title: hda6_rnaseq_rep3

description:
gene_hda6_vs_WT_exp.txt
TE_hda6_vs_WT_exp.txt

value: hda6 T-DNA insertion line


title: hda6_rnaseq_rep2

status: Public on May 10 2021

type: SRA

city: Shenzhen

first: Xishi

last: Zhou

address: No 7, Pengfei Road

country: China

institute: Shenzhen agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences

library_source: transcriptomic

data_processing:
RNA-seq: Illumina CASAVA software was used for basecalling
RNA-seq: sequenced reads were trimmed to remove adapter and low quality reads with Tim Galore v 0.6.6 program
RNA-seq: clean reads were mapped to the TAIR10 Arabidopsis genome using TopHat v 2.0.12 program with parameter --b2-very-sensitive
RNA-seq: the differentially expressed genes and TEs were identified using “Cuffdiff” program of Cufflinks v 2.2.1 , which uses the normalized RNA-seq fragment counts to measure the relative abundances of the genes
ChIP-seq: Illumina CASAVA software was used for basecalling
ChIP-seq: sequenced reads were trimmed to remove adapter and low quality reads with Tim Galore v 0.6.6 program
ChIP-seq: clean reads were mapped to the TAIR10 Arabidopsis genome using Bowtie v2.4.1 with default parameters
ChIP-seq: PCR duplicates were removed by Sambamba v 0.6.6 program
ChIP-seq: peaks were called using MACS2 v 2.1.1.20160309 program with parameters -g 1.2e8 -B -q 0.05
ChIP-seq:  differentially enriched peaks were determined by DiffBind R package in Bioconductor
ChIP-seq: the read count falling in each gene region which used for generating RPKM(reads per kilobase per million) value for each gene was calculated by “intersect” command from the BEDTools suite.
Genome_build: tair10
Supplementary_files_format_and_content: RNA-seq: tab-delimited text files include the log2(fold_change) of normalized read counts and P value for wild type and each mutant to figure out the differentially expressed genes and transposons(TEs)
Supplementary_files_format_and_content: ChIP-seq: tab-delimited text files include RPKM value of each gene for wild type, sant1234-null and hda6, and .csv files include  the log2 (fold_change) of  normalized read counts falling in each peak and FDR value for wild type, sant1234-null and hda6 to figure out the  differentially enriched peaks

molecule: total RNA

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Arabidopsis seeds were sown on 1/2 MS medium plates plates under a long-day photoperiod with 16 h of light at 24 °C and 8 h of darkness at 22 °C, and 12-day-old seedlings were harvested for RNA-seq and ChIP-seq experiments.

extract_protocol:
For RNA-seq: seedling samples were harvested and frozen immediately in liquid nitrogen and total RNA was extracted with TRIzol reagent (Invitrogen). For ChIP-seq: histone-DNA complexes were isolated with anti-acetylated Histone H3 antibody .
Both of the RNA-seq and ChIP-seq libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: untreated

tag: treatment

value: untreated

tag: genotype


title: ATAC-seq in HeLa cells in complete DMEM

city: Oxford

first: Thomas

middle: A

last: Milne

address: John Radcliffe Hospital, Headington

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

library_source: genomic

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using MACS2
Statistical analysis using Diffbind (EdgeR)

molecule: genomic DNA

organism: Homo sapiens

source_name: Cervical cancer cell line (HeLa)

growth_protocol: Cells were grown in normal or SILAC RPMI or DMEM medium (with the addition of arginine where indicated), supplemented with 10% FCS and glutamax (Life Technologies)

extract_protocol:
Cells were washed with PBS and lysed with 0.1% IGEPAL CA-630, followed by Tn5 transposase treatment
Libraries were made using the Nextera DNA library prep kit (Illumina)

treatment_protocol: Human CD4+ T-cells were purified from PBMCs isolated from commercially available leukocyte cones (NHS Blood and Transplant, Bristol, UK) by magnetic-activated cell sorting (MACS) purification using CD4 Microbead kits (Miltenyi Biotec) then stimulated (where indicated) using anti-CD3/CD28 antibodies (Life Technologies). Cells were cultured in full, low (20uM) arginine or arginine-free medium for 72h prior to harvest, with the addition of 20 nM rapamycin where indicated. HeLa cells were cultured in full or arginine-free medium for 72h prior to harvest.

tag: tissue

value: Cervical cancer cell line (HeLa)

value: Cells cultured in DMEM for 72h

tag: cell type

value: Cell line derived from human cervical carcinoma


title: ATAC-seq in unstimulated CD4 T-cells rep 5

source_name: Unstimulated human CD4 T-cells

value: Unstimulated human CD4 T-cells

value: Cells cultured in RPMI for 72h

value: Human CD4+ T-cells purified from PBMCs without stimulation


title: Control 3h 1

city: Aurora

first: Ian

middle: M

last: Cartwright

state: Colorado

department: Medicine

country: USA

institute: University of Colorado Anschutz Medical Campus

data_processing:
CASAVA software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
Mapping of clean reads to the reference genome was done using STAR software
Fragments Per Kilobase of transcipt per Mllion mapped reads (FPKM) were calculated.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each sample. Matrix table with raw gene counts for every gene and every sample

source_name: Intestinal epithelia cell

growth_protocol: T84 cells were grown to confluency in 6 well plates following protocol provided by ATCC

extract_protocol:
RNA was harvested using Tizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Media was replaced with Hanks buffered saline at pH 7.4 or 6.0. Cells were exposed for 3 or 6 hours

tag: cell line

value: Intestinal epithelia

value: pH 7.4, 3 hour


title: WT_chipseq_input_rep1

value: wild type


title: OL_WT_Pol II

city: Shanghai

first: Chenxi

last: He

address: 131 Dong'an Rd, Mingdao Bldg, Rm 512

institute: Fudan University

data_processing:
Basecalls performed using bcl2fastq
ChIP-seq reads (only R1) were aligned to the mm10 genome assembly using bowtie (version 1.2.2)
peaks were called using macs2(v2.1.2) with the following setting: macs2 callpeak -f BAM -g mm -q 0.05 -t ChIP.bam -n NAME -c INPUT.bam
Genome_build: mm10
Supplementary_files_format_and_content: bed files were generated using macs2

organism: Mus musculus

source_name: differentiated oligodendrocyte

growth_protocol: Neural stem cells were differentiated in Neurobasal medium containing B-27, 2 mM GlutaMAX-I, 30 ng/mL 3,3',5-Triiodo-L-thyronine (T3), 50 U/mL penicillin G, and 50 mg/mL streptomycin

extract_protocol:
Cells were crosslinked, sonicated and  then incubated with Qki-5, Srebp2, and Pol II antibodies. Protein-DNA complex were washed and ChIP'ed DNA were isolated for library preparation.
Libraries were prepared by KAPA Hyper Prep Kit (KK8504, Kapa Biosystems).

value: differentiated oligodendrocyte from neural stem cell

tag: passages

tag: strain

value: FvB/C57BL6 hybrid

tag: chip antibody

value: RNA polymerase II CTD repeat YSPTSPS (Abcam, Cat# ab817)


title: ATAC-seq in CD4 T-cells cells treated with rapamycin rep 5

source_name: Stimulated human CD4 T-cells

value: Stimulated human CD4 T-cells

value: Cells cultured in RPMI in the presence of 20 nM rapamycin for 72h

value: Human CD4+ T-cells purified from PBMCs, stimulated with anti-CD3/anti-CD28 beads


title: hda6_rnaseq_rep1

value: hda6 T-DNA insertion line


title: sant1234-null_rnaseq_rep3

description:
gene_sant1234-null_vs_WT_exp.txt
TE_sant1234-null_vs_WT_exp.txt

value: untreated

value: sant1234-null quadruple mutants


title: ATAC-seq in CD4 T-cells cells in arginine-free medium rep 5

value: Cells cultured in arginine-free RPMI for 72h


title: postnatal skeletal muscle at P4, biological rep2

type: RNA

city: Prague 2

first: Jana

last: Krizova

state: Non United States Or Canada

address: Ke Karlovu 2

department: Department of Pediatrics and Inherited Metabolic Disorders

country: Czech Republic

institute: Charles University in Prague, First Faculty of Medicine, and General University Hospital in Prague

description:
RaGene1_120313W_JZ22_B4
RaGene1_120313W_JZ01_B4
Gene expression data from neonatal skeletal muscle tissue, fourth postnatal day, suckling period.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45 °C on Rat Gene 1.0 ST Array. Arrays were scanned according to the protocol described in WT Sense Target Labeling Assay Manual (FS450_0007).

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with Expression console, using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

organism: Rattus norvegicus

source_name: Rat 4-day old skeletal muscle

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5.5 ug total RNA (RIN>8) using Ambion WT kit.

growth_protocol: The animals were kept and all rat tissues were obtained in the Department of Genetics of Model Diseases, Institute of Physiology CAS (Prague, Czech Republic). The experiments were performed in agreement with the Animal Protection Law of the Czech Republic and were approved by the Ethics Committee of the Institute of Physiology AS CR (Prague, Czech Republic).

extract_protocol: TriReagent extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: The fetuses were delivered by Caesarean section after sacrifice of pregnant Wistar rat mothers. Adult P90 controls were collected. All tissues were snap frozen in liquid nitrogen immediately. Tissues were stored for further analyses at -80 °C.

value: Wistar rat

tag: age

value: 4-day old newborn

value: skeletal muscle


title: fetal skeletal muscle at F22, biological rep4

description:
RaGene1_120313W_JZ14_D22
RaGene1_120313W_JZ01_D22
Gene expression data from fetal skeletal muscle tissue, last gestational day.

source_name: Rat 22-day old fetal skeletal muscle, last day before birth

value: 22-day old fetus


title: postnatal skeletal muscle at P1, biological rep2

description:
RaGene1_120313W_JZ02_B1
RaGene1_120313W_JZ01_B1
Gene expression data from neonatal skeletal muscle tissue, first postnatal day. Postanatal adaptation proceeds.

source_name: Rat newborn skeletal muscle, first day of life

value: 1-day old newborn


title: fetal skeletal muscle at F20, biological rep5

description:
RaGene1_120313W_JZ10_E20
RaGene1_120313W_JZ01_E20
Gene expression data from fetal skeletal muscle tissue, two day before birth.

source_name: Rat 20-day old fetal skeletal muscle

value: 20-day old fetus


title: postnatal skeletal muscle at P1, biological rep3

description:
RaGene1_120313W_JZ03_C1
RaGene1_120313W_JZ01_C1
Gene expression data from neonatal skeletal muscle tissue, first postnatal day. Postanatal adaptation proceeds.


title: postnatal skeletal muscle at P1, biological rep1

description:
RaGene1_120313W_JZ01_A1
RaGene1_120313W_JZ01_A1
Gene expression data from neonatal skeletal muscle tissue, first postnatal day. Postanatal adaptation proceeds.


title: fetal skeletal muscle at F22, biological rep3

description:
RaGene1_120313W_JZ13_C22
RaGene1_120313W_JZ01_C22
Gene expression data from fetal skeletal muscle tissue, last gestational day.


title: fetal skeletal muscle at F20, biological rep4

description:
RaGene1_120313W_JZ09_D20
RaGene1_120313W_JZ01_D20
Gene expression data from fetal skeletal muscle tissue, two day before birth.


title: postnatal skeletal muscle at P1, biological rep4

description:
RaGene1_120313W_JZ04_D1
RaGene1_120313W_JZ01_D1
Gene expression data from neonatal skeletal muscle tissue, first postnatal day. Postanatal adaptation proceeds.


title: postnatal skeletal muscle at P1, biological rep5

description:
RaGene1_120313W_JZ05_E1
RaGene1_120313W_JZ01_E1
Gene expression data from neonatal skeletal muscle tissue, first postnatal day. Postanatal adaptation proceeds.


title: fetal skeletal muscle at F22, biological rep1

description:
RaGene1_120313W_JZ11_A22
RaGene1_120313W_JZ01_A22
Gene expression data from fetal skeletal muscle tissue, last gestational day.


title: postnatal skeletal muscle at P4, biological rep3

description:
RaGene1_120313W_JZ23_C4
RaGene1_120313W_JZ01_C4
Gene expression data from neonatal skeletal muscle tissue, fourth postnatal day, suckling period.


