd_ID#09


title: HCT116, HU, input


title: Exer_d7_SKM.Qd_ID#08


title: HCT116, Ctrl, input


title: HAP3_3IAA_B_S11_RNA-seq


title: Exer_d2_SKM.Qd_ID#15


title: HCT116, HUWE1-CS, WRNIP1 Cut&Run, rep2

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 instrument (1 x 100 bp)
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2).
Reads were aligned to human genome (hg19) with STAR (2.5.4) and tag directories were generated using Homer (version 4.10.3)
Bedgraph files were generated using Homer makeUCSCfile script
Sequencing tag coverage was calculated using Homer annotatePeaks script
Assembly: hg19
Supplementary files format and content: Bedgraph
Library strategy: Cut&Run

extract_protocol:
Cells were fixed with 0.2% formaldehyde and Cut&Run assay was performed using the WRNIP1 antibody (sc-377402, Santa Cruz) and the NEB CUT&RUN kit (#86652P)
Sequencing libraries were prepared using NEB Ultra II DNA library Prep kit according to the manufacturer’s instructions.

value: WRNIP1 antibody (sc-377402, Santa Cruz)


title: E13.5 p27 positive progenitors, Sox4 ChIP, replicate3

city: Los Angeles

first: Neil

last: Segil

address: 1425 san pablo st, 503

department: DSR

institute: University of Southern California

data_processing:
the reads were trimmed to 37bp and aligned to GRCm38/mm10 genome assembly with STAR aligner
read duplicates were removed by MIDs using UMI-tools
Peaks were called by Model-based analysis of ChIP-Seq (MACS2; Feng et al., 2012) with FDR< 0.01 and disabled dynamic lambda (--nolambda) option for individual replicates
BigWig files were generated with deepTools
genome_build/assembly:mm10
supplementary_files_format_and_content:narrowPeak
Library strategy: Cut&Run

source_name: Cochlea

extract_protocol:
cochlea ducts were dissected at  E13.5 from p27kip1-GFP  mice and epithelial layer was isolated using enzymatic digestion with 0.25% dispase (Gibco) and collagenase I (Gibco) for 10 min. Cells are then dissociated and FACS sorted to obtain GFP positive cochlea epithelail progenitor cells.
CUT&RUN libraries were constructed using Accel-NGS 2S plus DNA prep kits with single index and MIDs (Swift Bioscience). At least 20 million paired-end reads were sequenced for each sample.

value: Cochlea

value: Cochlea p27 positive progenito cells

value: Wildtype

value: Guinea pig anti-Sox4 (Thein et al., 2010)


title: HAP3_3IAA_A_S10_RNA-seq

data_processing:
Paired-end sequencing reads were aligned to S. cerevisiae reference genome (sacCer3) and S. pombe reference genome (ASM294v2.20) with Bowtie2 using optional arguments “-I 10 -X 700 --local --very-sensitive-local --no-unal --no-mixed --no-discordant”.
SAM files for S. cerevisiae data were used as an input for HTseq-count with default settings. The GFF file with S. cerevisiae genomic features was downloaded from the Ensembl website.
HTSeq output files are used as input files for differential analysis using DESeq2 (using defaults settings)
Assembly: sacCer3 (S. cerevisiae), ASM294v2.20 (S. pombe)
Supplementary files format and content: Raw output files obtained from DESeq2 analysis


title: cortex_day_0_replicate_16

data_processing:
Reads were filtered to remove adapters, reads with polyA or polyG, reads with more than 5% unknown nucleotides, and reads with more than 20% low-quality bases (Q-value < 20) with Cutadapt.
Reads were mapped to the GRCmm39 genome assembly using STAR (v. 2.7.9)
Reads were counted with Subread (v. 2.0.3) in paired-end mode
Quality control and normalization was performed in R with the WGCNA, DESeq2, and edgeR packages.
Assembly: GRCmm39
Supplementary files format and content: comma-separated file gives raw read counts for each sample
Supplementary files format and content: comma-separated file gives variance-stabilized counts of only high-quality genes and samples

value: cortex


title: cortex_day_5_replicate_5


title: E13.5 p27 positive progenitors, Sox4 ChIP, replicate2


title: HCT116, HUWE1-WT, WRNIP1 Cut&Run, rep2

source_name: colon

value: colon

value: Colorectal carcinoma cell line


title: HAP2_DMSO_C_S21_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 HAP2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 HAP2-3xV5 IAA7::URA3


