title: A673 ETV6 dTAG cells - 6 hour dTAGV-1 treated  - input DNA reference - replicate 1


title: RARα KO, 10nM RA (H3k27ac)

status: Public on Oct 05 2022

type: SRA

city: Ann Arbor

first: Chang

last: Kim

address: 109 Zina Pitcher

country: USA

institute: University of Michigan

library_source: genomic

data_processing:
Reads were quality trimmed and Illumina adapter sequences were removed.
Alignment of reads to the GRCm38 mm10 Ensembl mouse genome was performed with Bowtie.
ChIP-seq coverage plots in bigWig files were created with bins of 100bp and normalized to reads per million.
Differences in H3k27ac enriched signal by subtracting normalized input with bigwigCompare.
Peaks were called uing MACS2
Assembly: mm10
Supplementary files format and content: bigWig files containing H3K27ac signal - input signal

molecule: genomic DNA

organism: Mus musculus

source_name: CD4 T cells

growth_protocol: Naïve CD4 T cells (>95% pure) were cultured in cRPMI (w/charcoal-stripped FBS) and activated with anti-CD3 and anti-CD28 in the presence of mIL-6 (20 ng/mL), mIL-1β (10 ng/mL), mIL-21 (10 ng/mL), mIL-23 (10 ng/mL), mTNFα (5 ng/mL), hTGFβ-1 (5 ng/mL), anti-IFNγ (10 μg/mL), and anti-IL-4 (10 μg/mL) for 16h.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. Samples were Mnase treated for 6 minutes and sonicated to achieve desired chromatin banding of 150-900bp. IP was performed overnight with clone D5E4 for H3k27ac using the magnetic SimpleChIP kit (Cell Signaling)
Indexed libraries were generated using the ThruPLEX DNA-seq kit (Takara; Mountain View, CA) with 13 cycles of amplification
ChIPseq. 1 x 50 bp sequencing was performed on a NovaSeq 6000 (Illumina; San Diego, CA).

treatment_protocol: Cells were cultured with or without RA at 10nM for the 16h of culture.

tag: cell type

value: CD4 T cells

tag: culture conditions

value: 16h w/ 10nM RA

tag: strain

tag: genotype

value: RAR{alpha} KO

tag: chip antibody


title: LIVE_ATAC, Rep1

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Data was processed using the nf-core atacseq pipeline (https://nf-co.re/atacseq) with the following options: --genome mm10  -r 1.2.0
Counts across the library consensus peak were used as input for DESeq2 to generate the consensus_peaks.mLb.vsd.csv file
Assembly: mm10
Supplementary files format and content: Counts across the library consensus peak were used as input for DESeq2 to generate the consensus_peaks.mLb.vsd.csv file

growth_protocol: Mouse ES cell lines were maintained in ES cell medium with 1000 U/ml LIF (Chemicon, Int ESG1107) on mitotically inactive primary mouse embryo fibroblasts (feeders) in ES cell medium (Dulbecco’s Modified Eagle Medium (DMEM) Knock Out (Gibco, Cat No. 10829-018) complemented with 10% Foetal Bovine Serum, Penicillin/Streptomycin (Gibco, Cat No. 15140122), 2mM L-Glutamine (Gibco, Cat No. 25030024), 2mM Non-essential amino acids (Gibco, Cat No. 11140-035), and 0.1 mM 2-mercaptoethanol (Gibco, Cat. No. 21985-023)). For spinal cord neural differentiation, ES cells were dissociated using 0.05% trypsin-EDTA (Gibco, Cat No. 25300054) and then plated onto 0.1% gelatinised (Gibco) tissue culture plates for three successive periods of 15 mins to remove feeders. Differentiations were carried out in N2B27 media (Advanced DMEM - F12 (Gibco, Cat No. 21331-020) and Neurobasal medium (Gibco, Cat No. A35829-01) (1:1), supplemented with 1xN2 (Gibco), 1xB27 (Gibco), 2 mM L-glutamine (Gibco, Cat No. 25030024), 40 μg/ml BSA (Sigma), and 0.1 mM 2-mercaptoethanol (Gibco, Cat. No. 21985-023)) with the indicated additives. Cells were plated onto 6-well plates (Corning, Cat. No. 353046) precoated in Matrigel (Corning, Cat. No. 356231) diluted 1/50 and 1/100 in Advanced DMEM - F12 (Gibco, Cat No. 21331-020) at a density of 20,000 cells per 35mm well in 1.5 ml. The media was supplemented on the different days as follows: Day 0 to Day 2, 10ng/ml bFGF (R&D, Cat No. 100-18B) and 5 μM LGK (Cayman Chemical Company, Cat. No. 1.800.364.9897); Day2 to Day 3 for 20 h, 10ng/ml bFGF (R&D, Cat No. 100-18B), 5 μM CHIR99021 (Axon Medchem, Cat. No. 1386), 10 μM SB-431542 (Tocris, Cat. No. S0400), and 2μM  DMH1 (Adooq Bioscience, Cat. No. A12820); from Day 3 to D5, 100 nM RA (Sigma, Cat No. R2625) and 100 nM SAG (Merck, Cat. No. 566660-5mg).