title: WT_chipseq_input_rep2

value: wild type


title: postnatal skeletal muscle at P4, biological rep1

description:
RaGene1_120313W_JZ21_A4
RaGene1_120313W_JZ01_A4
Gene expression data from neonatal skeletal muscle tissue, fourth postnatal day, suckling period.


title: fetal skeletal muscle at F22, biological rep5

description:
RaGene1_120313W_JZ15_E22
RaGene1_120313W_JZ01_E22
Gene expression data from fetal skeletal muscle tissue, last gestational day.


title: postnatal skeletal muscle at P4, biological rep5

description:
RaGene1_120313W_JZ25_E4
RaGene1_120313W_JZ01_E4
Gene expression data from neonatal skeletal muscle tissue, fourth postnatal day, suckling period.


title: postnatal skeletal muscle at P4, biological rep4

description:
RaGene1_120313W_JZ24_D4
RaGene1_120313W_JZ01_D4
Gene expression data from neonatal skeletal muscle tissue, fourth postnatal day, suckling period.


title: sant1234-null_rnaseq_rep2

description:
gene_sant1234-null_vs_WT_exp.txt
TE_sant1234-null_vs_WT_exp.txt


title: fetal skeletal muscle at F22, biological rep2

description:
RaGene1_120313W_JZ12_B22
RaGene1_120313W_JZ01_B22
Gene expression data from fetal skeletal muscle tissue, last gestational day.


title: ATAC-seq in CD4 T-cells cells in low arginine medium rep 5

value: Cells cultured in low (20uM) arginine RPMI for 72h


title: DNMT1-siRNA2 [si2_3]

city: Paris

first: Eric

last: Batsche

address: 7-9, Quai Saint Bernard

department: B2A Biological Adaptation and Ageing - UMR8256 CNRS

country: France

institute: IBPS - Institut Biologie Paris Seine

description: RMA expression value derived from Expression Console software; all-exon analysis

hyb_protocol: Samples were hybridized with GeneChip Human Exon 1.0 ST Arrays (Affymetrix) and scanned at the Institut Pasteur Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing:
Analysis was performed by GenoSplice (http://www.genosplice.com). Only genes expressed in the cells for at least in one of the two compared conditions and giving a signal of good quality probes were considered for further analysis. Significant variations (P< 0.05) in exon variation above 20% were taken into account.
affymetrix-algorithm-name = rma-exon-all : dabg
affymetrix-algorithm-version = 1.0
affymetrix-array-type = HuEx-1_0-st-v2
program-name = Expression Console
program-version = 1.0.2467.39138

label_protocol: Single-stranded cDNA was generated from the amplified cRNA with the WT cDNA Synthesis Kit (Affymetrix) and then fragmented and labeled with the WT Terminal Labeling Kit (Affymetrix).

growth_protocol: HeLa cells (CCL-2, from ATCC)  were maintained in Dulbecco’s modified Eagle’s medium (Gibco) supplemented with 7% (v/v) fetal bovine serum (Thermo Scientific) and 100 U/ml penicillin-streptomycin (Gibco).

extract_protocol: Cytoplasmic enriched total RNA was extracted by homogenizing the cells in TMS buffer (10 mM TRIS pH8, 250 mM NaCl, 1 mM MgCl2 , 1% NP40, 20 mM DTT, 1U/µL RNasin) for 15 min on ice. After quickly spinning out the nuclei and debris, supernatant was supplemented with 0.5% SDS and 2 mM EDTA before extraction by phenol-chloroform, and isopropanol-precipitation. RNase-free TURBO DNase (Ambion; Sigma) -treated RNAs were checked on agarose gel for their quality

treatment_protocol: HeLa cells were transfected twice with 2 independent siRNA (20 nM) targeting DNMT1 and GAPDH used as negative control, and RNAi Max reagent (Life Technologies) according to the reverse transfection protocol. The second round of transfection was performed 48 h after the first one, and the cells were collected after 72h.

tag: cell line background

value: HeLa

tag: genotype/variation


title: mbd124_rnaseq_rep3

description:
gene_mbd124_vs_WT_exp.txt
TE_mbd124_vs_WT_exp.txt

value: mbd1/2/4 triple mutants


title: mbd124_rnaseq_rep2


title: fetal skeletal muscle at F20, biological rep2

description:
RaGene1_120313W_JZ07_B20
RaGene1_120313W_JZ01_B20
Gene expression data from fetal skeletal muscle tissue, two day before birth.


title: fetal skeletal muscle at F20, biological rep3

description:
RaGene1_120313W_JZ08_C20
RaGene1_120313W_JZ01_C20
Gene expression data from fetal skeletal muscle tissue, two day before birth.


title: fetal skeletal muscle at F20, biological rep1

description:
RaGene1_120313W_JZ06_A20
RaGene1_120313W_JZ01_A20
Gene expression data from fetal skeletal muscle tissue, two day before birth.


title: sant1234-null_rnaseq_rep1


title: ATAC-seq in CD4 T-cells cells treated with rapamycin rep 4

value: Stimulated human CD4 T-cells


title: ATAC-seq in CD4 T-cells cells in arginine-free medium rep 4


title: Control 3h 3

value: Intestinal epithelia

value: pH 7.4, 3 hour


title: hhp1_rnaseq_rep3

description:
gene_hhp1_vs_WT_exp.txt
TE_hhp1_vs_WT_exp.txt

value: hhp1 T-DNA insertion line


title: fetal skeletal muscle at F16, biological rep1

description:
RaGene1_120313W_JZ26_A16
RaGene1_120313W_JZ01_A16
Gene expression data from fetal skeletal muscle tissue.

source_name: Rat 16-day old fetal skeletal muscle

value: 16-day old fetus


title: fetal skeletal muscle at F16, biological rep5

description:
RaGene1_120313W_JZ30_E16
RaGene1_120313W_JZ01_E16
Gene expression data from fetal skeletal muscle tissue.


title: ATAC-seq in CD4 T-cells cells in full medium rep 5

value: Cells cultured in RPMI for 72h

value: Human CD4+ T-cells purified from PBMCs, stimulated with anti-CD3/anti-CD28 beads


title: mbd124_rnaseq_rep1

value: untreated


title: ATAC-seq in CD4 T-cells cells in low arginine medium rep 4


title: GAPDH-siRNA (control) [C_2]

source_name: HeLa_GAPDH-siRNA (control)

value: GAPDH-siRNA (control)


title: fetal skeletal muscle at F16, biological rep4

description:
RaGene1_120313W_JZ29_D16
RaGene1_120313W_JZ01_D16
Gene expression data from fetal skeletal muscle tissue.

value: Wistar rat

value: skeletal muscle


title: fetal skeletal muscle at F16, biological rep2

description:
RaGene1_120313W_JZ27_B16
RaGene1_120313W_JZ01_B16
Gene expression data from fetal skeletal muscle tissue.


title: postnatal adult liver, biological rep2

description:
RaGene1_91812W_JZ22_22
RaGene1_91812W_JZ01_22
Gene expression data from adult liver tissue, 3-month old rat on standard chow.

source_name: Rat adult control liver

value: 90-day old adult

value: liver


title: fetal skeletal muscle at F16, biological rep3

description:
RaGene1_120313W_JZ28_C16
RaGene1_120313W_JZ01_C16
Gene expression data from fetal skeletal muscle tissue.


title: hhp1_rnaseq_rep2


title: postnatal adult liver, biological rep3

description:
RaGene1_91812W_JZ23_23
RaGene1_91812W_JZ01_23
Gene expression data from adult liver tissue, 3-month old rat on standard chow.


title: postnatal adult liver, biological rep4

description:
RaGene1_91812W_JZ24_24
RaGene1_91812W_JZ01_24
Gene expression data from adult liver tissue, 3-month old rat on standard chow.


title: DNMT1-siRNA2 [si2_2]


title: postnatal adult liver, biological rep1

description:
RaGene1_91812W_JZ21_21
RaGene1_91812W_JZ01_21
Gene expression data from adult liver tissue, 3-month old rat on standard chow.


title: ATAC-seq in CD4 T-cells cells in full medium rep 4


title: hhp1_rnaseq_rep1


title: postnatal liver at P4, biological rep3

description:
RaGene1_91812W_JZ19_19
RaGene1_91812W_JZ01_19
Gene expression data from neonatal liver tissue, fourth postnatal day.

source_name: Rat 4-day old liver

value: 4-day old newborn


title: postnatal liver at P4, biological rep4

description:
RaGene1_91812W_JZ20_20
RaGene1_91812W_JZ01_20
Gene expression data from neonatal liver tissue, fourth postnatal day.


title: WT_rnaseq_rep3

value: wild type


title: ATAC-seq in unstimulated CD4 T-cells rep 3

description:
Tcell_ATAC_ArgVsUnstim_Diffbind.txt.gz
Tcell_ATAC_noArgVsUnstim_Diffbind.txt.gz

value: Unstimulated human CD4 T-cells

value: Human CD4+ T-cells purified from PBMCs without stimulation


title: ATAC-seq in unstimulated CD4 T-cells rep 2


title: WT_rnaseq_rep2


title: DNMT1-siRNA1 [si1_1]

description: RMA expression value derived from Expression Console software; all-exon analysis

value: HeLa


title: WT_rnaseq_rep1


title: ATAC-seq in unstimulated CD4 T-cells rep 1


title: postnatal liver at P4, biological rep2

description:
RaGene1_91812W_JZ18_18
RaGene1_91812W_JZ01_18
Gene expression data from neonatal liver tissue, fourth postnatal day.


title: GAPDH-siRNA (control) [C_3]


title: GAPDH-siRNA (control) [C_1]


title: CD4 T-cell ATF4/CEBPb noArg rx Input

description:
Input for reference-normalized ATF4 and CEBPb ChIP-seq in THP1 cells cultured in the absence of arginine
Tcell_ATF4_noArg_rx_peaks.txt.gz
Tcell_CEBPb_noArg_rx_peaks.txt.gz

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using Homer v4.7

growth_protocol: Cells were grown in RPMI medium supplemented with 10% FCS and glutamax (Life Technologies)

extract_protocol:
Cells were washed with PBS and fixed in 2mM DSG for 30 minutes and 1% FA for 30 minutes. Fixed Drosophila S2 cells were added at a 1:4 ratio (Dm:Hs) to allow reference normalization. Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

treatment_protocol: THP1 cells were cultured in full, low arginine (20uM), or arginine-free medium for 72h prior to harvest. Human CD4+ T-cells were purified from PBMCs isolated from commercially available leukocyte cones (NHS Blood and Transplant, Bristol, UK) by magnetic-activated cell sorting (MACS) purification using CD4 Microbead kits (Miltenyi Biotec) then stimulated using anti-CD3/CD28 antibodies (Life Technologies). Cells were cultured in full, low (20uM) arginine or arginine-free medium for 72h prior to harvest.

value: Stimulated human CD4 T-cells

value: Cells cultured in arginine-free RPMI for 72h


title: postnatal liver at P4, biological rep1

description:
RaGene1_91812W_JZ17_17
RaGene1_91812W_JZ01_17
Gene expression data from neonatal liver tissue, fourth postnatal day.