title: E13.5 p27 positive progenitors, Sox4 ChIP, replicate1

data_processing:
the reads were trimmed to 37bp and aligned to GRCm38/mm10 genome assembly with STAR aligner
read duplicates were removed by MIDs using UMI-tools
Peaks were called by Model-based analysis of ChIP-Seq (MACS2; Feng et al., 2012) with FDR< 0.01 and disabled dynamic lambda (--nolambda) option for individual replicates
BigWig files were generated with deepTools
genome_build/assembly:mm10
supplementary_files_format_and_content:narrowPeak, bed, bigwig
Library strategy: Cut&Run


title: cortex_day_0_replicate_14

description: brain_clean_VST_counts.csv column 3


title: HCT116, HUWE1-CS, WRNIP1 Cut&Run, rep1


title: HAP2_DMSO_B_S20_RNA-seq


title: E13.5 cochlea, whole organ, SoxC double knockout, replicate2

data_processing:
the reads were trimmed to 37bp and aligned to GRCm38/mm10 genome assembly with STAR aligner
PCR-duplicated reads were marked and removed based on fragment genomic coordinates
Peaks were called by Model-based analysis of ChIP-Seq (MACS2; Feng et al., 2012) with FDR< 0.01 and disabled dynamic lambda (--nolambda) option for individual replicates
BigWig files were generated with deepTools
genome_build/assembly:mm10
supplementary_files_format_and_content:narrowPeak

extract_protocol:
cochlea ducts were dissected at  E13.5 from SoxC double knockout mice and epithelial layer was isolated using enzymatic digestion with 0.25% dispase (Gibco) and collagenase I (Gibco) for 10 min.
Whole epithelia were lysed in the buffer containing 10mM TrisHCl (pH=8.0), 5mM MgCl2, 10% DMF, 0.2% NP40 in ddH2O. Transposition buffer containing 10 mM Tris-HCL (pH=8.0), 5 mM MgCl2, 10% DMF, 0.2% NP40, and Tn5 transposes was then added and incubate at 37°C for 20 min. After DNA purification, amplification and library construction was performed through PCR.

value: Cochlea duct epithelia cells

value: SoxC double knockout


title: HAP3_DMSO_A_S7_RNA-seq


title: HCT116, HUWE1-WT, WRNIP1 Cut&Run, rep1


title: cortex_day_0_replicate_8

description: brain_clean_VST_counts.csv column 1

value: F


title: HAP2_DMSO_A_S19_RNA-seq


title: cortex_day_5_replicate_6

description: brain_clean_VST_counts.csv column 5

value: M


title: HCT116, HUWE1-CS, input for Cut&Run

value: none (input)


title: cortex_day_0_replicate_7


title: HAP2_3IAA_C_S24_RNA-seq


title: cortex_day_0_replicate_6


title: HAP2_3IAA_B_S23_RNA-seq


title: HAP2_3IAA_A_S22_RNA-seq


title: E13.5 cochlea, whole organ, wildtype, replicate2

data_processing:
Peaks were called by Model-based analysis of ChIP-Seq (MACS2; Feng et al., 2012) with FDR< 0.01 and disabled dynamic lambda (--nolambda) option for individual replicates
PCR-duplicated reads were marked and removed based on fragment genomic coordinates
Peaks were called by Model-based analysis of ChIP-Seq (MACS2; Feng et al., 2012) with FDR< 0.01 and disabled dynamic lambda (--nolambda) option for individual replicates
BigWig files were generated with deepTools
genome_build/assembly:mm10
supplementary_files_format_and_content:narrowPeak

extract_protocol:
cochlea ducts were dissected at  E13.5 from wildtype mice and epithelial layer was isolated using enzymatic digestion with 0.25% dispase (Gibco) and collagenase I (Gibco) for 10 min.
Whole epithelia were lysed in the buffer containing 10mM TrisHCl (pH=8.0), 5mM MgCl2, 10% DMF, 0.2% NP40 in ddH2O. Transposition buffer containing 10 mM Tris-HCL (pH=8.0), 5 mM MgCl2, 10% DMF, 0.2% NP40, and Tn5 transposes was then added and incubate at 37°C for 20 min. After DNA purification, amplification and library construction was performed through PCR.