extract_protocol:
Trasposition was performed as previously described with 50,000 cells.
Transposed DNA was first amplified as described in Corces et al (2017) and Ma et al (2020)

tag: cell line

value: NPs


title: H3K9me3-HeLa-2_S6_L001

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

library_source: transcriptomic

data_processing:
Paired end reads from 3 replicates each for H3K9me3 and H3Q5ser modifications in HeLa cell line (with a single input sample) were processed by trimming the adapter sequences using Trim Galore.
Trimmed reads were further aligned to the hg38 Ensembl v90 human reference genome using HISATv2.2.1.
Peak calling was performed using MACS software to obtain sites of H3K9me3 and H3Q5ser histone modifications.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file

molecule: total RNA

organism: Homo sapiens

source_name: HeLa

extract_protocol:
Adherent HeLa S3 cells were crosslinked with 1% formaldehyde for 10 minutes, and the reaction was stopped with 0.125 M glycine for 10 minutes. Chromatin was sheared by sonication (Covaris S220) to 200-800 bp in ChIP lysis buffer (50 mM Hepes, pH 7.4, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% Na-deoxycholate, 0.5 mM PMSF). 5-10 ug of sonicated chromatin were incubated with H3K9me3 antibody (Active Motif, #39161) and H3Q5ser antibody (Millipore Sigma, #ABE1791) at 4°C for 4 h, then incubated with washed Protein A/G Dynabeads (Invitrogen, #10001D) at 4°C for 2 h. The beads were washed once with ChIP Lysis Buffer, High Salt Buffer (50 mM Tris, pH 7.4, 500 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate), LiCl Buffer (20 mM Tris, pH 7.4, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Na-deoxycholate) and TE Buffer (10 mM Tris PH8.0, 1 mM EDTA) in sequence. The beads were resuspended with Elution Buffer (50 mM Tris, pH 8.0, 10 mM EDTA, 1% SDS) and incubated at 65°C for overnight. The crosslink-reversed ChIP product was then treated using RNase A and Proteinase K. The final sample was extracted using QIAquick PCR Purification Kit (Qiagen).
ChIP-seq library is prepared using a SWIFT Accel-NGS® 2S DNA Library Kit

value: H3K9me3 (Active Motif, #39161)

value: HeLa


title: RARα KO, 10nM RA (input)


title: RARα TG, 0nM RA (H3k27ac)

value: 16h w/o RA

value: RAR{alpha} TG


title: A673 ETV6 dTAG cells - 6 hour dTAGV-1 treated  - FLI1 ChIP-seq - replicate 2

city: Boston

first: Kenneth

middle: N

last: Ross

state: MA

address: 450 Brookline Ave., Room LC6115

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

data_processing:
The raw Illumina sequencer output was converted to FASTQ format using the program bcl2fastq (v2.17).
Sequencing read quality was examined using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.9).
Trimming of low-quality reads and clipping of sequencing adapters was done using the program Trimmomatic (v0.36) and all reads shorter than 40bp after trimming were dropped.
Reads were aligned to the human genome (hg19) using Bowtie2 (v2.3.5) using the ‘—very_sensitive’ preset collection of parameters.
Bam to Sam file conversion was done with SamTools (v1.9) and duplicate reads were removed using Picard-tools (v2.19.0) (http://picard.sourceforge.net).
ChIP-seq peaks were called using MACS2 (v2.1.4) with the command callpeak with the ChIP-seq treatment and control bam files and minimum False Discovery Rates (FDR) set to q < 0.01
BigWig files were created from bam files using the program bamCoverage in the python deeptools software suite (v3.3.0) with a default read extension length of 180. For parental cell line samples and untreated ETV6 dTAG samples, bamCoverage was run on the deduplicated bam files from picard tools.  For the DMSO and dTAGV-1 treated ETV6 dTAG samples, deduplicated read counts were adjusted to normalize to the fly spike-in control levels using picard DownsampleSam before running bamCoverage.
Genome_build: hg19
Supplementary_files_format_and_content: *.xls files are tab delimited text files with ChIP-seq peaks data from MACS2; *.bw files are read coverage files in bigWig format from bamCoverage