title: Human kidney sample - snATAC-seq_rep2

city: Philadelphia

first: Xin

last: Sheng

institute: University of Pennsylvania

data_processing:
Basecalls performed using cellranger-atac mkfastq. Read alignment, deduplication and transposase cut site identification were performed using the Cell Ranger ATAC (version 1.1.0 from 10×Genomics®). Sequencing reads were aligned to the hg19 (b37) reference genome and the resulted sorted bam files were hierarchically structured into hdf5 snapfiles (single-nucleus accessibility profiles) using snaptools (version 1.4.8). Quality control was further conducted using SnapATAC (version 1.0.0). Only cells with logUMI in [3-5] and promoter ratio in [0.25-0.6] were retained. The top 5% cells with high mitochondria ratio were removed for each sample. We binarized fragments into 5 kb bins and removed bins overlapping with the ENCODE blacklist, mitochondria, chrX, chrY and ambiguous chromosomes, as well as the top 5% bins that overlap with invariant features (such as housekeeping gene promoters). Cells with bin coverage less than 1,000 were excluded. A nonlinear diffusion map algorithm embedded in function runDiffusionMaps of the SnapATAC package was utilized to perform dimensionality reduction and 50 eigenvectors were analyzed and the first 22 eigenvectors were then selected in order to generate K Nearest Neighbor (KNN) graph with K=18. Batch effect correction was performed using an iterative batch correction method Harmony (v1.0). We next performed clustering using Leiden algorithm (leiden package version 0.3.3) with a resolution of 0.5. and 2 UMAP (uniform Manifold Approximation and Projection) embeddings were generated using UMAP package (version 0.2.5.0) to visualize the data. Fragments originating from cells belonging to the same clusters were pooled using snaptools. For each cluster, peaks were called on the Tn5-corrected insertions (each end of the Tn5-corrected fragments) for each cell type separately using MACS2 (v2.2.6) with parameters “--nomodel --keep-dup all --shift 100 --ext 200 --qval 5e-2 -B --SPMR --call-summits --nolambda”.
Genome_build: hg19 (b37)
Supplementary_files_format_and_content: Compressed bed (open chromatin regions) and txt files (cluster labels)

source_name: Human kidney

growth_protocol: Human kidney samples were obtained from the non-tumor tissue of partial or radical nephrectomy patients from the Hospital of the University of Pennsylvania

extract_protocol:
Kidneys were minced and lysed in 2 mL lysis buffer for 15 min. Tissue lysis reaction was then blocked by adding 10 mL 1x PBS into each tube, and solution was passed through a 40 μm cell strainer. Cell debris and cytoplasmic contaminants were removed by Nuclei PURE Prep Nuclei Isolation Kit (Sigma, NUC-201) after centrifugation at 13,000 RPM for 45 min.
Libraries were prepared according to 10x Genomics's instructions (CG000209) accompanying the Chromium Next GEM Single Cell ATAC Reagent Kits v1.1.
Single nuclei ATAC-seq

tag: gender

value: Male

tag: race

value: African American

value: Kidney

tag: disease state

value: Healthy


title: postnatal liver at P1, biological rep2

description:
RaGene1_91812W_JZ14_B
RaGene1_91812W_JZ01_B
Gene expression data from neonatal liver tissue, first postnatal day. Postanatal adaptation proceeds.

source_name: Rat newborn liver, first day of life

value: 1-day old newborn


title: postnatal liver at P1, biological rep3

description:
RaGene1_91812W_JZ15_D
RaGene1_91812W_JZ01_D
Gene expression data from neonatal liver tissue, first postnatal day. Postanatal adaptation proceeds.


title: CD4 T-cell ATF4/CEBPb fullArg rx Input

description:
Input for reference-normalized ATF4 and CEBPb ChIP-seq in THP1 cells cultured in complete RPMI
Tcell_ATF4_Arg_rx_peaks.txt.gz
Tcell_CEBPb_Arg_rx_peaks.txt.gz

value: Cells cultured in RPMI for 72h

value: Human CD4+ T-cells purified from PBMCs, stimulated with anti-CD3/anti-CD28 beads


title: postnatal liver at P1, biological rep1

description:
RaGene1_91812W_JZ13_14
RaGene1_91812W_JZ01_14
Gene expression data from neonatal liver tissue, first postnatal day. Postanatal adaptation proceeds.

value: Wistar rat


title: postnatal liver at P1, biological rep4

description:
RaGene1_91812W_JZ16_F
RaGene1_91812W_JZ01_F
Gene expression data from neonatal liver tissue, first postnatal day. Postanatal adaptation proceeds.


title: CD4 T-cell ATF4/CEBPb lowArg rx Input

description:
Input for reference-normalized ATF4 and CEBPb ChIP-seq in THP1 cells cultured under low (20uM) arginine conditions
Tcell_ATF4_lowArg_rx_peaks.txt.gz
Tcell_CEBPb_lowArg_rx_peaks.txt.gz

value: Cells cultured in low (20uM) arginine RPMI for 72h


title: DNMT1-siRNA1 [si1_2]


title: DNMT1-siRNA1 [si1_3]


title: DNMT1-siRNA2 [si2_1]


title: fetal liver at F22, biological rep3

description:
RaGene1_91812W_JZ11_11
RaGene1_91812W_JZ01_11
Gene expression data from fetal liver tissue, last gestational day.

source_name: Rat 22-day old fetal liver, last day before birth

value: 22-day old fetus

value: liver


title: THP1 ATF4/CEBPb noArg rx Input

description:
Input for reference-normalized ATF4 and CEBPb ChIP-seq in THP1 cells cultured in the absence of arginine
THP1_ATF4_noArg_rx_peaks.txt.gz
THP1_CEBPb_noArg_rx_peaks.txt.gz

source_name: Leukemia cell line (THP1)

value: Leukemia cell line (THP1)

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation


title: fetal liver at F22, biological rep2

description:
RaGene1_91812W_JZ10_10
RaGene1_91812W_JZ01_10
Gene expression data from fetal liver tissue, last gestational day.


title: fetal liver at F20, biological rep4

description:
RaGene1_91812W_JZ08_8
RaGene1_91812W_JZ01_8
Gene expression data from fetal liver tissue, hemopoietic function declining.

source_name: Rat 20-day old fetal liver

value: 20-day old fetus


title: Human kidney sample - snATAC-seq_rep1

value: Female

value: White


title: fetal liver at F22, biological rep1

description:
RaGene1_91812W_JZ09_9
RaGene1_91812W_JZ01_9
Gene expression data from fetal liver tissue, last gestational day.


title: fetal liver at F20, biological rep2

description:
RaGene1_91812W_JZ06_6
RaGene1_91812W_JZ01_6
Gene expression data from fetal liver tissue, hemopoietic function declining.


title: THP1 ATF4/CEBPb lowArg rx Input

description:
Input for reference-normalized ATF4 and CEBPb ChIP-seq in THP1 cells cultured under low (20uM) arginine conditions
THP1_ATF4_lowArg_rx_peaks.txt.gz
THP1_CEBPb_lowArg_rx_peaks.txt.gz


title: THP1 ATF4/CEBPb fullArg rx Input

description:
Input for reference-normalized ATF4 and CEBPb ChIP-seq in THP1 cells cultured in complete RPMI
THP1_ATF4_Arg_rx_peaks.txt.gz
THP1_CEBPb_Arg_rx_peaks.txt.gz


title: fetal liver at F20, biological rep3

description:
RaGene1_91812W_JZ07_7
RaGene1_91812W_JZ01_7
Gene expression data from fetal liver tissue, hemopoietic function declining.


title: fetal liver at F16, biological rep4

description:
RaGene1_91812W_JZ04_4
RaGene1_91812W_JZ01_4
Gene expression data from fetal liver tissue, hemopoietic function.

source_name: Rat 16-day old fetal liver

value: 16-day old fetus


title: Capture C_Tn-1 (CD4+CD25-CD62L+CD44- Tn cells sorted from male B6 mice)

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

data_processing:
Library strategy: Capture-C
Paired-end reads of 150bp were first trimmed for adapters by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 6 -O 25 ”).
Then trimmed seqeunces were processed by HiC-Pro17 using mouse genome mm9 (MGSCv37 from Sanger) with restriction fragments annotation based on DpnII(^GATC).
We then generate bigwig files using make_viewpoints.py script from HiC-Pro. We used “chrX:7154229-7156816” as viewpoint for Foxp3 promoter. bigwig tracks height was normalized to 500k contact within 5 million bp, that is we double the track height if we observed a sample have 250k contact within 5 million bp from viewpoint.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig

source_name: Naïve CD4 T cells sorted from male B6 mice

growth_protocol: CD4 naive T cells and nTreg cells were FACS sorted from male mice  and used for Capture-C without in vitro culture. iTreg cells were induced, from CD4 naïve T cells of male Foxp3-gfp reporter mice, in vitro (iTr) by plate-bound anti-CD3 and anti-CD28 antibodies, recombinant Interleukin-2 (IL-2), and TGF-beta, and ascorbic acid-2-phosphate. Four days later, iTr cells were sorted by GFP expression for Capture C.

extract_protocol:
10 million mouse primary T cells were fixed in 1% formaldehyde for 10 min at RT with gentle rotation. The reaction was quenched by 0.125 M glycine followed. Cells were then resuspended in 5 mL lysis buffer and incubated on ice for 20 min. Cells were pelleted and resuspended in 1 mL of 1x DpnII digestion buffer and transferred to a 2 mL tube for homogenization followed with centrifugation at 14,000 rpm for 5 min at 4°C. Complete homogenization was confirmed under microscope and the supernatant was removed. The remaining pellets were subjected to DpnII (NEB) digestion, T4 DNA ligation (Thermo Fisher Scientific), and de-crosslinking. The resulting 3C library DNA was precipitated, and a small portion was separated by electrophoresis with an agarose gel to assess the digestion and ligation efficiency.
5 µg of the 3C DNA library was sheared to approximately 200 bp followed by end-repair, adaptor ligation, and PCR enrichment of adaptor ligated DNA. Two rounds of captures were conducted at 47°C by using 2 µg of DNA, 5 µg mouse Cot-1 DNA (Thermo Fisher Scientific), biotinylated DNA oligonucleotide probes, 1 µl xGen Universal Blocking Oligo i7, and 1 µl xGen Universal Blocking Oligo i5 (IDT DNA Technologies).
Amplicon sequencing

treatment_protocol: iTreg cells were treated with 0.25 mM ascorbic acid 2-phosphate for 4 days during Treg induction to induce Tet-mediated DNA demethylation.

value: CD4 naive T cells


title: Capture C_Tn-2 (CD4+CD25-CD62L+CD44- Tn cells sorted from male B6 mice)


title: Commercially available PSC-derived astrocytes_replicate 3

city: Leuven

first: Jonathan

last: De Smedt

address: ON4 - Herestraat 49 PB804

department: Development and Regeneration

country: Belgium

institute: Stem Cell Institute Leuven

description:
iCell_3
iCellAstr3@S24@TCGATATC@ACACGAGT
countfile.txt

data_processing:
Low quality ends of reads were trimmed (<Q20) with FastX 0.0.14 followed by adapter trimming using cutadapt 1.15.
Poly-A-reads, ambiguous reads, artifact reads and low-quality reads (more than 50% of bases <Q25) were removed using FastX 0.0.14 and ShortRead 1.40.0.
Contaminants were removed using bowtie 2.3.3.1.
Reads were aligned to reference genome Homo_Sapiens.Ensembl.GRCh38.88 using STAR 2.5.2b (--outSAMprimaryFlag OneBestScore --twopassMode Basic --alignIntronMin 50 --alignIntronMax 500000 --outSAMtype BAM SortedByCoordinate). Following sorting and indexing was performed with samtools 1.5.
Genome_build: GRCh38
Supplementary_files_format_and_content: Raw counts are provided in countfile.txt. Columns contain samples, rows contain Ensembl identifiers. Counts are raw, i.e. not normalised in any manner.

source_name: Astrocytes

growth_protocol: Single cell suspensions of iSOX9 PSCs were cultured in neural induction medium containing 1 μM LDN-193189 and 10 μM SB431542 to allow dual SMAD inhibition for 12 days. Afterwards, cells were replated and cultured in astrocyte maturation medium containing 0.1 mM dbcAMP, 10 ng/ml CNTF, 10 ng/ml BMP4 and 5 ng/ml HB-EGF supplemented with 3 µg/ml doxycycline to allow SOX9 overexpression for 6 days. From then onwards, cells were cultured in astrocyte maturation medium without doxycycline and split when approximately 90% confluency was reached.

extract_protocol:
RNA was extracted using Trizol followed by column-based extraction.
RNA libraries were prepared for sequencing using the library prep kit TruSeq followed by single-end sequencing (Illumina HiSeq 4000, 50 cycles).