title: HUWE1-CS, shWRNIP1, ChIP pS2-RNAPII, rep2

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 instrument (1 x 100 bp)
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2).
Bedgraph files were generated using Homer makeUCSCfile script
Reads were aligned to human genome (hg19) with STAR (2.5.4) and differentially expressed genes were determined using EdgeR (3.26.8).
Assembly: hg19
Supplementary files format and content: Bedgraph
Supplementary files format and content: ChIP-seq tag coverage was calculated using Homer annotatePeaks script

extract_protocol:
For each ChIP sample, 4 - 6 x107 HCT116 cells per condition were fixed with 1% PFA for 4 min at room temperature and the reaction was quenched by adding 200 mM glycine for 4 min. Cells were scraped in ice cold PBS and lysed in 200 µl PBS, 0.5% (v/v) TritonX-100, 1 mM dithiothreitol, 5 mM MgCl2, 5 mM CaCl2 and protease/phosphatase inhibitors (Sigma) for 10 min on ice. Chromatin was fragmented with 1 µl micrococcal nuclease (NEB M0247S) for 3 min at 37°C and 20 µl 500 mM EDTA was added to suppress enzyme activity. After diluting samples with 800 µl TNT-300 (25 mM Tris, 300 mM NaCl, 1% (v/v) Triton-X100, pH 7.4, with protease/phosphatase inhibitor cocktails), chromatin was further fragmented by sonication for 3x 2 min with 30% amplitude, 2 W power and a 45 s on / 15 s off cycle with an UP200St sonicator (Hielscher) on ice. Lysates were cleared by centrifugation for 10 min at 17,000xg and 2% of each sample were separated as input. For each immunoprecipitation 1.5 - 2 µg of target specific antibody was added to the lysate and rotated overnight at 4°C. To capture proteins of interest, 10 µl magnetic protein A or protein G bead slurry (Thermo) were added per sample and rotated for 2 h. Beads were washed three times with TNT-300, 0.1% SDS and RNA was digested with 1 µl RNAseA (Thermo) in 10 mM Tris pH 8, 1 mM EDTA, 0.5% SDS, 250 mM NaCl for 1 h at 50°C. Proteins were digested with 2 µl proteinase K (Thermo) at 50°C for 1 h followed by 65°C overnight. Fragmented DNA was purified using phenol/chloroform/isoamyl (Roth A156.1)
Sequencing libraries were prepared using NEB Ultra II DNA library Prep kit according to the manufacturer’s instructions.

value: HUWE1-CS, shWRNIP1

value: pS2-RNAPII (Active Motif; Cat# 61083; Lot# 32820004)


title: HUWE1-CS, shCtrl, ChIP pS2-RNAPII, rep2

value: HUWE1-CS, shCtrl


title: E13.5 cochlea, Pax2creSoxCfl/fl strain, SoxC double knockout

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
genome_build/assembly:mm10
supplementary_files_format_and_content:Tab-separated values files and matrix files

extract_protocol:
cochlea ducts were dissected at  E13.5 from SoxC double knockout mice and epithelial layer was isolated using enzymatic digestion with 0.25% dispase (Gibco) and collagenase I (Gibco) for 10 min.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.


title: HAC1_DMSO_C_S3_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 HAC1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 HAC1-3xV5 IAA7::URA3


title: cortex_day_0_replicate_11

description: brain_clean_VST_counts.csv column 2


title: HAC1_DMSO_B_S2_RNA-seq


title: E13.5 cochlea, whole organ, wildtype, replicate1

data_processing:
the reads were trimmed to 37bp and aligned to GRCm38/mm10 genome assembly with STAR aligner
PCR-duplicated reads were marked and removed based on fragment genomic coordinates
Peaks were called by Model-based analysis of ChIP-Seq (MACS2; Feng et al., 2012) with FDR< 0.01 and disabled dynamic lambda (--nolambda) option for individual replicates
genome_build/assembly:mm10
supplementary_files_format_and_content:narrowPeak

value: Cochlea


title: astrocyte differentiation (fgf1,bmp4), 72hour

city: New York

first: Paul

last: Frazel

state: NY

address: 435 E 30th St

institute: NYU Langone Medical Center

data_processing:
After demultiplexing, cell calling was performed via Cellranger v6.0.1 or Cellranger ARC v4.0.5 for multiomic data.
Assembly: mm10, GRCh38-2020-A
Supplementary files format and content: Processed data type: h5 file for gene expression, atac fragments for snATACseq. Can be used for tertiary scRNAseq analysis

source_name: astrocyte differentiation

extract_protocol:
Single cell suspensions were generated with papain dissociation. Single nuclei generated with Sigma EZ Lysis buffer.
10X Genomics manufacturer's instructions (Illumina dual-index library)