source_name: A673 Ewing sarcoma cell line

growth_protocol: All cell lines were genotyped by short tandem repeat analysis and Mycoplasma tested. Additionally, whole exome sequencing and RNA-sequencing were previously performed to validate cell line identity. A673 and EW8 Ewing sarcoma cells were grown in Dulbecco’s Modified Eagle’s Media (DMEM) (Thermo Fisher Scientific, # MT10013CM), supplemented with 10% Fetal Bovine Serum (Sigma-Aldrich, #F2442) and 1% Penicillin-Streptomycin (Life Technologies, #15140163). For dTAG cell lines, A673 and EW8 Ewing sarcoma parental cells were co-transduced with the following lentivirally packaged constructs. Four sgRNAs targeting exon-intron junctions of the endogenous ETV6 gene were cloned into a version of the LentiCRISPRv2 plasmid backbone conferring blasticidin resistance (Addgene 83480). The sgRNA sequences used were (1) sgETV6-endo-1, 5’-TCCTGCTCAGTGTAGCATTA-3’, (2) sgETV6-endo-2, 5’-GAACACTCACGCAGGTGCGC-3’, (3) sgETV6-endo-3, 5’-TCCAGACTCTCACCTGAATG-3’, and (4) sgETV6-endo-4, 5’-AGTTCATAGAGCACATCACC-3’. A codon-optimized gblock encoding coding sequences of ETV6 was cloned into the pLEX_305 vector backbone (Addgene 91798) to C-terminally tag the ETV6 protein with the FKBP12F36V protein domain and a HA epitope tag. Cells were incubated for 24 hours, after which viral media was replaced by media containing 1 µg/ml puromycin and 5 µg/ml blasticidin (Life Technologies, #A1113903) and supplemented with 40% FBS for 48-72 hours. Non-infected control cells were treated with puromycin or blasticidin to confirm selection. Cells were cultured in Dulbecco’s Modified Eagle’s Media supplemented with 15% FBS and 1% penicillin streptomycin glutamine, as well as 0.5 µg/ml puromycin and 2.5 µg/ml blasticidin to maintain selection. Cells were split at a ratio of 1:5 every other day.

extract_protocol:
Prior to immunoprecipitation (IP), antibodies targeting proteins of interest were conjugated to magnetic beads as follows. For each IP, 100 µl of magnetic Protein A Dynabeads (Thermo Fisher Scientific, 10002D) were washed three times in 1 ml BSA blocking solution (0.5% w/v sterile-filtered Bovine Serum Albumin in H2O) and resuspended in 250 µl of the solution. Beads were then rotated overnight at 4ºC with antibody, using 5 µg of antibody to detect H3K27ac (Abcam, # 4729) or 10 µg of antibody to detect TFs (anti-HA, Abcam, # ab9110; anti-FLI1, Abcam, ab15289). For comparative studies (i.e., comparing the relative binding of EWS/FLI), 2 µg of spike-in antibody recognizing a Drosophila-specific histone variant was added (Active Motif, # 61686). The following morning, the antibody-conjugated beads were washed four times in 1 ml BSA blocking solution and then resuspended in 100 µl of the solution and stored at 4ºC until use. To prepare sheared chromatin, Ewing sarcoma cells (20 million cells per ChIP reaction) were collected in a 1.5 ml reaction tube and washed twice in 1 ml PBS. Cells were then crosslinked by resuspension in 1 ml PBS containing 1% methanol-free formaldehyde (Thermo Fisher Scientific, # 28906) and rotated for 10 minutes at room temperature at 12 RPM. The fixation reaction was quenched by adding 100 µl of 1.25M glycine (Sigma Aldrich, # G7126) and 100 µl 1M Tris-HCl pH 8.0 (Thermo Fisher Scientific, # 15568025). Cell pellets were washed twice with 1 ml PBS at room temperature and resuspended in 1 ml of SDS Lysis Buffer (0.5% SDS, 5 mM EDTA, 50 mM Tris-HCl pH 8.0) supplemented with protease inhibitor cocktail (Thermo Fisher Scientific, # PI78429) and incubated at room temperature for 2 minutes with gentle agitation. Lysates were centrifuged at 15,000xg for 10 minutes at 4°C. The supernatant was discarded and the transparent nuclear pellet was re-suspended in 950 µl of ChIP IP Buffer (2 parts SDS Lysis Buffer and 1 part Triton Dilution Buffer, which was composed of 100 mM Tris-HCl pH 8.0, 100mM NaCl, 5mM EDTA, 0.2% NaN3, and 5% Triton X-100) supplemented with protease inhibitor cocktail and transferred to a milliTUBE (Covaris Inc, # 520130) for shearing of chromatin. Sonication was performed on an E220 Focus Ultra Sonicator (Covaris) using the settings 5% duty cycle, 140W peak power, 200 cycles per burst, at 4°C, at 30 minutes per milliTUBE. Following sonication, sheared chromatin was transferred to a 1.5 ml reaction tube and centrifuged at 15,000xg for 10 minutes at 4°C to pellet debris. The supernatant, constituting cleared sheared chromatin, was transferred to a new reaction tube. To prepare the ChIP DNA Input sample, 5 µl of sheared chromatin was transferred to a PCR strip-tube and mixed with 40 µl de-crosslinking buffer (100 mM NaHCO3 and 1% SDS buffer), 1 µl RNAse A (Thermo Fisher Scientific, # 12091021), and 1 µl Proteinase K (Thermo Fisher Scientific, # AM2546). The tube was incubated for 2 hours at 65°C in a thermal cycler to de-crosslink DNA-protein covalent bonds. DNA was then isolated using Agencourt AMPure XP bead-based purification at a 1.2X ratio (Beckman Coulter, # A63881), eluted in 50 µl H2O, and stored at -20ºC. The remaining sheared chromatin was divided or pooled according to the target of interest; at least 5 million cells were used for immunoprecipitation of histone marks and 40 million cells for transcription factors (TFs). Each IP reaction was brought up to a total volume of at least 1 ml with ChIP IP buffer in a 1.5 ml tube. Pooled reactions were conducted in 2 ml or 5 ml reaction tubes. 50 ng of Drosophila spike-in chromatin was added for each H3K27ac ChIP reaction, while 20 ng of spike-in chromatin was added for each TF ChIP reaction. The 100 µl conjugated bead-antibody solution was then added to the sheared chromatin. IP reactions were rotated overnight at 4°C. The following day, ChIP reactions were washed twice in 1 ml low salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl), then twice in 1 ml high salt buffer (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 500 mM NaCl), then twice in 1 ml lithium chloride buffer (0.25 M LiCl, 1% IGEPAL-CH 630, 1% sodium deoxycholate, 10 mM Tris-HCl pH 8.0, 1 mM EDTA), and then once in 700 µl Tris-EDTA buffer (Sigma Aldrich, # 93283). All washes were performed on ice using buffers that had been stored at 4ºC. Chromatin was eluted from beads using 100 µl fresh ChIP Elution Buffer (1% SDS, 0.1M NaHCO3) and rotated at room temperature for 15 minutes. Eluate was transferred to PCR tubes and mixed with 8 µl 2.5M NaCl, 1 µl RNAse A, and 1 µl Proteinase K. Samples were de-crosslinked for 12-16 hours at 65°C on a thermal cycler. ChIP DNA was extracted from the de-crosslinked samples using AMPure XP beads at a 1.2X ratio and eluted in 20 µl of H2O. DNA from input and ChIP samples were quantified using a Qubit fluorometer (Thermo Fisher) and the Qubit dsDNA high sensitivity assay (# Q32851).
ChIP-seq libraries were prepared using the SMARTer ThruPLEX DNA-Seq kit (Takara Bio, # R400674). H3K27ac ChIP-seq samples were amplified 4 PCR cycles. TF ChIP-Seq samples were amplified 10 PCR cycles. Samples were single-indexed (Takara Bio, # R400695). The concentration of DNA in each library was measured by Qubit and the average of DNA fragment sizes was measured by Tapestation. The approximate molarity of each library was calculated. Each library was diluted to a concentration of 4 nanomolar and equal volumes of each library were pooled. The approximate molarity of the pool was then determined by Qubit and Tapestation and adjusted for sequencing according to Illumina standards. Libraries were sequenced, in 37-basepair paired-end fashion for 75 cycles (Illumina Inc, # 20024906), at a depth of roughly 30 million reads per sample, on the Illumina NextSeq 500 instrument.