value: induced pluripotent stem cell-derived astrocytes

tag: overexpressed transcription factor

value: no TF overexpression

tag: differentiation day

value: not known


title: Commercially available primary human fetal astrocytes_replicate 2

description:
fHA_2
PHA2@S20@ACAGGCGC@CTCTGCCT
countfile.txt

value: Primary human fetal astrocytes

value: no differentiation


title: Commercially available primary human fetal astrocytes_replicate 3

description:
fHA_3
PHA3@S21@GTGAATAT@TCTCATTC
countfile.txt


title: Capture C_nTreg-1(CD4+YFP+ Treg cells sorted from male Foxp3-YFP-Cre mice)

source_name: nTreg cells sorted from male Foxp3-YFP-Cre mice

value: nTreg cells


title: Capture C_ASC-treated iTreg-3 (CD4+GFP+ iTreg cells induced from naive T cells of male Foxp3-GFP mice)

source_name: ASC-treated iTreg cells induced from naïve T cells of male Foxp3-GFP mice

value: ASC-treated induced Treg cells

value: in vitro iTreg induction with the addition of ASC


title: CD4 T-cell CEBPb noArg rx

description:
Reference-normalized CEBPb ChIP-seq in THP1 cells cultured in the absence of arginine
Tcell_CEBPb_noArg_rx_peaks.txt.gz

source_name: Stimulated human CD4 T-cells

value: Stimulated human CD4 T-cells

value: Cells cultured in arginine-free RPMI for 72h

value: Human CD4+ T-cells purified from PBMCs, stimulated with anti-CD3/anti-CD28 beads

value: Bethyl A302-738A


title: CD4 T-cell CEBPb lowArg rx

description:
Reference-normalized CEBPb ChIP-seq in THP1 cells cultured under low (20uM) arginine conditions
Tcell_CEBPb_lowArg_rx_peaks.txt.gz

value: Cells cultured in low (20uM) arginine RPMI for 72h


title: Capture C_nTreg-2(CD4+GFP+ Treg cells sorted from male Foxp3-DTR-GFP mice)

source_name: nTreg cells sorted from male Foxp3-DTR-GFP mice


title: fetal liver at F16, biological rep2

description:
RaGene1_91812W_JZ02_2
RaGene1_91812W_JZ01_2
Gene expression data from fetal liver tissue, hemopoietic function.

value: Wistar rat

value: liver


title: fetal liver at F20, biological rep1

description:
RaGene1_91812W_JZ05_5
RaGene1_91812W_JZ01_5
Gene expression data from fetal liver tissue, hemopoietic function declining.

value: 20-day old fetus


title: fetal liver at F16, biological rep3

description:
RaGene1_91812W_JZ03_3
RaGene1_91812W_JZ01_3
Gene expression data from fetal liver tissue, hemopoietic function.

value: 16-day old fetus


title: fetal liver at F16, biological rep1

description:
RaGene1_91812W_JZ01_1
RaGene1_91812W_JZ01_1
Gene expression data from fetal liver tissue, hemopoietic function.


title: Capture C_ASC-treated iTreg-2 (CD4+GFP+ iTreg cells induced from naive T cells of male Foxp3-GFP mice)


title: CD4 T-cell CEBPb fullArg rx

description:
Reference-normalized CEBPb ChIP-seq in THP1 cells cultured in complete RPMI
Tcell_CEBPb_Arg_rx_peaks.txt.gz

value: Cells cultured in RPMI for 72h


title: Commercially available primary human fetal astrocytes_replicate 1

description:
fHA_1
PHA1@S19@CATAGAGT@TGCCACCA
countfile.txt

value: no TF overexpression


title: Commercially available PSC-derived astrocytes_replicate 1

description:
iCell_1
iCellAstr1@S22@TACTCATA@CCTGTGGC
countfile.txt

value: induced pluripotent stem cell-derived astrocytes

value: not known


title: ATAC-seq in unstimulated CD4 T-cells rep 4

source_name: Unstimulated human CD4 T-cells

value: Unstimulated human CD4 T-cells

value: Human CD4+ T-cells purified from PBMCs without stimulation


title: CD4 T-cell ATF4 noArg rx

description:
Reference-normalized ATF4 ChIP-seq in THP1 cells cultured in the absence of arginine
Tcell_ATF4_noArg_rx_peaks.txt.gz

value: Cell Signaling Technology 11815


title: Capture C_ASC-treated iTreg-1 (CD4+GFP+ iTreg cells induced from naive T cells of male Foxp3-GFP mice)

value: ASC-treated induced Treg cells

value: in vitro iTreg induction with the addition of ASC


title: Healthy iSOX9-astrocytes_30 days after doxy removal_replicate 2

description:
Astro_Sigma_late2
Astr@Sigma@late2@S5@TTCCTGTT@AGTATCTT
countfile.txt


title: Capture C_Tn-3 (CD4+GFP+CD62L+CD44- naive T cells sorted from male Foxp3-GFP mice)

source_name: Naïve CD4 T cells sorted from Foxp3-GFP male mice

value: CD4 naive T cells


title: CD4 T-cell ATF4 lowArg rx

description:
Reference-normalized ATF4 ChIP-seq in THP1 cells cultured under low (20uM) arginine conditions
Tcell_ATF4_lowArg_rx_peaks.txt.gz

value: Stimulated human CD4 T-cells

value: Human CD4+ T-cells purified from PBMCs, stimulated with anti-CD3/anti-CD28 beads


title: Capture C_Tn-2 (CD4+GFP+CD62L+CD44- naive T cells sorted from male Foxp3-GFP mice)


title: Commercially available PSC-derived astrocytes_replicate 2

description:
iCell_2
iCellAstr2@S23@CGTCTGCG@TTCACAAT
countfile.txt


title: CD4 T-cell ATF4 fullArg rx

description:
Reference-normalized ATF4 ChIP-seq in THP1 cells cultured in complete RPMI
Tcell_ATF4_Arg_rx_peaks.txt.gz


title: THP1 CEBPb lowArg rx

description:
Reference-normalized CEBPb ChIP-seq in THP1 cells cultured under low (20uM) arginine conditions
THP1_CEBPb_lowArg_rx_peaks.txt.gz

value: Leukemia cell line (THP1)

value: Cells cultured in low (20uM) arginine RPMI for 72h

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation

value: Bethyl A302-738A


title: THP1 CEBPb noArg rx

description:
Reference-normalized CEBPb ChIP-seq in THP1 cells cultured in the absence of arginine
THP1_CEBPb_noArg_rx_peaks.txt.gz

value: Cells cultured in arginine-free RPMI for 72h


title: Healthy iSOX9-astrocytes_5 days after doxy removal_replicate 1

description:
Astro_Sigma_early1
Astr@Sigma@early1@S1@TTGCCTAG@ACCACTTA
countfile.txt


title: Healthy iSOX9-astrocytes_5 days after doxy removal_replicate 3

description:
Astro_Sigma_early3
Astr@Sigma@early3@S3@ACACTAAG@ATCCATAT
countfile.txt


title: Healthy iSOX9-astrocytes_5 days after doxy removal_replicate 2

description:
Astro_Sigma_early2
Astr@Sigma@early2@S2@CCATTCGA@GTTGTCCG
countfile.txt


title: S18: CNS3KO

data_processing:
Library strategy: TCR-seq
VDJ gene assignments were calculated and filtered with MIGEC software. VDJtools v1.2.1 software was applied for filtering non-functional TCR and decontaminate samples
Genome_build: mm10
Supplementary_files_format_and_content: Processed data contains CDR3 nucleotide sequence, CDR3 amino acid sequence, V gene usage, D gene usage and J gene usage. And different TCR counts and frequency.

source_name: Lymphocytes of male mice

extract_protocol:
CD4+Foxp3-GFP+ nTreg cells were sorted from the spleen, skin draining LN, and mLN of individual WT GFP, CNS3, CNS0, and CNS3,0 mice at 16 days of age. Total RNA was extracted by TRIzol according to the manufacturer’s instructions. cDNA was synthesized by SMARTScribe Reverse Transcriptase with primers targeting the constant regions of mouse TCRa (5’-AGTCAAAGTCGGTGAAC-3’) or TCRb (5’-ATCTCTGCTTTTGATG-3’) chains and template switch adapter (5’-AAGCAGUGGTAUCAACGCAGAGUNNNNUNNNNUNNNNUCTTrGrGrGrG-3’).
TCRa and TCRb chains were further amplified by a two-step protocol. Sequencing adaptors were then added by Kapa Hyper Prep Kit (Kapa Biosystems). Samples were pooled and sequenced by Nova Seq with at least 10x coverage relative to the numbers of Treg cell used.

value: nTreg

tag: Sex

value: male


title: S17: GFP

value: GFP


title: S16: CNS3KO


title: THP1 CEBPb fullArg rx

description:
Reference-normalized CEBPb ChIP-seq in THP1 cells cultured in complete RPMI
THP1_CEBPb_Arg_rx_peaks.txt.gz

tag: treatment

value: Cells cultured in RPMI for 72h


title: Healthy iSOX9-astrocytes_30 days after doxy removal_replicate 3

description:
Astro_Sigma_late3
Astr@Sigma@late3@S6@CCTTCACC@GACGCTCC
countfile.txt

value: induced pluripotent stem cell-derived astrocytes


title: CD4 T-cell no Arg rep 1

description: replicate 1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina iScan cscanning protocol

data_processing: The data were normalised using quantile normalisation in R and poor quality probes were removed

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted using the RNeasy minikit (Qiagen; 74104)

treatment_protocol: THP1 cells were cultured in full or arginine-free medium for 72h prior to harvest. Human CD4+ T-cells were purified from PBMCs isolated from commercially available leukocyte cones (NHS Blood and Transplant, Bristol, UK) by magnetic-activated cell sorting (MACS) purification using CD4 Microbead kits (Miltenyi Biotec) then stimulated using anti-CD3/CD28 antibodies (Life Technologies). Cells were cultured in full or arginine-free medium for 72h prior to harvest.

value: Cells cultured in RPMI without arginine


title: S14: GFP

tag: genotype


title: CD4 T-cell full Arg rep 3

description: replicate 3

tag: tissue

value: Cells cultured in full RPMI


title: CD4 T-cell no Arg rep 3

description: replicate 3


title: THP1 ATF4 noArg rx

description:
Reference-normalized ATF4 ChIP-seq in THP1 cells cultured in the absence of arginine
THP1_ATF4_noArg_rx_peaks.txt.gz

tag: cell type

value: Cell Signaling Technology 11815


title: ALS-mutant iSOX9-astrocytes_30 days after doxy removal_replicate 3

description:
Astro_RH_late3
Astr@RH@late3@S12@TGGCCGGT@TAGAGCGC
countfile.txt

value: induced pluripotent stem cell-derived astrocytes (ALS mutant)


title: CD4 T-cell full Arg rep 2

description: replicate 2


title: THP1 ATF4 fullArg rx

description:
Reference-normalized ATF4 ChIP-seq in THP1 cells cultured in complete RPMI
THP1_ATF4_Arg_rx_peaks.txt.gz


title: CD4 T-cell full Arg rep 1

description: replicate 1


title: Capture C_Tn-1 (CD4+GFP+CD62L+CD44- naive T cells sorted from male Foxp3-GFP mice)

value: CD4 naive T cells


title: S12: GFP


title: ALS-mutant iSOX9-astrocytes_30 days after doxy removal_replicate 2

description:
Astro_RH_late2
Astr@RH@late2@S11@CAATTAAC@CGAGATAT
countfile.txt


title: S13: CNS3KO


title: THP1 ATF4 lowArg rx

description:
Reference-normalized ATF4 ChIP-seq in THP1 cells cultured under low (20uM) arginine conditions
THP1_ATF4_lowArg_rx_peaks.txt.gz


title: S11: CNS03DKO


title: S15: GFP


title: Healthy iSOX9-astrocytes_30 days after doxy removal_replicate 1

description:
Astro_Sigma_late1
Astr@Sigma@late1@S4@GTGTCGGA@GCTTGCGC
countfile.txt


title: ALS-mutant iSOX9-astrocytes_30 days after doxy removal_replicate 1

description:
Astro_RH_late1
Astr@RH@late1@S10@GTCTACAC@GCCAAGGT
countfile.txt


title: S10: CNS03DKO


title: ALS-mutant iSOX9-astrocytes_5 days after doxy removal_replicate 3

description:
Astro_RH_early3
Astr@RH@early3@S9@ACTCGTGT@ATTGGAAC
countfile.txt


title: K562 siC RNH-treated DRIP-seq rep1

city: Seville

first: Andrés

last: Aguilera

address: Av. Américo Vespucio 24

department: Genome BIology

country: Spain

institute: CABIMER, Universidad de Sevilla

description:
DRIP-seq
DNA from RNA:DNA hybrids

data_processing:
Paired-end sequencing reads were subjected to quality control pipeline using the FASTQ Toolkit v.1.0.0 software
Reads from different sequencing lanes but same condition were concatenated and mapped to the human reference genome hg38 using BWA (DRIP-seq) or HISAT2 (RNA-seq)
PCR duplicates were removed
For RNA-seq data, reads were counted using FeatureCounts and RPKM-normalized.
For DRIP-seq data, bigwig files were generated using bedtools bamcoverage
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files (coverage)
Supplementary_files_format_and_content: txt file (tab-delimited text file include RPKM values for each gene)

source_name: K562 cells

growth_protocol: K562 (ATCC, CCL-243) cells were cultured in Iscove's Modified Dulbecco's medium (IMDM; GIBCO) supplemented with 10% heat-inactivated fetal bovine serum (Sigma Aldrich) and 1% antibiotic-antimycotic (BioWEST) at 37ºC (5% CO2).