value: astrocyte differentiation

value: cells


title: HUWE1-WT, shWRNIP1, ChIP pS2-RNAPII, rep2

value: HUWE1-WT, shWRNIP1


title: E13.5 cochlea, p27GFP strain, wildtype

description: 10x Genomics

extract_protocol:
cochlea ducts were dissected at  E13.5 from wildtype mice and epithelial layer was isolated using enzymatic digestion with 0.25% dispase (Gibco) and collagenase I (Gibco) for 10 min.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Wildtype


title: astrocyte differentiation (fgf1,bmp4), no embryoid body step


title: E13.5 cochlea, whole organ, SoxC double knockout, replicate1


title: HAC1_DMSO_A_S1_RNA-seq


title: HUWE1-WT, shCtrl, ChIP pS2-RNAPII, rep2

value: colon

value: HUWE1-WT, shCtrl


title: E13.5 cochlea, whole organ, wildtype, replicate3


title: astrocyte differentiation (fgf1,bmp4), 24hour


title: astrocyte differentiation (fgf1,bmp4), 48hour


title: HUWE1-CS, shWRNIP1, ChIP RNAPII, rep2

value: Colorectal carcinoma cell line

value: RNAPII (Active Motif; Cat# 101307; Lot# 08322043)


title: adherent differentiation, 4day diff

source_name: adherent differentiation

value: adherent differentiation


title: Wildtype replicate 5

city: Bethesda

first: Tamara

last: Haque

state: MD

address: 10 Center Drive

institute: NIAID

data_processing:
Raw fastq files were trimmed for quality and adapter contamination using Cutadapt v2.10
Trimmed reads were mapped to the mm10 mouse reference genome and Ensembl v103 transcriptome using STAR v2.5.3
Gene-level expression quantification was performed using RSEM v1.3.0
Differential expression analysis was performed using the R package DESeq2
Assembly: mm10/Ensembl 103
Supplementary files format and content: tab delimited text with expected counts

source_name: Peyer's patch

extract_protocol:
Peyer’s patch CD4+CXCR5+PD1+ Tfh cells were sorted on a BD FACS Aria and stored in Trizol. Total RNA was collected using the chloroform and ethanol isolation method.
Clontech SMART-Seq Ultra Low Input Non-Stranded mRNA Library Prep was used on a total of 300pg of RNA according to manufacturer’s protocol.

value: Peyer's patch

value: Total Tfh cells, CD4+CXCR5+PD1+

value: WT


title: HUWE1-CS, shCtrl, ChIP RNAPII, rep2


title: HAC1_3IAA_B_S5_RNA-seq


title: Wildtype replicate 4


title: HCT116, HUWE1-WT, input for Cut&Run

value: none (input)


title: Wildtype replicate 3


title: Wildtype replicate 1


title: embryoid bodies, 4day diff

source_name: embryoid body

value: embryoid body


title: HAC1_3IAA_A_S4_RNA-seq


title: HUWE1-WT, shWRNIP1, ChIP RNAPII, rep2


title: HUWE1-WT, shCtrl, ChIP RNAPII, rep2


title: TGFBR1 WT/mut, replicate 10

value: WT/Mut


title: embryoid bodies, 2day diff, rep3


title: HAA1_DMSO_C_S15_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 HAA1-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 HAA1-3xV5 IAA7::URA3


title: HUWE1-CS, shWRNIP1, input, rep2

value: HUWE1-CS, shWRNIP1


title: embryoid bodies, 2day diff, rep2


title: HAC1_3IAA_C_S6_RNA-seq

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 HAC1-3xV5 IAA7::URA3


title: TGFBR1 WT/mut, replicate 9


title: HUWE1-CS, shCtrl, input, rep2

value: HUWE1-CS, shCtrl


title: HAA1_DMSO_B_S14_RNA-seq


title: embryoid bodies, 2day diff, rep1

value: cells


title: HUWE1-WT, shWRNIP1, input, rep2

value: HUWE1-WT, shWRNIP1


title: TGFBR1 WT/mut, replicate 8


title: HAA1_DMSO_A_S13_RNA-seq


title: HAA1_3IAA_C_S18_RNA-seq


title: HUWE1-WT, shCtrl, input, rep2

value: colon


title: TGFBR1 WT/mut, replicate 7


title: TGFBR1 WT/mut, replicate 6


title: HAA1_3IAA_B_S17_RNA-seq


title: HUWE1-CS, shWRNIP1, ChIP WRNIP1, rep1

value: WRNIP1 (Santa Cruz Biotechnology; Cat# sc-377402; Lot# l1516)