treatment_protocol: The dTAGV-1 molecule was generously provided by the Gray Laboratory (Dana-Farber Cancer Institute, Boston, MA) and used at a stock concentration of 10 millimolar suspended in DMSO. For ChIP-seq experiments, A673 ETV6-dTAG cells were seeded at 5 million cells per 15 cm dish for the 6-hour time point and 1 million cells per 15 cm dish for the 72-hour time point. EW8 ETV6-dTAG cells were seeded at 7.7 million cells per 15 cm dish for the 6-hour time point and at 1 million cells per 15 cm dish for the 72-hour time point. Following seeding, cells were allowed to adhere for 24 hours prior to treatment. Existing media was aspirated and DMSO or dTAGV-1-containing media was added. For all experiments, dTAGV-1 was used at a final concentration of 1 micromolar. Equivalent volumes of DMSO were used as control.

tag: chip anti-body

value: FLI1 (Abcam, ab15289)

tag: modification type

value: dTAG

tag: modification

value: ETV6 dTAG

tag: time

value: 6 hours

tag: treatment


title: H3Q5ser-HeLa-1_S2_L001

value: H3Q5ser (Millipore Sigma, #ABE1791)


title: 7w_4

city: Illkirch-Graffenstaden

first: Jocelyn

last: Laporte

address: 1 rue Laurent Fries

country: France

institute: IGBMC

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Preprocessing was performed with cutadapt version 1.10.
Read mapping was performed using STAR version 2.5.3a.
Gene expression quantification was performed from uniquely aligned reads using htseq-count version 0.6.1p1 with annotations from Ensembl version 96 and union mode.
Assembly: mm10
Supplementary files format and content: merged_htseqcount.tsv: Tab-separated text file containing the matrix of raw counts per gene generated using htseqcount.

source_name: RNA extracts from skeletal muscle of 7 weeks old mice

extract_protocol:
RNA was isolated from tibialis anterior muscle pieces using TRI Reagent.
TruSeq Stranded mRNA Library Prep Kit.