extract_protocol:
Genomic DNA from K562 cells enzimatically fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Monoclonal S9.6 antibody was used to immunoprecipitate RNA-DNA hybrids.
Library constructed using the ThruPLEX DNA-Seq 6S kit (Rubicon Genomics) according to manufacturer’s guidelines.

treatment_protocol: Cells were transfected with 50nM siC (D-001810-10) using DharmaFECT 1 (Dharmacon) and extracted genomic DNA was treated in vitro with RNase H (New England Biolabs) prior to immunoprecipitation

value: lymphoblast

tag: disease

value: chronic myelogenous leukaemia

tag: drip antibody

value: S9.6 Ab (hybridoma HB-8730)

value: RNH-treated siC-transfected


title: CD4 T-cell no Arg rep 2

description: replicate 2

value: Stimulated human CD4 T-cells


title: ALS-mutant iSOX9-astrocytes_5 days after doxy removal_replicate 2

description:
Astro_RH_early2
Astr@RH@early2@S8@ATTGTGAA@TGCATTGC
countfile.txt


title: K562 siC untreated DRIP-seq rep1

description:
DRIP-seq
DNA from RNA:DNA hybrids

treatment_protocol: Cells were transfected with 50nM siC (D-001810-10) using DharmaFECT 1 (Dharmacon)

value: untreated siC-transfected


title: K562 siBRG1 RNA-seq rep1

description:
RNA-seq
Total RNA

extract_protocol:
RNA purification was performed using RNeasy Mini kit (Qiagen) according to manufacturer’s conditions.
Library constructed using TruSeq Stranded Total RNA Library Prep (Illumina) according to manufacturer’s guidelines.

treatment_protocol: Cells were transfected with 50nM siBRG1 (L-010431-00) using DharmaFECT 1 (Dharmacon)


title: ALS-mutant iSOX9-astrocytes_5 days after doxy removal_replicate 1

description:
Astro_RH_early1
Astr@RH@early1@S7@GCCACAGG@CATGCCAT
countfile.txt


title: S8: GFP

tag: strain


title: K562 siBRG1 DRIPc-seq rep1

data_processing:
Library strategy: DRIPc-seq
Paired-end sequencing reads were subjected to quality control pipeline using the  FASTQ Toolkit v.1.0.0 software
Reads from different sequencing lanes but same condition were concatenated and mapped to the human reference genome hg38 using Bowtie2
PCR duplicates were removed and reads assigned to Watson and Crick strand
Peak calling was performed using MACS2 package
Bigwig files were generated using bedtools bamcoverage
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files (coverage)
Supplementary_files_format_and_content: bed files (peaks)

extract_protocol:
Genomic DNA from K562 cells enzimatically fragmented using HindIII, EcoRI, BsrGI, XbaI and SspI. Monoclonal S9.6 antibody was used to immunoprecipitate RNA-DNA hybrids.
Libraries were prepared using TruSeq Stranded Total RNA Library Prep (Illumina) as determined by the company

treatment_protocol: Cells were transfected with 50nM siRNA (siC (D-001810-10) or siBRG1(L-010431-00)) using DharmaFECT 1 (Dharmacon)

tag: cell line

tag: sequenced molecule

value: RNA moiety from RNA:DNA hybrids


title: S7: CNS0KO

value: nTreg


title: K562 siBRG1 DRIPc-seq rep2


title: RUNX1_D5_0hr_r2

first: Erinke

last: van Grinsven

address: Roosevelt Drive

department: Kennedy Institute of Rheumatology

data_processing:
Reads were mapped to the mm10 genome using STAR with the options: “—runMode alignReads –outFilterMismatchNmax 2.” Uniquely mapped read pairs were counted over annotated genes using feature Counts with the options: “-T 18 -s 2 -Q 255.” Differential expression was then analysed with DESeq2
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: featurecount table

molecule: polyA RNA

source_name: ER-Hoxb8 neutrophils

growth_protocol: ER-Hoxb8 progenitor cells were routinely cultured in RMPI-1640 medium supplemented with 10% FCS, 30 mM β-mercaptoethanol, 1% supernatant from stem cell factor (SCF)-producing CHO cells and 1 μM β-estradiol. Differentiation was induced by estrogen removal and culture in medium containing 1% SCF supernatant. The progenitor cells were differentiated into neutrophils by culturing with complete RPMI 1640 medium supplemented with 30 mM b-mercaptoethanol, 4% SCF containing supernatant and 20 ng/mL G-CSF in 5% CO2 tissue culture incubator at 37°C.

extract_protocol: Total RNA of Hoxb8 neutrophils  were extracted using RNeasy mini kit (Qiagen) according to the manufacturer’s instruction.

treatment_protocol: HoxB8 neutrophils differentiated for five days were incubated with Zymosan(50ug/ml) or DMSO vehicle for two hours.

value: ER-Hoxb8 neutrophils

tag: phenotype

tag: number of days of in vitro differentiation

value: DMSO 2h

tag: replicate


title: K562 siC DRIPc-seq rep1


title: S6: CNS0KO

value: male


title: SA_rep1

first: Sandy

last: Martin

state: CO

department: Cell and Developmental Biology

institute: University of Colorado School of Medicine

data_processing:
Library strategy: GRO-seq
The raw sequencing reads were trimmed with serial runs through cutadapt to remove the adaptor sequence and polyA, short sequences with settings -z, -m32 (Martin, 2011). Trimmed reads were mapped to the HiC_Itri_2 genome (Fu et al., 2021) using BWA. Existing transcript annotations were modified by building fstitch annotations, first for each state using the merged triplicate reads. These were then merged across all states to generate maximal called transcript regions which were intersected with the HiC_Itri_2 annotations. In cases where the fstitch annotation extended further 3’, the fstitch annotation was substituted for that gene’s annotation, otherwise the annotation was unchanged.  All overlapping genes were then merged, with the gene name retaining all merged gene names separated by a “:”. These fstitch gene annotations were further processed to exclude the first 500nt (based on TSS annotation). Read counts were re-quantified on this new annotation using featureCounts. DE genes among the GRO-seq reads mapping to each of these unique gene bodies were identified using DESeq2 and further filtered to exclude gene bodies overlapping multiple genes or annotations <= 50 nt in length. Fu, R., Gillen, A.E., Grabek, K.R., Riemondy, K.A., Epperson, L.E., Bustamante, C.D., Hesselberth, J.R., and Martin, S.L. (2021). Dynamic RNA regulation in the brain underlies physiological plasticity in a hibernating mammal. Frontiers in Physiology 11.
Genome_build: HiC_Itri_2, NCBI genome accession JAESOR000000000, PRJNA647389
Supplementary_files_format_and_content: csv file with GRO-seq read counts calculated with FeatureCounts using Fstitch supplemented annotations

organism: Ictidomys tridecemlineatus

source_name: liver

growth_protocol: laboratory housed 13-lined ground squirrels purchased from University of Wisconsin Oshkosh breeding colony

extract_protocol:
frozen liver tissue was homogenized by dounce in 10 mM Tris pH 7.5, 2 mM MgCl2, 3 mM CaCl2, 2 U/ml Superase-In, as described in Fang et al., 2014, Cell 159:1140
nascent RNA was labeled with BrdU in a 7 min nuclear run-on incubation at 30oC, purified by immunoprecipitation and converted to sequencing libraries as described in Fang et al., 2014 Cell 159:1140

treatment_protocol:
animals were surgically implanted with radiotelemeters and ibuttons to measure body temperature and therefore track hibernation physiology. Tissues were collected from 4 stages of hibernation based on Tb and time (IBA, Ent, ET and LT for interbout aroused, entrance into torpor, early torpor and late torpor) plus SA from the homeothermic period prior to the onset of hibernation
liver was immediately frozen in N2l and stored continuously at <-70oC until use

value: liver

tag: hibernation state

value: SA

tag: animal number

value: female

tag: rna population

value: nuclear RNA


title: KLF6_D5_0hr_r1


title: RUNX1_D5_0hr_r1


title: SA_rep2


title: S5: CNS0KO


title: THP1 no Arg rep 2

description: replicate 2

source_name: THP1 cells

value: THP1 cells

value: Cells cultured in RPMI without arginine


title: THP1 no Arg rep 3

description: replicate 3


title: LT_rep3

value: LT


title: THP1 full Arg rep 1

description: replicate 1

value: Cells cultured in full RPMI


title: THP1 lowArg ATAC rep 3

description: ATAC-seq in THP1 cells in low arginine medium rep 3

treatment_protocol: THP1 cells were cultured in full, low (20uM) arginine or arginine-free medium for 72h prior to harvest. Human CD4+ T-cells were purified from PBMCs isolated from commercially available leukocyte cones (NHS Blood and Transplant, Bristol, UK) by magnetic-activated cell sorting (MACS) purification using CD4 Microbead kits (Miltenyi Biotec) then stimulated using anti-CD3/CD28 antibodies (Life Technologies). Cells were cultured in full, low (20uM) arginine or arginine-free medium for 72h prior to harvest.

value: Leukemia cell line (THP1)

value: Cells cultured in low (20uM) arginine RPMI for 72h

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation


title: THP1 full Arg rep 2

description: replicate 2


title: THP1 full Arg rep 3

description: replicate 3


title: KLF6_D5_0hr_r2


title: THP1 no Arg rep 1

description: replicate 1


title: S4: CNS03DKO


title: S9: GFP

value: GFP


title: SA_rep3


title: THP1 fullArg ATAC rep 3

description: ATAC-seq in THP1 cells in full medium rep 3

value: Cells cultured in RPMI for 72h


title: LT_rep2


title: Eomes_1

city: Lyon

first: Thierry

last: Walzer

address: 21 avenue tony garnier

institute: CIRI, centre international de recherche en infectiologie

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome mm10 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm10
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b).

source_name: NK cells

extract_protocol:
Spleen NK cells were purified by negative selection (Miltenyi MACS)  before lysis an chromatin ip.
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 0-10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5X ends were ligated to the 5X end of the genomic DNA, leaving a nick at the 3X end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3X ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 + 2 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: NK cells

tag: chip antibody

value: HA (CST, catalog number 3724)

value: HAV5-tagged Eomes


title: THP1 noArg ATAC rep 2

description: ATAC-seq in THP1 cells in arginine-free medium rep 2

source_name: Leukemia cell line (THP1)

extract_protocol:
Cells were washed with PBS and lysed with 0.1% IGEPAL CA-630, followed by Tn5 transposase treatment
Libraries were made using the Nextera DNA library prep kit (Illumina)

value: Cells cultured in arginine-free RPMI for 72h


title: Eomes_2


title: Tbet_2

value: HAV5-tagged T-bet


title: THP1 noArg ATAC rep 3

description: ATAC-seq in THP1 cells in arginine-free medium rep 3


title: ET_rep3

value: liver

value: ET

tag: Sex


title: THP1 lowArg ATAC rep 2

description: ATAC-seq in THP1 cells in low arginine medium rep 2

tag: treatment


title: LT_rep1

value: female

value: nuclear RNA


title: S1: GFP

value: nTreg

tag: genotype

value: male


title: S2: CNS03DKO


title: THP1 fullArg ATAC rep 2

description: ATAC-seq in THP1 cells in full medium rep 2

tag: tissue


title: ET_rep2


title: Tbet_1

tag: cell type


title: WT_2

value: WT


city: Cambridge

first: Brian

middle: Yee Hong

last: Lam

address: Box 289 Addenbookes Hospital, Hills Road

department: Metabolic Research Laboratories

institute: University of Cambridge

description:
nascent RNA
Mouse AP/NTS overnight fasted repitition 2

data_processing:
Fastq files were mapped and genes were counted using CellRanger v4.0
Genome_build: GRCm38
Supplementary_files_format_and_content: gene level counts for all cells in hdf5 format

source_name: AP/NTS

extract_protocol:
an area of the brainstem containing the Area Postrema and Nucleus of the Solitary tract was dissected, and a single nucleus suspension was created using a dounce homogenizer and purified using Fluoresence activated cell sorting (FACs)
Library constriction was perfomed using 10X Genomics Chromium Single Cell 3’ Reagent kits (Version 3) according to the standardised protocol.
Single nucleus RNA-sequencing

treatment_protocol: 6 mice were fed ad libitum and 6 mice were fasted for 16 hours prior to dissection

value: hindbrain

tag: age

value: 6-8 weeks

value: overnight fasted


title: THP1 noArg ATAC rep 1

description: ATAC-seq in THP1 cells in arginine-free medium rep 1

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using MACS2
Statistical analysis using Diffbind (EdgeR)

value: Leukemia cell line (THP1)