title: adherent differentiation, 2day diff


title: HAA1_3IAA_A_S16_RNA-seq


title: normal_inpt_nme2wt_m302

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

data_processing:
Trimming: The raw fastq files were processed by 5 prime trimming, keeping 30bp-length fragments, using fastx_trimmer [http://hannonlab.cshl.edu/fastx_toolkit/. Accessed 28 Feb. 2022.], with options -l 30 -Q33.
Alignment: The trimmed fastq files were aligned on the UCSC Mus_musculus mm10 genome using the Bowtie2 aligner (Langmead and Salzberg 2012) [PMID: 22388286], with options –end-to-end, –no-mixed, –no-discordant.
Assembly: UCSC Mus_musculus mm10 genome
Supplementary files format and content: big wig files (.bw) containing normalized integrated aligned read count signals.

source_name: liver

extract_protocol:
The RNA was isolated and purified from the liver tissue by NucleoSpin RNA kit (Machery-Nagel- 740955.50).
For sequencing, ChIP libraries were prepared using MicroPlex Library Preparation Kit v2 (Diagenode) according to manufacturer’s instructions. Each library was quantified on Qubit with Qubit® dsDNA HS Assay Kit (Life Technologies) and size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
The ChIP libraries were sequenced on a High-output flow cell (400M clusters) using the NextSeq® 500/550 High Output v2.5 150 cycles kit (Illumina), in paired-end 75/75nt mode, according to manufacturer’s instructions at the TGML Platform of Aix-Marseille University (France). Base calling was performed using RTA version 2.

tag: genotype/variation

tag: diet

value: normal

value: inpt


title: HUWE1-CS, shCtrl, ChIP WRNIP1, rep1

value: Colorectal carcinoma cell line

tag: genotype


title: CD8+ T cells, KO3 (p38α-/-p38beta-/-), biol rep 3

city: Xiamen

first: Lichen

last: Hu

state: Fujian

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

department: School of Life Sciences

institute: Xiamen University

data_processing:
Sequence reads were obtained from image data using CASAVA base discrimination
Sequence reads were trimmed for adaptor sequence/reads with undefined base/low-quality sequence (base with Qphred <= 20 at a proportion greater than 50%)
Trimmed sequence reads were mapped to GRCm38/mm10 using HISAT2 v2.0.5
New transcripts were predicted using StringTie (1.3.3b) (Mihaela Pertea.et al. 2015)
Read count extraction and normalization were performed using featureCounts (1.5.0-p3)
Assembly: GRCm38/mm10
Supplementary files format and content: txt file includes raw counts for each Sample
Supplementary files format and content: txt file includes FPKM values for each Sample

source_name: spleen

extract_protocol:
RNA was extracted using RNAiso Plus (Takara). 1 μg of total RNA was used for the construction of sequencing libraries.
mRNA was enriched from total RNA using Oligo(dT) magnetic bead, and then fragmented ramdonly. cDNA was synthesized from mRNA fragments using ramdon primers by M-MuLV reverse transcriptase. Thereafter RNA was degraded by RNaseH and the complementary DNA strand was synthesized by DNA polymerase I using dNTPs. After end repairing, polyA elongation and adding sequencing adaptor, around 370-420bp purified double strand cDNA was selected using AMPure XP beads. The cDNA was PCR amplified and further purified using AMPure XP beads to obtain the cDNA library.

treatment_protocol: 8 weeks old male mice were intraperitoneally infected with LCMV Armstrong at a dose of 2*105 PFU. 8 days later, splenic Db-GP33-41-tetramer+ CD8+ T cells were sorted by flowcytometry.

value: spleen

value: CD8+ T cell

value: Db-GP33-41-tetramer+ CD8+ T cell

value: LCMV, Day 8


title: CD8+ T cells, KO4 (p38α-/-p38beta-/-), biol rep 4


title: CD8+ T cells, KO2 (p38α-/-p38beta-/-), biol rep 2


title: HUWE1-WT, shWRNIP1, ChIP WRNIP1, rep1


title: GZF3_DMSO_C_S57_RNA-seq

city: SEATTLE

first: Lakshmi

last: Mahendrawada

address: 1100 FAIRVIEW AVE N

institute: Fred Hutchinson Cancer Center

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 GZF3-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GZF3-3xV5 IAA7::URA3