tag: tissue

value: tibialis anterior muscle

tag: age

value: 7 weeks

tag: genetic background

value: WT


title: 7w_3


title: ZBTB7A-infection-4

city: Durham

first: Nicholas

last: Heaton

state: NC

address: 213 Research Drive, 426 CARL Building

department: Molecular Genetics and Microbiology

institute: Duke University School of Medicine

data_processing:
Sequences for TruSeq Illumina adapters were removed from the raw reads using Trimmomatic v0.32 (Bolger et al., 2014).
Reads were aligned against the latest human reference genome (GRCh38) using the aligner STAR v2.4.1a following the proposed 2-pass strategy, removing alignments containing non-canonical splice junctions (--outFilterIntronMotifs RemoveNoncanonical)
Aligned reads were assigned to genes in the GENCODE v22 comprehensive gene annotation using the featureCounts command in the subread package with default settings (v1.4.6-p4)
Differential expression analysis was performed using DESeq2 (v1.22.0) running on R (v3.5.1). Briefly, raw counts were imported and filtered to remove genes with low or no expression, that is, keeping genes having two or more counts per million (CPMs) in two or more samples.
Genome_build: hg38
Supplementary_files_format_and_content: Mapped reads

source_name: human hepatoma Huh7 cell line

growth_protocol: Huh7 cells were cultured with DMEM containing 10% FBS

extract_protocol:
Total RNA was extracted and further purified with a NEBNext Poly(A) messenger RNA (mRNA) Magnetic Isolation Module. RT-PCR for the mRNA was performed.
Total RNA was extracted with Monarch Total RNA Miniprep Kit (NEB, T2010S).   Samples were prepared with a NEBNext Poly(A) messenger RNA (mRNA) Magnetic Isolation Module (NEB #E74905). The NEBNext Ultra II RNA Library Prep Kit (E7770S) was used to prepare libraries with NEBNext Multiplex Oligos for Illumina (E7335S, E7500S).

treatment_protocol: ZBTB7A-Huh7 cells and control cells were seeded into 6-well plates and mock-infected or infected with HCoV-229E at 1 MOI. Each group contained 4 duplicates. The cells were collected 24 hpi.

value: human hepatoma cell line

value: HCoV-229E infected


title: A673 ETV6 dTAG cells - 6 hour dTAGV-1 treated  - FLI1 ChIP-seq - replicate 1


title: A673 ETV6 dTAG cells - 6 hour DMSO treated  - H3K27ac ChIP-seq - replicate 2

value: DMSO


title: RARα KO, 0nM RA (H3k27ac)

value: CD4 T cells

value: RAR{alpha} KO


title: 7w_2


title: RARα KO, 0nM RA (input)


title: A673 ETV6 dTAG cells - 6 hour DMSO treated  - FLI1 ChIP-seq - replicate 2


title: A673 ETV6 dTAG cells - 6 hour DMSO treated  - FLI1 ChIP-seq - replicate 1


title: 7w_1


title: ZBTB7A-infection-2


title: ZBTB7A-infection-3


title: A673 ETV6 dTAG cells - 6 hour DMSO treated  - H3K27ac ChIP-seq - replicate 1


title: siRNA-NC-B

type: RNA

city: Wuhan

first: Xing-Xing

last: He

state: Hubei

address: 1095# Jie-Fang Avenue

department: Institute of Liver and Gastrointestinal Diseases

country: China

institute: Tongji Hospital

description: Gene expression after transfected with siRNA-NC

hyb_protocol: Each slide was hybridized with 600 ng Cy3-labeled cRNA using Gene Expression Hybridization Kit (Cat.# 5188-5242, Agilent technologies, Santa Clara, CA, US) in Hybridization Oven (Cat.# G2545A, Agilent technologies, Santa Clara, CA, US), according to the manufacturer’s instructions. After 17 hours hybridization, slides were washed in staining dishes (Cat.# 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit(Cat.# 5188-5327, Agilent technologies, Santa Clara, CA, US), followed the manufacturer’s instructions

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit.

data_processing: Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US). Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: Control Group

label_protocol: Total RNA was amplified and labeled by Low Input Quick Amp Labeling Kit, One-Color (Cat.# 5190-2305, Agilent technologies, Santa Clara, CA, US), following the manufacturer’s instructions. Labeled cRNA were purified by RNeasy mini kit (Cat.# 74106, QIAGEN, GmBH, Germany).

growth_protocol: SMMC-7721 cells were cultured in  six well plates and incubated in a 37 °C, 5% CO2 humidified incubator

extract_protocol: 48h after transient introduction of si-YWHAZ or siRNA-NC, total RNA was extracted and purified by RNeasy mini kit (Cat#74106, QIAGEN, GmBH, Germany) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).

treatment_protocol: Each well of  SMMC-7721 cells in  six well plates  was  transfected by 10 nmol si-YWHAZ or the control siRNA-NC  using Lipofectamine 3000 (Invitrogen, USA) according to the manufacturer’s instructions.

tag: cell line

value: hepatoma cell line SMMC-7721

tag: genotype/variation

value: control


title: WT, 10nM RA (H3k27ac)

value: 16h w/ 10nM RA


title: Si-YWHAZ-1-C

description: Gene expression after silencing YWHAZ

source_name: Experimental Group

value: YWHAZ knockdown


title: siRNA-NC-C


title: Si-YWHAZ-1-A

description: Gene expression after silencing YWHAZ


title: WT, 10nM RA (input)


title: Si-YWHAZ-1-B

description: Gene expression after silencing YWHAZ


title: siRNA-NC-A


title: EW8 ETV6 dTAG cells - untreated - input DNA reference for ETV6 HA-tag sample

source_name: EW8 Ewing sarcoma cell line


title: H3K9me3-HeLa-1_S5_L001

value: H3K9me3 (Active Motif, #39161)