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation


title: WT_1

value: NK cells


description:
nascent RNA
Mouse AP/NTS overnight fasted repitition 1


title: ET_rep1


title: Ent_rep3

value: Ent


title: THP1 lowArg ATAC rep 1

description: ATAC-seq in THP1 cells in low arginine medium rep 1

value: Cells cultured in low (20uM) arginine RPMI for 72h


title: Tbet Ho CD11b- rep3

description:
Tbet-/- CD11b- rep3
TRWR104

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Raw data were preprocessed using cutadapt 1.10 in order to remove adaptor and low-quality sequences (Phred quality score below 20). Reads shorter than 40 bp were removed for further analysis. Remaining reads were mapped to mouse rRNA sequences using bowtie 2.2.8 and reads mapped to rRNA sequences were discarded for further analysis.
Remaining reads were aligned to mm10 assembly of the mouse genome with STAR 2.5.3a.
Gene quantification was performed with htseq-count 0.6.1p1 using “union” mode and Ensembl 96 annotations.
Genome_build: mm10
Supplementary_files_format_and_content: Tab-separated text file with raw read counts per Ensembl Gene.

extract_protocol:
Spleen NK cells were purified by negative selection (Miltenyi MACS)  before flow cytometry-based sorting of NK1.1+ CD3-CD11b-CD27+ or NK1.1+  CD3-CD11b+CD27- cells, that were then processed for RNA extraction.
RNA libraries were prepared as previously described (Picelli, S. et al. 2014). Briefly, total RNA was purified using the Direct-Zol RNA microprep kit (Zymo Research) according to manufacturer instructions and was quantified using QuantiFluor RNA system (Promega). 1µl of 10µM Oligo-dT primer and 1µl of 10mM dNTPs mix were added to 0.15ng of total RNA in a final volume of 2.3µl. Oligo-dT were hybridized 3min at 72°C and reverse transcription (11 cycles) was performed. PCR pre-amplification was then conducted using 16 cycles. cDNA were purified on AmpureXP beads (Beckman Coulter) and cDNA quality was checked on D5000 screen tape and analysed on Tape station 4200 (Agilent). 3ng of cDNA were tagmented using Nextera XT DNA sample preparation kit (Illumina). Tagged fragments were further amplified and purified on AmpureXP beads (Beckman Coulter). Tagged library quality was checked on D1000 screen tape and analyzed on Tape station 4200 (Agilent).

tag: cell state

value: CD11b- NK cells


description:
nascent RNA
Mouse AP/NTS ad libitum fed repitition 2

tag: strain

value: ad libitum fed


title: Tbet Ho CD27- rep3

description:
Tbet-/- CD27- rep3
TRWR103

value: CD27- NK cells


title: S3: CNS03DKO


title: fetal liver at F22, biological rep4

description:
RaGene1_91812W_JZ12_12
RaGene1_91812W_JZ01_12
Gene expression data from fetal liver tissue, last gestational day.

source_name: Rat 22-day old fetal liver, last day before birth

extract_protocol: TriReagent extraction of total RNA was performed according to the manufacturer's instructions.

value: Wistar rat

value: 22-day old fetus

value: liver


title: Ent_rep2

value: female

value: nuclear RNA


description:
nascent RNA
Mouse AP/NTS ad libitum fed repitition 1


title: THP1 fullArg ATAC rep 1

description: ATAC-seq in THP1 cells in full medium rep 1

value: Cells cultured in RPMI for 72h


title: Tbet WT CD11b- rep3

description:
Tbet WT CD11b- rep3
TRWR102

value: WT


title: CD4 T-cell noArg ATAC rep 3

description: ATAC-seq in CD4 T-cells cells in arginine-free medium rep 3

value: Stimulated human CD4 T-cells

value: Cells cultured in arginine-free RPMI for 72h

value: Human CD4+ T-cells purified from PBMCs, stimulated with anti-CD3/anti-CD28 beads


title: Ent_rep1


title: IBA_rep3

value: IBA


title: TNF3

city: Beijing

first: Dan

last: Wu

address: No. 16, Nei Nanxiao Street, Dongzhimen, Dongcheng District

institute: Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences

data_processing:
Briefly, The poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads.
Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers.
This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H.
These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters.
The products are then purified and enriched with PCR to create the final cDNA library.
Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).
Supplementary_files_format_and_content: Expression value of genes and transcripts

source_name: murine macrophage-like cell line

growth_protocol: The murine macrophage-like cell line (RAW264.7) was obtained from Cell Resource Center, IBMS, CAMS/PUMC (Beijing, China) and cultured in DMEM supplemented with 10% heat-inactivated fetal bovine serum and antibiotics (100 U/mL penicillin and 100 U/mL streptomycin) at 37 °C in a humidified atmosphere containing 95% O2 and 5% CO2 atmosphere.

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany) according to the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The quantity of total RNA samples was measured using Qubit®3.0 Fluorometer (Thermo Fisher Scientific, USA) and NanoDrop One (Wilmington, DE, USA).
Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA). The sequencing work was undertaken by Beijing Zhimei Yinuo Biotechnology Co., Ltd (Beijing, China).

value: macrophage

value: treated with TNF-α for 24 hours

value: BALB/c


title: CD4 T-cell lowArg ATAC rep 3

description: ATAC-seq in CD4 T-cells cells in low arginine medium rep 3

value: Cells cultured in low (20uM) arginine RPMI for 72h


title: TNF2


title: IBA_rep2


title: CD4 T-cell fullArg ATAC rep 3

description: ATAC-seq in CD4 T-cells cells in full medium rep 3


title: TNF1


title: Tbet WT CD27- rep3

description:
Tbet WT CD27- rep3
TRWR101

value: NK cells


title: Eomes Ho CD27- rep3

description:
Eomes-/- CD27- rep3
TRWR99

value: Eomes-/-

value: CD27- NK cells


title: Eomes Ho CD11b- rep3

description:
Eomes-/- CD11b- rep3
TRWR100

value: CD11b- NK cells


title: IBA_rep1

value: liver


title: TNF_P3

value: treated with WBP and TNF-α for 24 hours


title: Recipient Alveolar Macrophages r588

city: Pittsburgh

first: Mark

middle: E

last: Snyder

state: PA

address: 200 Lothrop Street, BST12

institute: University of Pittsburgh

data_processing:
hisat2
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using Kallisto
Raw count matrix generated using TxImport
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: NA - primary cells obtained from BAL

extract_protocol:
FACS Sorted based on donor and recipient HLA; alveolar macrophages defined as CD45+, live, lineage-, CD64+ CD206+
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Untreated

tag: subject group

value: lung transplant recipient

value: alveolar macrophages derived from the bronchoalveolar lavage


title: CD4 T-cell lowArg ATAC rep 2

description: ATAC-seq in CD4 T-cells cells in low arginine medium rep 2


title: TNF_P2


title: CD4 T-cell noArg ATAC rep 2

description: ATAC-seq in CD4 T-cells cells in arginine-free medium rep 2


title: NK-Cre CD11b- rep3

description:
NK-Cre CD11b- rep3
TRWR98

value: Cre


title: Recipient Alveolar Macrophages r563


title: Tbet Ho CD11b- rep2

description:
Tbet-/- CD11b- rep2
TRWR96


title: NK-Cre CD27- rep3

description:
NK-Cre CD27- rep3
TRWR97


title: Recipient Alveolar Macrophages r557


title: Con3

value: untreated


title: Donor Alveolar Macrophages d588

value: donor


title: CD4 T-cell lowArg ATAC rep 1

description: ATAC-seq in CD4 T-cells cells in low arginine medium rep 1

value: Stimulated human CD4 T-cells

value: Human CD4+ T-cells purified from PBMCs, stimulated with anti-CD3/anti-CD28 beads


title: Tbet Ho CD27- rep2

description:
Tbet-/- CD27- rep2
TRWR95


title: CD4 T-cell fullArg ATAC rep 2

description: ATAC-seq in CD4 T-cells cells in full medium rep 2

value: Cells cultured in RPMI for 72h


title: CD4 T-cell fullArg ATAC rep 1

description: ATAC-seq in CD4 T-cells cells in full medium rep 1


title: Donor Alveolar Macrophages d563


title: Tbet WT CD27- rep2

description:
Tbet WT CD27- rep2
TRWR93

value: WT


title: Con2

value: macrophage

value: BALB/c


title: Donor Alveolar Macrophages d557


title: CD4 T-cell H3K27me3 lowArg Input

description: Input for H3K27me3 ChIP-seq in stimulated CD4 T-cells cutured under low (20uM) arginine conditions

extract_protocol:
Cells were washed with PBS and fixed in either 1% FA for 10 minutes (histones) or 2mM DSG for 30 minutes and 1% FA for 30 minutes (transcription factors). Cells were sonicated to give fragments of 100-300bp followed by IP.
DNA libraries were made using the NEBnext ultra DNA library preparation kit for Illumina (Cat no. E7370).

treatment_protocol: THP1 cells were cultured in full or arginine-free medium for 72h prior to harvest. Human CD4+ T-cells were purified from PBMCs isolated from commercially available leukocyte cones (NHS Blood and Transplant, Bristol, UK) by magnetic-activated cell sorting (MACS) purification using CD4 Microbead kits (Miltenyi Biotec) then stimulated using anti-CD3/CD28 antibodies (Life Technologies). Cells were cultured in low (20uM) arginine or arginine-free medium for 72h prior to harvest.

value: Cells cultured in low (20uM) arginine RPMI for 72h


title: TNF_P1


title: CD4 T-cell H3K27me3 lowArg

description: H3K27me3 ChIP-seq in stimulated CD4 T-cells cutured under low (20uM) arginine conditions

value: Millipore 07-449


title: Eomes Ho CD11b- rep2

description:
Eomes-/- CD11b- rep2
TRWR92

value: NK cells

value: Eomes-/-


title: CD4 T-cell noArg ATAC rep 1

description: ATAC-seq in CD4 T-cells cells in arginine-free medium rep 1

value: Cells cultured in arginine-free RPMI for 72h


title: Eomes Ho CD27- rep2

description:
Eomes-/- CD27- rep2
TRWR91

value: CD27- NK cells


title: CD4 T-cell H3K27me3 noArg Input

description: Input for H3K27me3 ChIP-seq in stimulated CD4 T-cells cutured in the absence of arginine


title: CD4 T-cell H3K27me3 noArg

description: H3K27me3 ChIP-seq in stimulated CD4 T-cells cutured in the absence of arginine


title: NK-Cre CD11b- rep2

description:
NK-Cre CD11b- rep2
TRWR90

value: CD11b- NK cells


title: 01_051_J10

first: Melissa

last: Saichi

address: 1 avenue Claude Vellefaux

institute: Human Immunology Pathophysiology Immunotherapy (HIPI)- Inserm

data_processing:
sample de-multiplexing and alignment was performed using Cell Ranger Single Cell Software Suite (v3.1.0)
Fastq were aligned on Grch38 reference genome
Bam files and filtered expression matrices were generated using “cellranger_count”
All expression matrices were loaded into R 4.0.0 using “Read10X” function from Seurat library (3.1.5)
Seurat suite was used to perform downstream analyses
Genome_build: Grch38
Supplementary_files_format_and_content: Processed files are  separate “Seurat .Rds” files for each processed sample separately (“RNA” assay) whose names are specified in the “Processed data file” column table ; along with integrated Seurat objects with the original uncorrected matrix, in the "RNA" assay, and the batch-corrected matrix in the "SCT" assay (DiscoverySet_EDTA_SeuratObj.Rds and  ValidationSet_RPMI_SeuratObj.Rds)