title: GZF3_DMSO_B_S56_RNA-seq


title: CD8+ T cells, KO1 (p38α-/-p38beta-/-), biol rep 1


title: normal_inpt_nme2ko_m293


title: HUWE1-WT, shCtrl, ChIP WRNIP1, rep1

value: HUWE1-WT, shCtrl


title: mESCs, undifferentiated

source_name: embryonic stem cell

value: embryonic stem cell


title: CD8+ T cells, WT4 (p38α+/+p38beta+/+), biol rep 4


title: GZF3_3IAA_C_S60_RNA-seq


title: CD8+ T cells, WT3 (p38α+/+p38beta+/+), biol rep 3


title: HUWE1-CS, shWRNIP1, ChIP pS2-RNAPII, rep1

value: HUWE1-CS, shWRNIP1

value: pS2-RNAPII (Active Motif; Cat# 61083; Lot# 32820004)


title: normal_chip_nme2wt_m302

value: chip


title: HUWE1-CS, shCtrl, ChIP pS2-RNAPII, rep1

value: HUWE1-CS, shCtrl


title: normal_inpt_nme2ko_m291


title: GZF3_3IAA_B_S59_RNA-seq


title: HUWE1-WT, shWRNIP1, ChIP pS2-RNAPII, rep1

value: HUWE1-WT, shWRNIP1


title: CD8+ T cells, WT1 (p38α+/+p38beta+/+), biol rep 1


title: GZF3_DMSO_A_S55_RNA-seq


title: normal_chip_nme2ko_m293


title: HUWE1-WT, shCtrl, ChIP pS2-RNAPII, rep1

value: colon


title: normal_chip_nme2ko_m291


title: Untreated adult mouse - rep 4

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Raw sequencing data were processed using the 10 Genomics Space Ranger pipeline to generate Fastq files
Sequences were aligned to the mm10 reference genome to produce gene expression counts using Space Ranger's default settings
Gene expression level of RefSeq coding genes were quantified using Space Ranger's default settings
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene Ids
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of th etissue and spots
Supplementary files format and content: scalefactors_jason.json.gz: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatual barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Liver

extract_protocol:
Livers were collected and snap frozen in isopentane, then embedded in Killik OCT on dry ice. 5-µm slices were cut using Leica cryostat CM1860 and put on commercial Visium 10X slides
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manifacturer's construction

value: Liver

value: Adult

value: Untransduced


title: HUWE1-CS, shWRNIP1, ChIP RNAPII, rep1

value: Colorectal carcinoma cell line

value: RNAPII (Active Motif; Cat# 101307; Lot# 08322043)


title: GLN3_DMSO_B_S8_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 GLN3-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GLN3-3xV5 IAA7::URA3


title: GZF3_3IAA_A_S58_RNA-seq


title: GLN3_DMSO_C_S9_RNA-seq


title: CD8+ T cells, WT2 (p38α+/+p38beta+/+), biol rep 2

value: spleen

value: CD8+ T cell

value: Db-GP33-41-tetramer+ CD8+ T cell


title: GLN3_DMSO_A_S7_RNA-seq


title: normal_inpt_nme2wt_m301

value: normal

value: inpt


title: HUWE1-CS, shCtrl, ChIP RNAPII, rep1


title: HUWE1-WT, shWRNIP1, ChIP RNAPII, rep1


title: Untreated adult mouse - rep 3


title: normal_chip_nme2wt_m301


title: hghfat_inpt_nme2wt_m300

value: high fat diet (hghfat)


title: GLN3_3IAA_C_S12_RNA-seq


title: Untreated adult mouse - rep 2


title: Untreated adult mouse - rep 1


title: hghfat_inpt_nme2ko_m292


title: HUWE1-WT, shCtrl, ChIP RNAPII, rep1

value: HUWE1-WT, shCtrl


title: HUWE1-CS, shWRNIP1, input, rep1

value: HUWE1-CS, shWRNIP1

value: none (input)


title: LV treated adult mouse - rep 4

value: LV-transduced


title: hghfat_inpt_nme2ko_m273


title: LV treated adult mouse - rep 3


title: GLN3_3IAA_B_S11_RNA-seq


title: hghfat_inpt_nme2wt_m303


title: GCR2_DMSO_C_S57_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 GCR2-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GCR2-3xV5 IAA7::URA3