value: HeLa


title: ZBTB7A-infection-1


title: WT, 0nM RA (H3k27ac)

value: 16h w/o RA


title: 2w_3

source_name: RNA extracts from skeletal muscle of 2 weeks old mice

value: 2 weeks


title: WT, 0nM RA (input)


title: ZBTB7A-4

value: Uninfected


title: EW8 ETV6 dTAG cells - untreated - ETV6 HA-tag ChIP-seq

value: HA (Abcam, # ab9110)

value: dTAG

value: ETV6 dTAG


title: Parental EW8 cell line - input DNA reference for EW8 H3K27ac sample


title: ZBTB7A-3

value: human hepatoma cell line


title: 2w_2

value: tibialis anterior muscle

value: WT


title: TIL_Cx3cr1-cre replicate 2

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

data_processing:
Filtering out low-quality reads or reads without poly(T) tails presented in their first ends.
Extracting cell barcodes and UMI sequences for each read pair.
Trimming adapters and poly(A) tails (i.e., a stretch of 18 A’s) from the second ends of the filtered reads by cutadapt (v1.17)
Read alignment to the mouse reference genome (mm10) with gene annotation (ensembl v102) using STAR (version 2.7.7a).
UMI-based deduplication, and counting the numbers of reads mapped to individual genes for every cell barcode using featureCounts (v2.0.1).
Assembly: mm10
Supplementary files format and content: tar ball of mtx, tsv: UMI counts of individual genes in single cells

source_name: tumor

growth_protocol: Mice were housed in conventional cages in an animal room at constant temperature (19–23 °C) and humidity (55 ± 10%) under a 12-h light–dark cycle and were allowed access to standard diet and water ad libitum.

extract_protocol:
Single-cell suspensions (1×105 cells/ml) with PBS were loaded into microfluidic devices using the Singleron Matrix® Single Cell Processing System (Singleron)
The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron)
single-cell RNA-seq

treatment_protocol: 1×105 B16F10 cells were implanted subcutaneously into Cx3cr1-cre and Gsdmdfl/fl Cx3cr1-cre mice, aPD-L1 (200mg) or vehicle were intraperitoneally injected on day 4, 8.

tag: mouse pool replicate


title: 2w_1


title: ZBTB7A-2

tag: cell type


title: E18.5_4

source_name: RNA extracts from skeletal muscle of E18.5 mice


title: Parental EW8 cell line - H3K27ac ChIP-seq


title: TIL_Gsdmdfl/fl Cx3cr1-cre replicate 2

value: Gsdmdfl/fl Cx3cr1-cre


title: Control-infection-4

value: HCoV-229E infected


title: E18.5_3


title: 2w_4


title: TIL_Gsdmdfl/fl Cx3cr1-cre replicate 1


title: Control-infection-3


title: E18.5_2


title: Parental A673 cell line - input DNA reference for A673 H3K27ac sample


title: Parental A673 cell line - H3K27ac ChIP-seq


title: E18.5_1


title: Control-infection-2


title: Parental A673 cell line - input DNA reference for A673 FLI1 sample


title: RNAseq, PS, AZ, rep2

city: Davis

first: Satoshi

middle: H

last: Namekawa

state: CA

address: One Shields Avenue

department: Department of Molecular and Cellular Biology

institute: University of California, Davis

data_processing:
Raw sequence reads were trimmed and filtered using trimmomatic v0.39.
Trimmed sequence reads were aligned to the mouse genome (GRCm38/mm10) using STAR version 2.5.4b with --outFilterMultimapNmax 1 options for unique alignments.
Aligned read counts for each gene were generated using featureCounts v2.0.1 based on the UCSC mouse refGene annotation.
The TPM normalization were performed on Microsoft excel softwere.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes TPM values for each Sample

source_name: testis

extract_protocol:
Total RNA was extracted using the RNeasy plus Micro Kit (QIAGEN, Cat # 74034) according to the manufacturer’s instructions.
Library preparation was performed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina® (NEB, E6420S) according to the manufacturer’s instruction.  Prepared RNA-seq libraries were sequenced on the HiSeq 4000 system (Illumina) with paired-ended 150-bp reads.

treatment_protocol: The isolated pachytene spermatocytes were cultured with DMSO or 10 µM AZ20 for 24 h at 34 C at 5% CO2.

value: testis

value: pachytene spermatocytes

value: 10µM AZ20


title: Control-infection-1


title: Parental EW8 cell line - input DNA reference for EW8 FLI1 sample


title: Mll4-knockout B16-F10 cells, Input

city: Tianjin

first: Shan

last: Huang

address: Qi Xiangtai Road

institute: Tianjin Medical University

data_processing:
Raw paired-end reads of H3K4me1 and H3K27ac were trimmed by Trim Galore (0.6.4), and then aligned to mouse genome mm10 using Bowtie2 (2.4.3) with default parameters.
Samtools (1.7) was used to remove all unmapped reads and keep one assigned position with the best matched score of non-uniquely mapped reads.
For subsequent analyses, reads were extended to 200 bp and normalized to Reads Per Kilobase per Million mapped reads (RPKM) to generate bigwig files by deepTools (2.0).
mm10
Bigwig files generated by deepTools (2.0).