source_name: Antigen Presenting Cells

extract_protocol: RNA from all the samples was extracted according to the Single Cell 3' Reagent Kits V2

treatment_protocol: Blood samples (20ml) were collected from each patient at days 1 and 4 post-hospital admission, and from HC. PBMC were isolated by centrifugation on a density gradient (Lymphoprep, Proteogenix). After FICOLL (GE Healthcare and Lymphoprep StemCell) gradient centrifugation, total PBMC were enriched in CD14+ monocytes using the human CD14 microbeads (Miltenyi Biotec) for positive magnetic selection according to the manufacturer’s instructions. The negative fraction remaining after the positive selection of CD14+ cells was used for pan-DC enrichment employing the EasySep human pan-DC enrichment kit (StemCell Technologies). Total pan-DC were resuspended with 20,000 CD14+ cells and sent for sequencing. Monocyte and pan-DC enrichment were performed immediately after sampling. To avoid DC-T cell clusters that often form in DC-enriched preparations, EDTA-containing medium (DPBS 1X, 0.5% EDTA, 1% Human Serum) was used for sample enrichment in the first set “Discovery set”. The latter was composed of  a total of 12 samples from 2 healthy donors, 3 moderate and 4 severe patients from both day-1 and day-4 time points. Because EDTA can decrease Reverse Transcription efficiency, we validated the findings derived from the discovery set by using RPMI for all enrichment steps (1640 + Glutamax, 2% BSA, 1% Penicillin/Streptomycin, 1% Sodium Puryvate, 1% MEM NEAA) in  a second set of samples, including a total of 15 samples, defined as “validation set”. The latter included 2 healthy donors, 2 moderate and 6 severe patients.

tag: suspension medium

value: RPMI

tag: dataset name

value: Validation Set

value: Antigen Presenting Cells

value: Blood

tag: gender

value: Male

tag: disease state

tag: disease severity

value: Severe

tag: timepoint

value: Day 10


title: 4-HPAA replicate 3

city: Cleveland

first: Lucas

last: Osborn

state: Ohio

address: 9500 Euclid Ave

institute: Cleveland Clinic Foundation

data_processing:
Basecalls performed using Illumina RTA3
Paired-end 100 bp reads were controlled for quality with FastQC (v0.11.9, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Reads were aligned to the Mus musculus reference transcriptome (NCBI GRCm38.p6 transcript annotations downloaded August, 2020) using the Kallisto pseudo-alignment (v0.46.0.4, https://pachterlab.github.io/kallisto/ ) [Bray et al., 2016] with standard parameters using Galaxy (https://galaxyproject.org/) [Afgan et al., 2018].
Pseudo counts were loaded into R (http://www.R-project.org/) (R Development Core Team, 2015) and DESeq2 [Love et al., 2014] (v.1.28.1, https://bioconductor.org/packages/release/bioc/html/DESeq2.html) was used to perform differential expression (DE) analysis on genes with 10 counts per sample with alpha set to 0.05. P-values were adjusted using the Benjamini-Hochberg method and genes with p<0.05 were considered statistically significant.
Heat maps were generated of top 50 differentially expressed transcripts using pheatmap [Kolde 2012] and RColorBrewer [Neuwirth, 2011]. Non-metric multidimensional scaling (NMDS) analysis was performed using the plotMDS function of edgeR [Robinson et al., 2010] using the top 500 DE genes as sorted by log2 fold change. Pathway analysis on the top 250 DE genes was performed using Metascape [Zhou et al., 2019].
Genome_build: NCBI GRCm38.p6
Supplementary_files_format_and_content: .txt file containing Kallisto-assigned pseudo counts

source_name: Liver tissue

extract_protocol:
QIAGEN Rneasy
First, RNA quality was checked using a Bio-analyzer (Agilent). Then, libraries were prepared using the Illumina mRNA TruSEQ Directional library kit. Sequencing was performed using an Illumina NovaSeq 6000

treatment_protocol: Either normal saline or 4-HPAA was administered intraportally for 2 weeks following necropsy and subsequent RNA sequencing.

value: Liver


title: CD4 T-cell CEBPb noArg Input

first: Thomas

last: Milne

description: Input for C/EBPbeta ChIP-seq in stimulated CD4 T-cells cutured in the absence of arginine

data_processing:
Alignment to the genome (Bowtie) maintaining strict read order
Trim_galore (to remove sequencing adaptors)
FLASH (to reconstruct paired end reads into single reads where possible)
Removal of PCR duplicates, parsing of informative reads using samtools rmdup
Genome_build: hg19
Peak calling using Homer v4.7

value: Stimulated human CD4 T-cells

value: Human CD4+ T-cells purified from PBMCs, stimulated with anti-CD3/anti-CD28 beads


title: 4-HPAA replicate 4


title: 01_43_J0


title: 01_051

value: Day 1


title: 4-HPAA replicate 2


title: 4-HPAA replicate 1


title: Tbet WT CD11b- rep2

description:
Tbet WT CD11b- rep2
TRWR94

value: WT


title: NK-Cre CD27- rep2

description:
NK-Cre CD27- rep2
TRWR89

value: NK cells

value: Cre


title: Normal Saline replicate 4

value: Normal Saline


title: 01_42_J16

value: Day 16


title: Con1

value: macrophage

value: untreated

value: BALB/c


title: 01_42_J0

value: RPMI

value: Validation Set

value: Antigen Presenting Cells


title: CD4 T-cell CEBPb noArg

description: C/EBPbeta ChIP-seq in stimulated CD4 T-cells cutured in the absence of arginine

value: Cells cultured in arginine-free RPMI for 72h

value: Bethyl A302-738A


title: Tbet Ho CD27- rep1

description:
Tbet-/- CD27- rep1
TRWR87

value: CD27- NK cells


title: Normal Saline replicate 3

value: Liver


title: CD4 T-cell ATF4 lowArg Input

description: Input for ATF4 ChIP-seq in stimulated CD4 T-cells cutured under low (20uM) arginine conditions

value: Stimulated human CD4 T-cells

value: Cells cultured in low (20uM) arginine RPMI for 72h

value: Human CD4+ T-cells purified from PBMCs, stimulated with anti-CD3/anti-CD28 beads


title: Tbet WT CD11b- rep1

description:
Tbet WT CD11b- rep1
TRWR86

value: NK cells

value: WT

value: CD11b- NK cells


title: 01-053

value: Blood

value: Male

value: Severe

value: Day 1


title: 01_050

value: RPMI


title: Tbet WT CD27- rep1

description:
Tbet WT CD27- rep1
TRWR85


title: WGBS-regulatory T cells- Foxp3 enhancer CNS0 and CNS2 double knockout-replicate 2

description: Genome-wide bisulfite sequencing (WGBS)

data_processing:
Whole-genome bisulfite sequencing (WGBS) data were aligned to mouse genome mm9 assembly by using BSMAP2.74.
The methylation ratio for each CpG site was extracted by methratio.py from BSMAP2.74. The methylation ratio was then converted to bw file for visualization. Regions covered by < 5 reads were marked as -0.2.
Genome_build: mm9(MGSCv37 )
Supplementary_files_format_and_content: bigwig

source_name: Regulatory T cells were sorted by GFP expression from mixed bone marrow chimeric mice generated with bone marrows from male donors of CD45.1 wild-type mice and CD45.2 mice of indicated genotypes

extract_protocol:
Genetic DNA was extracted by proteinase K digestion followed by phenol-chloroform extraction and isopropanol precipitation.
Standard protocols for genome-wide bisulfite sequencing.

value: FACS sorted regulatory T cells (CD4+GFP+)


title: Normal Saline replicate 1

value: Normal Saline


title: CD4 T-cell ATF4 lowArg

description: ATF4 ChIP-seq in stimulated CD4 T-cells cutured under low (20uM) arginine conditions

source_name: Stimulated human CD4 T-cells

value: Cell Signaling Technology 11815


title: 01_047

value: Validation Set

value: Antigen Presenting Cells


title: Eomes Ho CD11b- rep1

description:
Eomes-/- CD11b- rep1
TRWR84

value: Eomes-/-


title: CD4 T-cell ATF4 noArg Input

description: Input for ATF4 ChIP-seq in stimulated CD4 T-cells cutured in the absence of arginine

value: Stimulated human CD4 T-cells

value: Cells cultured in arginine-free RPMI for 72h


title: Tbet Ho CD11b- rep1

description:
Tbet-/- CD11b- rep1
TRWR88


title: CD4 T-cell ATF4 noArg

description: ATF4 ChIP-seq in stimulated CD4 T-cells cutured in the absence of arginine

value: Human CD4+ T-cells purified from PBMCs, stimulated with anti-CD3/anti-CD28 beads


title: WGBS-regulatory T cells- Foxp3 enhancer CNS0 knockout-replicate 2

description: Genome-wide bisulfite sequencing (WGBS)

value: Foxp3 enhancer CNS0 knockout


title: NK-Cre CD11b- rep1

description:
NK-Cre CD11b- rep1
TRWR82

value: NK cells

value: Cre


title: 04_01_J0

value: Blood

value: Moderate


title: WGBS-regulatory T cells- Foxp3 enhancer CNS0 and CNS2 double knockout-replicate 1

description: Genome-wide bisulfite sequencing (WGBS)


title: HeLa ATF4 noTrp

description: ATF4 ChIP-seq in HeLa cells cutured in the absence of tryptophan

source_name: Cancer cell line (HeLa)

value: Cancer cell line (HeLa)

value: Cells cultured in tryptophan-free DMEM for 72h

value: Immortalized cell line derived from cervical cancer


title: 01_048_J5

value: RPMI

value: Male


title: NK-Cre CD27- rep1

description:
NK-Cre CD27- rep1
TRWR81

value: CD27- NK cells


title: 01_042_J4

value: Validation Set

value: Severe


title: 04_001_J5

value: Antigen Presenting Cells

value: Day 1


title: WGBS-regulatory T cells- Foxp3 enhancer CNS0 knockout-replicate 1

description: Genome-wide bisulfite sequencing (WGBS)

value: FACS sorted regulatory T cells (CD4+GFP+)


title: THP1 noArg Input

description: Input for ATF4 and C/EBPbeta ChIP-seq in THP1 cells cutured in the absence of arginine

value: Leukemia cell line (THP1)

value: Cells cultured in arginine-free RPMI for 72h

value: Paediatric monocytic cell line derived from AML M5 with t(9;11)(q21;q23) translocation


title: WGBS-regulatory T cells- Foxp3 enhancer CNS2 knockout-replicate 2

description: Genome-wide bisulfite sequencing (WGBS)

value: Foxp3 enhancer CNS2 knockout


title: Normal Saline replicate 2

value: Normal Saline

value: Liver


title: 01_048_J0

value: Blood

value: Moderate


title: THP1 CEBPb noArg

description: C/EBPbeta ChIP-seq in THP1 cells cutured in the absence of arginine

value: Bethyl A302-738A


title: KO2

city: Bethesda

first: Yuhong

last: Luo

state: MD

address: 37 Convent Dr

department: NCI

institute: NATIONAL INSTITUTES OF HEALTH

description: Raw gene counts matrix.txt

data_processing:
reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (Mouse - mm10) and the annotated transcripts using STAR.
The mapping statistics were calculated using Picard software. Library complexity was measured in terms of unique fragments in the mapped reads using Picard’s MarkDuplicate utility. The gene expression quantification analysis was performed for all samples using STAR/RSEM tools.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: intestine

extract_protocol:
Total RNA was isolated from mice liver using RNeasy Plus Mini Kit (Qiagen, Germantown, MD, #74136) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using Illumina TruSeq Stranded mRNA Library Prep.

treatment_protocol: 7-8 weeks old male MycΔIE, ERT2 and Mycfl/fl mice were injected intraperitoneally with tamoxifen and fed an 60% HFD for 2 weeks.