title: GCR2_DMSO_B_S56_RNA-seq


title: LV treated adult mouse - rep 2

value: Liver


title: LV treated adult mouse - rep 1

value: Adult


title: HUWE1-WT, shCtrl, input, rep1

value: colon


title: hghfat_chip_nme2ko_m292

value: chip


title: GCR2_DMSO_A_S55_RNA-seq


title: GCR2_3IAA_C_S60_RNA-seq


title: Untreated juvenile mouse - rep 4

value: Juvenile

value: Untransduced


title: nme2wt_normal_rep4

data_processing:
Aligment: The sequenced reads from the raw sequence (.fastq files) were aligned on the UCSC mm10 genome using the STAR software (2.7.1a) (Dobin et al. 2013) [PMID:23104886] to produce bam files.
Counts: The aligned reads (.bam files) were counted using HTSeq framework (0.11.2) (Anders et al. 2015) [PMID:25260700], with options: -t exon -f bam -r pos –stranded=reverse -m intersection-strict –nonunique none.
Assembly: UCSC mm10
Supplementary files format and content: counts

extract_protocol:
The RNA was isolated and purified from the liver tissue by NucleoSpin RNA kit (Machery-Nagel- 740955.50). Four independent RNA extractions were performed for each condition.
For each sample, one µg of RNA (RIN = 10) was used for library preparation with TruSeq Stranded Total RNA (RiboZero Human/Mouse/Rat) Library Prep (Illumina, Cat#RS-122-2201) according to the manufacturer’s instructions. Each library was quantified on Qubit with the Qubit® dsDNA HS Assay Kit (Life Technologies) and the size distribution was examined on the Fragment Analyzer with High Sensitivity NGS Fragment Analysis kit (Agilent).
The libraries were then sequenced on the Illumina NextSeq 500 (paired-end 75) at the TGML Platform of Aix-Marseille University (France).

value: liver


title: hghfat_chip_nme2ko_m273


title: HCT116 cells, HUWE1-WT, rep 3

description:
CS_vs_WT.txt
RNAseq_FC19EE32_WT_rep3

data_processing:
Sequencing was performed on the Illumina NovaSeq 6000 instrument (1 x 100 bp)
Demultiplexing of the sequencing reads was performed with Illumina bcl2fastq (2.20). Adapters were trimmed with Skewer (version 0.2.2).
Reads were aligned to human genome (hg19) with STAR (2.5.4) and differentially expressed genes were determined using EdgeR (3.26.8).
Assembly: hg19
Supplementary files format and content: Tab-delimited text files (EdgeR output) include differential expression (log2FC) and average logCPM values for each pair of samples
Supplementary files format and content: Tab-delimited text files (EdgeR output) include tag counts per gene and sample

extract_protocol:
RNA was harvested using TRI Reagent® (Sigma). 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared NEBNext® Ultra™ II RNA Library Prep Kit for Illumina with the magnetic mRNA isolation module following manufacturer's protocols.

value: Colorectal carcinoma cell line


title: GLN3_3IAA_A_S10_RNA-seq

extract_protocol:
Experiments were done as previously described (Donczew et al., 2021 [PMID: 34137374]). Detailed protocol is available in publication accompaning this submission.
Ovation Universal RNA-seq System kit (Tecan) was used for library construction.

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GLN3-3xV5 IAA7::URA3


title: hghfat_chip_nme2wt_m303


title: Untreated juvenile mouse - rep 3


title: GCR2_3IAA_B_S59_RNA-seq


title: LV treated juvenile mouse - rep 4


title: HUWE1-CS, shCtrl, input, rep1

value: HUWE1-CS, shCtrl


title: GCR2_3IAA_A_S58_RNA-seq


title: nme2wt_normal_rep3

value: normal


title: nme2wt_normal_rep2


title: HCT116 cells, HUWE1-WT, rep 2

description:
CS_vs_WT.txt
RNAseq_FC19EE29_WT_rep2


title: hghfat_chip_nme2wt_m300

value: high fat diet (hghfat)


title: HUWE1-WT, shWRNIP1, input, rep1

value: HUWE1-WT, shWRNIP1


title: LV treated juvenile mouse - rep 3


title: Untreated juvenile mouse - rep 2


title: nme2wt_normal_rep1


title: GCN4_DMSO_SM_120_B_S18_RNA-seq

source_name: MATα ∆ade2::hisG his3∆200 leu2∆0 lys2∆0 met15∆0 trp1∆63 ura3∆0 pGPD1-OSTIR::HIS3 GCN4-3xV5 IAA7::URA3