source_name: B16-F10 cells

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FBS) and 1% penicillin/streptomycin.

extract_protocol:
Lysates were clarified from sonicated nuclei but not immuno-precipitated.
DNA libraries were prepared for sequencing according to standard Illumina protocols.


title: TIL_Cx3cr1-cre replicate 1


title: Wild-type B16-F10 cells, Input

value: Wild-type


title: ZBTB7A-1


title: Parental A673 cell line - FLI1 ChIP-seq

value: FLI1 (Abcam, ab15289)


title: RNAseq, PS, AZ, rep1


title: Parental EW8 cell line - FLI1 ChIP-seq


title: Control-3


title: RNAseq, PS, Ctrl, rep2

value: DMSO


title: Wild-type B16-F10 cells, H3K27ac

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing according to standard Illumina protocols.

value: H3K27ac (abcam, cat. no. ab4729)


title: Control-4


title: A673 cells with CRISPR sgETV6-3 KO at 3 days - replicate C

data_processing:
The raw Illumina sequencer output was converted to FASTQ format using the program bcl2fastq (v2.17).
Sequencing read quality was examined using FastQC (http://www.bioinformatics.babraham.ac.uk) (v0.11.9).
Reads were aligned to the human genome (hg19) using STAR (v2.7.2b)
Transcript-level quantifications were calculated using RSEM (v1.3.126)
Gene counts from STAR were then used to quantify differentially expressed genes between the experimental and control conditions using the R Bioconductor package DESeq2 (v1.30.1) using the approximate posterior estimation for GLM coefficients (apeglm) method for effect size.
Normalized expression values for individual samples were obtained from RSEM log2 TPM values with the RSEM log2(TPM+1) values used for GSEA and producing RNA-seq heat map plots.
Genome_build: hg19
Supplementary_files_format_and_content: RSEM output files with gene TPM and FPKM (*.rsem.genes.results) and STAR output files with read counts for genes (*.ReadsPerGene.out.tab)

molecule: polyA RNA

growth_protocol: A673 and EW8 Ewing sarcoma parental cells were co-transduced with the following lentivirally packaged constructs. Four sgRNAs targeting exon-intron junctions of the endogenous ETV6 gene were cloned,  into a version of the LentiCRISPRv2 plasmid backbone conferring blasticidin resistance (Addgene 83480). The sgRNA sequences used were (1) sgETV6-endo-1, 5’-TCCTGCTCAGTGTAGCATTA-3’, (2) sgETV6-endo-2, 5’-GAACACTCACGCAGGTGCGC-3’, (3) sgETV6-endo-3, 5’-TCCAGACTCTCACCTGAATG-3’, and (4) sgETV6-endo-4, 5’-AGTTCATAGAGCACATCACC-3’. A codon-optimized gblock encoding coding sequences of ETV6 was cloned into the pLEX_305 vector backbone (Addgene 91798) to C-terminally tag the ETV6 protein with the FKBP12F36V protein domain and a HA epitope tag. Ewing sarcoma cells were spin-infected as described above. Cells were incubated for 24 hours, after which viral media was replaced by media containing 1 µg/ml puromycin and 5 µg/ml blasticidin (Life Technologies, #A1113903) and supplemented with 40% FBS for 48-72 hours. Non-infected control cells were treated with puromycin or blasticidin to confirm selection. Cells were cultured in Dulbecco’s Modified Eagle’s Media supplemented with 15% FBS and 1% penicillin streptomycin glutamine, as well as 0.5 µg/ml puromycin and 2.5 µg/ml blasticidin to maintain selection. Cells were split at a ratio of 1:5 every other day.

extract_protocol:
All RNA-seq experiments were performed using total RNA that was extracted with a silica column-based kit (Qiagen, # 74104) and treated with an on-column DNAse digestion per the kit protocol. ERCC RNA spike-ins were added to each sample for normalization, per kit instructions (Thermo Fisher Scientific, # 4456740).
RNA-seq library preparation and sequencing were performed by Novogene (Sacramento, CA, https://en.novogene.com) at a depth of roughly twenty million reads per sample. Per Novogene correspondence, the quality control for the RNA samples was performed using Qubit fluorometric quantitation (Thermo Fisher Scientific) and the Bioanalyzer instrument (Agilent). Libraries were then prepared using New England Biolabs NEBNext Ultra II non-directional RNA Library Prep kit. Library quality and concentrations were assessed with Labchip (Perkin Elmer) and qPCR. Libraries were then sequenced in 150-basepair paired-end fashion on the Novaseq6000 instrument (Illumina).