value: intestine

value: Myc<delta>IE, ERT2


title: Eomes Ho CD27- rep1

description:
Eomes-/- CD27- rep1
TRWR83

value: NK cells

value: Eomes-/-

value: CD27- NK cells


title: WGBS-regulatory T cells-wild type Foxp3-GFP-replicate 2

description: Genome-wide bisulfite sequencing (WGBS)

value: wild type Foxp3-gfp


title: HeLa ATF4 noTrp Input

institute: University of Oxford

description: Input for ATF4 ChIP-seq in HeLa cells cutured in the absence of tryptophan

value: Cancer cell line (HeLa)

value: Cells cultured in tryptophan-free DMEM for 72h

value: Immortalized cell line derived from cervical cancer


title: CTRL_RPMI

value: RPMI

value: Validation Set

value: Antigen Presenting Cells

value: Male

value: Healthy

value: Day 1


title: KO1

description: Raw gene counts matrix.txt


title: CTRL_02020

value: Blood


title: WT3

description: Raw gene counts matrix.txt

value: Mycfl/fl


title: RNA Pol II-CutRun-regulatory T cells-Foxp3 CNS0 and CNS2 double knockout (CNS02DKO)

data_processing:
Library strategy: Cut&Run
Paired-end reads of 50bp were mapped mouse genome mm9 (MGSCv37 from Sanger) by BWA (version 0.7.12-r1039, default parameter) after trimming for adapters by cutadapt(version 1.9, paired-end mode, default parameter with “ -m 25 -O 6 ”), duplicated reads were then marked with biobambam2(version v2.0.87).
Only non-duplicated reads have been kept by samtools (parameter “-q 1 -F 1804” version 1.2).
All samples have more than 5M fragments as suggested by Cut&Run protocols paper after merging replicates. We then generated bigwig files by using the center 80bp of fragments smaller than 2000bp and normalized to 10M fragments. We confirmed clear peak patterns.
Genome_build: mm9(MGSCv37 )
Supplementary_files_format_and_content: bigwig

growth_protocol: Regulatory T cells were sorted by GFP expression from mixed bone marrow chimeric mice.

extract_protocol:
Cut&Run was performed according to a method recently described (PMID: 28079019).
Libraries were constructed according to standard protocols for Cut&Run sequencing.

value: FACS sorted regulatory T cells (CD4+GFP+)

value: deficiency of Foxp3 enhancer CNS0 and CNS2 (CNS02DKO)


title: WT2

description: Raw gene counts matrix.txt

value: intestine


title: M3B: mouse 3 - non-wounded tissue

city: La Jolla

first: Deborah

last: Witherden

state: CA

address: 10550 North Torrey Pines Rd

institute: Scripps Research

data_processing:
Alignment to mouse (genome build mm10) and quantification were conducted using Salmon
Statistical analysis of differential gene expression was conducted using edgeR
Genome_build: mm10
Supplementary_files_format_and_content: matrix tables with raw gene counts ("counts" tab) and expression levels in transcripts per million ("TPM" tab) for every gene in every sample

source_name: whole epidermis

extract_protocol:
Epidermis was separated from dermis following incubation in trypsin solution. RNA was harvested using Trizol followed by Qiagen Rneasy kit.
RNA libraries were prepared for sequencing poly-dT capture and sequencing

treatment_protocol: 6-8 week old mice were wounded with a 3mm punch biopsy in back (8 wounds). Tissue was collected 2 hours post-wounding

value: 6-8 weeks

value: epidermis


title: 03_01_J1

value: EDTA

value: Discovery Set

value: Severe


title: KO3

description: Raw gene counts matrix.txt

value: Myc<delta>IE, ERT2


title: M3W: mouse 3 - wounded tissue


title: WT1

description: Raw gene counts matrix.txt


title: GSK rep3

description: Raw gene counts matrix.txt

source_name: liver tumor

extract_protocol:
Total RNA was isolated from mice liver using RNeasy Plus Mini Kit (Qiagen, Germantown, MD, #74136) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using Illumina TruSeq Stranded Total RNA Library Prep.

treatment_protocol: LAP-tTA-tetO-MYC mice was administered doxycycline (DOX) in drinking water at 100 mg/L until the mice reached 4 weeks of age. Then the MYC transgene was turned on by withdraw DOX in the drinking water.MYC-ON mice were treated with vehicle or 50 mg/kg/day GSK3326595 for 2 weeks after turned on MYC transgene for 8 weeks.

value: FVB/N

value: liver tumor


title: 037-J0

value: Antigen Presenting Cells


title: P037-J4

value: Male


title: M2B: mouse 2 - non-wounded tissue


title: GSK rep2

description: Raw gene counts matrix.txt


title: RNA Pol II-CutRun-regulatory T cells-Foxp3 CNS2 knockout

value: deficiency of Foxp3 enhancer CNS2 (CNS2KO)


title: RNA Pol II-CutRun-regulatory T cells-WT Foxp3-GFP

value: wild type Foxp3-GFP


title: M2W: mouse 2 - wounded tissue


title: M1W: mouse 1 - wounded tissue


title: M1B: mouse 1 - non-wounded tissue


title: 01_054_J0

value: Blood

value: Day 1


title: WGBS-regulatory T cells-wild type Foxp3-GFP-replicate 1

description: Genome-wide bisulfite sequencing (WGBS)

value: FACS sorted regulatory T cells (CD4+GFP+)

value: wild type Foxp3-gfp


title: GSK rep1

description: Raw gene counts matrix.txt


title: H3K27ac-CutRun-regulatory T cells-Foxp3 CNS0 and CNS2 double knockout (CNS02DKO)

value: deficiency of Foxp3 enhancer CNS0 and CNS2 (CNS02DKO)


title: H3K27ac-CutRun-regulatory T cells-Foxp3 CNS0 knockout

value: deficiency of Foxp3 enhancer CNS0 (CNS0KO)


title: 01_049


title: chondrocyte stimulated by activated macrophages using cartilage fragments 3

city: Sapporo

first: Mohamad Alaa

last: Terkawi

state: Hokkaido

address: Kita-15, Nish-7, Kita-ku

department: Department of Orthopedic Surgery

country: Japan

institute: Hokkaido University

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped by alignment to mouse genome (mm10) using TopHat and Bowtie, normalized using the Trimmed Mean of M values (TMM) process, and then annotated using Cufflinks and Cuffdiff. Low calculated fragments per kilobase of transcript per million mapped reads (FPKM) were removed.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.gtf: Tab-delimited text files include FPKM values for each Sample.

source_name: Primary mouse chondrocyte

growth_protocol: Cartilages were harvested from mouse knee joint. After exposing to collagenase D solution overnight, chondrocytes were isolated and cultured in DMEM supplemented with 10% FBS and 25mg/l penicillin/streptomycin and 2mM L-glutamine.

extract_protocol:
Chondrocytes were lysed with TRIzol Reagent and harvested for RNA purification. RNA was purified using RNeasy Mini kit columns according to the manufacturer's instructions, and integrity of samples was assessed by determining 28S/18S ribosomal RNA bands with an Agilent 2100 Bioanalyzer.
High-quality DNA-free RNA with integrity score > 9.0 was further used for RNA-seq. Each library was generated from 0.5-1 μg pooled RNA of 3 donors (equal quantity) using the TruSeq® Stranded mRNA Sample Preparation Kit. Quality of libraries was examined by Bioanalyzer High sensitivity DNA kit, and then paired-end reads (101 bp) were obtained by Illumina HiSeq 2500, with an average of 69 million reads per sample. Reads were mapped by alignment to mouse genome (mm10) using TopHat and Bowtie, normalized using the Trimmed Mean of M values (TMM) process, and then annotated using Cufflinks and Cuffdiff.

treatment_protocol: Chondrocytes were indirectly co-cultured with activated macrophages by cartilage fragments using transwell inserts for 48 hours as earlier described. Control chondrocytes were cultured alone.

value: knee cartilage

value: chondrocytes

value: macrophages activated by cartilage fragments


title: vehicle rep3

description: Raw gene counts matrix.txt

value: vehicle


title: 03_01_J5

value: EDTA

value: Discovery Set

value: Severe


title: 05-01-J4

value: Antigen Presenting Cells

value: Moderate


title: 05_02

value: Female


title: chondrocyte stimulated by activated macrophages using cartilage fragments 1


title: H3K27ac-CutRun-regulatory T cells-WT Foxp3-GFP

value: wild type Foxp3-GFP


title: vehicle rep1

description: Raw gene counts matrix.txt

value: FVB/N

value: liver tumor


title: WGBS-regulatory T cells- Foxp3 enhancer CNS2 knockout-replicate 1

description: Genome-wide bisulfite sequencing (WGBS)

value: FACS sorted regulatory T cells (CD4+GFP+)

value: Foxp3 enhancer CNS2 knockout


title: H3K4me3-CutRun-regulatory T cells-Foxp3 CNS0 and CNS2 double knockout (CNS02DKO)

value: deficiency of Foxp3 enhancer CNS0 and CNS2 (CNS02DKO)


title: 01_052

value: Blood

value: Male

value: Day 1


title: H3K4me3-CutRun-regulatory T cells-Foxp3 CNS0 knockout

value: deficiency of Foxp3 enhancer CNS0 (CNS0KO)


title: control chondrocyte 2

value: knee cartilage

value: chondrocytes

value: control


title: CTRL_02022

value: EDTA

value: Discovery Set

value: Healthy


title: Noncachexia2

first: Diya

last: Sun

address: Dongan Street

institute: Zhongshan Hospital Fudan University

data_processing:
Illumina CASAVA 1.7software was used for basecalling
Raw reads generated during high-throughput sequencing were fastq format sequences. In order to get high-quality reads that could be used for later analysis, raw reads needed to be further quality filtered. Trimmomatic version 0.36 software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out. Finally, we got high-quality clean reads.
Using hisat2 version 2.2.1.0 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment.
Genome_build: Genome Database GRCh38.p12
Supplementary_files_format_and_content: Table with raw gene counts or normalized abundance measurements for every gene and every sample

source_name: Adipose tissue_noncachexia

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA)
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions. Then these libraries were sequenced on the Illumina sequencing platform and 150 bp/125bp paired-end reads were generated.

tag: subject status

value: noncachexia cancer patient

tag: tumor stage

value: II stage

value: Adipose tissue


title: vehicle rep2

description: Raw gene counts matrix.txt

value: FVB/N

value: liver tumor

value: vehicle


title: control chondrocyte 3


title: 05_01_J1

value: Antigen Presenting Cells

value: Moderate


title: H3K4me3-CutRun-regulatory T cells-Foxp3 CNS2 knockout

value: FACS sorted regulatory T cells (CD4+GFP+)

value: deficiency of Foxp3 enhancer CNS2 (CNS2KO)

tag: chip antibody


title: control chondrocyte 1

tag: treatment


title: Noncachexia3

value: Male


title: Noncachexia1


title: H3K4me3-CutRun-regulatory T cells-WT Foxp3-GFP

tag: genotype

value: wild type Foxp3-GFP


title: chondrocyte stimulated by activated macrophages using cartilage fragments 2

tag: tissue

value: knee cartilage

value: chondrocytes

value: macrophages activated by cartilage fragments


title: H3K27ac-CutRun-regulatory T cells-Foxp3 CNS2 knockout

tag: cell type


title: Cachexia3

source_name: Adipose tissue_Cachexia

value: Cancer-associated cachexia (CAC) patient

value: III stage


title: 15717X16 SJL PLX CD8 rep 2

city: Salt Lake City

first: Ana Beatriz

last: DePaula-Silva

state: UT

address: 15N Medical Drive East room 2800

department: Pathology

institute: University of Utah

data_processing:
The mouse GRCm38 FASTA and GTF files were downloaded from Ensembl release 94.
The reference database was created using STAR version 2.6.1b with splice junctions optimized for 50 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1.
Differentially expressed genes were identified using a 5% false discovery rate with DESeq2 version 1.20.0
Supplementary_files_format_and_content: FeatureCount output files combined into tab-delimited file

source_name: Brain

extract_protocol:
RNA was extracted using RNeasy
Illumina TruSeq stranded RNA Kit with Ribo-Zero Gold

treatment_protocol: PLX5622 or control diet

tag: mouse strain

value: SJL/J

tag: diet

value: PLX

value: CD8 T cells


title: CTRL_02021

value: EDTA

value: Discovery Set

value: Blood

value: Female

tag: age

value: Healthy

value: Day 1