value: MAT{alpha} {delta}ade2::hisG his3{delta}200 leu2{delta}0 lys2{delta}0 met15{delta}0 trp1{delta}63 ura3{delta}0 pGPD1-OSTIR::HIS3 GCN4-3xV5 IAA7::URA3

value: SM starvation


title: HCT116 cells, HUWE1-CS, rep 3

description:
CS_vs_P.txt
RNAseq_FC19EE33_CS_rep3


title: Untreated juvenile mouse - rep 1


title: HCT116 cells, parental, rep 2

description:
WT_vs_P.txt
RNAseq_FC19EE28_P_rep2

value: parental


title: nme2wt_hghfat_rep4

value: hghfat


title: GCN4_DMSO_SM_120_A_S6_RNA-seq


title: HCT116 cells, HUWE1-CS, rep 1

description:
CS_vs_P.txt
RNAseq_FC19EE27_CS_rep1


title: nme2wt_hghfat_rep3


title: HCT116 cells, parental, rep 3

description:
WT_vs_P.txt
RNAseq_FC19EE31_P_rep3


title: GCN4_DMSO_SM_60_C_S29_RNA-seq


title: HCT116 cells, HUWE1-CS, rep 2

description:
CS_vs_P.txt
RNAseq_FC19EE30_CS_rep2


title: GCN4_DMSO_SM_120_C_S30_RNA-seq


title: LV treated juvenile mouse - rep 2

value: Liver

value: LV-transduced


title: nme2wt_hghfat_rep2


title: HCT116 cells, HUWE1-WT, rep 1

description:
CS_vs_WT.txt
RNAseq_FC19EE26_WT_rep1


title: nme2wt_hghfat_rep1


title: LV treated juvenile mouse - rep 1


title: GCN4_DMSO_SM_60_B_S17_RNA-seq


title: Untreated newborn mouse - rep 4

value: Newborn


title: GCN4_DMSO_SM_60_A_S5_RNA-seq


title: HCT116 cells, parental, rep 1

description:
WT_vs_P.txt
RNAseq_FC19EE25_P_rep1


title: GCN4_DMSO_SM_30_C_S28_RNA-seq


title: D, spatial transcriptomics

city: Chengdu

first: Hao

last: Xu

state: China

address: No.17 section3 renmin south road, chengdu

institute: Sichuan university

description:
This library only has one sample, D_sample1 (female, 54 years old). This sample was obtained from buccal mucosa. According to whether erosion of oral mucosa in the biopsy, this sample was grouped as: EOLP. And according to whether erosion occurred in oral mucosa more than once within a one-year follow-up, this sample was grouped as: NA.
10x_visium

data_processing:
The data was processed by FastQC software and Space Ranger software (https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: spatial transcriptomics

source_name: buccal mucosa

extract_protocol:
Samples were frozen embedded on dry ice. Frozen tissues were sectioned (10μm) and attached to ST microarrays (https://www.10xgenomics.com/). On the one hand, slides were dehydrated, stained with HE, and imaged by a 3D HISTECH Pannoramic MIDI FL scanner.
On the other hand, slides were permeated and obtained fluorescently labeled cDNA. The cDNA was digested and fragmented to construct the NDA library. And the NDA library was sequenced using the lllumina novaseq 6000 system.

value: buccal mucosa


title: nme2ko_normal_rep4


title: C, spatial transcriptomics

description:
This library has two different samples, including C_sample1 (male, 47 years old) and C_sample2 (male, 43 years old). These samples were both obtained from normal oral buccal mucosa.
10x_visium


title: nme2ko_normal_rep3


title: GCN4_DMSO_SM_30_B_S16_RNA-seq


title: Untreated newborn mouse - rep 3


title: nme2ko_normal_rep2


title: Untreated newborn mouse - rep 1


title: B2, spatial transcriptomics

description:
This library has three different samples, including B2_sample1 (female, 45 years old), B2_sample2 (female, 50 years old), and B2_sample3 (female, 38 years old). These samples were obtained from buccal mucosa. According to whether erosion of oral mucosa in the biopsy, these samples were grouped as: NEOLP (B2_sample1), NEOLP (B2_sample2), and NEOLP (B2_sample3). And according to whether erosion occurred in oral mucosa more than once within a one-year follow-up, these samples were grouped as: NA (B2_sample1), EOLP (B2_sample2), and NEOLP (B2_sample3).
10x_visium


title: Untreated newborn mouse - rep 2


title: nme2ko_normal_rep1