treatment_protocol: The dTAGV-1 molecule was generously provided by the Gray Laboratory (Dana-Farber Cancer Institute, Boston, MA) and used at a stock concentration of 10 millimolar suspended in DMSO. A673 ETV6-dTAG cells were seeded at 1 million cells per 6 cm dish for the 6-hour time point, 0.5 million cells per 6 cm dish for the 24-hour time point, and 0.5 million cells per 10 cm dish for the 72-hour time point. EW8 ETV6-dTAG cells were seeded at 0.75 million cells per 6 cm dish for the 6-hour time point, 0.5 million cells per 10 cm dish for the 24-hour time point, and 0.2 million cells per 10 cm dish for the 72-hour time point. For each time point, 3 separate dishes were seeded and treated per DMSO or dTAGV-1 condition. At the appropriate time point, cells from each sample were taken for total RNA extraction and western blot validation.  Existing media was aspirated and DMSO or dTAGV-1-containing media was added. For all experiments, dTAGV-1 was used at a final concentration of 1 micromolar. Equivalent volumes of DMSO were used as control.

value: CRISPR

value: day 3


title: Control-2

value: Uninfected


title: A673 cells with CRISPR sgETV6-3 KO at 3 days - replicate B


title: A673 cells with CRISPR sgETV6-3 KO at 3 days - replicate A


title: Wild-type B16-F10 cells, H3K4me1

value: H3K4me1 (Cell Signaling Technology, cat. no. 5326)


title: RNAseq, PS, Ctrl, rep1


title: 12week Homo Heart

city: Nishinomiya

first: Takuma

last: Yamamoto

address: 1-1 Mukogawa-Cho

country: Japan

institute: Hyogo Medical University

data_processing:
The sequencing reads were trimmed using Cutadapt v1.1 and Trimmomatic v0.32 with the following options:  --match-read-wildcards -O 1 (Cutadapt) / -phred33 LEADING:0 TRAILING:0 SLIDINGWINDOW:20:20 MINLEN:50 (Trimmomatic).
Trimmed  reads were aligned to the GRCm38 genome assembly using TopHat v2.0.14 and bowtie v1.1.1 with the following options: --microexon-search --bowtie1.
Aligned reads were used as input for PSI.sh v2.0 to determine alternative splicing expression levels (PSI).
Assembly: GRCm38
tab-delimited text files include PSI values for each Sample

source_name: Heart

extract_protocol:
Total RNAs from mouse heart were extracted by using RNeasy Plus Universal Mini Kit (Qiagen). Representative libraries were generated for each groups (Wild-type, Heterozygote and Homozygote) by RNA-seq with SMART-seq v4 Ultra Low Input RNA kit for sequencing (Takara Bio Inc.) and Nextera XT DNA Library Prep Kit (Illumina, Tokyo, Japan) and sequenced on a NovaSeq 6000 instrument (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Heart

value: Homozygote


title: Control-1

value: human hepatoma cell line


title: 12week Hetero Heart

value: Heterozygote


title: A673 cells with CRISPR sgETV6-2 KO at 3 days - replicate C


title: RNA-seq of Mll3-knockout B16-F10 cells, rep2

data_processing:
The quality, adapter content and duplication rates of raw reads were confirmed by FastQC (0.11.9) with default parameters, and reads were trimmed by Cutadapt.
And then, reads were aligned to mouse genome version mm10 using HISAT(2.2.1).
The count of each gene was calculated by htseq-count.
mm10
Tab-delimited text files include raw count of each gene for each sample.

growth_protocol: Cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum (FBS) and 1% penicillin/streptomycin before implantation.

extract_protocol:
Total RNAs were extracted follow the protocol of TRIzol (Invitrogen, USA) reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Cells were infected with eGFP-expression lentivirus which packaged by 293T cells to establish eGFP-expression cells, respectively. These eGFP+ B16F10 cells (1 × 106) were implanted subcutaneously into the right flank of 6- to 8-week-old C57BL/6 male mice. On day 14 post implantation, tumors were excised and mechanically minced, and treated with collagenase ( 0.2mg/ml, Sigma, USA) and DNase I for 15 min at 37 °C. Cells were passed through a 70 μm filter and taken for flow cytometry. eGFP+ B16F10 cells were sorted and lysed to extract total RNA.


title: G-etv3

city: Paris

first: Javiera

last: Villar

address: 25 rue d'Ulm

institute: Institut Curie

data_processing:
Quality of RNA-seq data was assessed using FastQC.
Reads were aligned using STAR
Differential gene expression analysis was performed using DESeq2.
Genome_build: hg38
Supplementary_files_format_and_content: Count matrix (raw counts) was obtained using FeatureCounts or HTSeq-Counts

source_name: human monocytes

growth_protocol: Monocytes were cultured with M-CSF, IL4 and TNF for 3 days in presence of lentivirus expressing shRNA control or against ETV3 or ETV6

extract_protocol:
Cells were lyzed and mRNA extracted using Qiagen RNEasy Mini kit including on-column DNAse digestion.
Sequencing was performed in the same sequencing unit of NovaSeq (Illumina) (100-nt-length reads, paired end) with an average depth of 15 million reads per sample.

tag: donor

value: G

tag: shRNA


title: A673 cells with CRISPR sgETV6-2 KO at 3 days - replicate B


title: Mll4-knockout B16-F10 cells, H3K27ac

tag: strain


title: 12week Wild Heart

tag: genotype

value: Wildtype


title: G-ctrl

value: ctrl


title: Mll4-knockout B16-F10 cells, H3K4me1

tag: cell line

tag: chip antibody


title: RNA-seq of Mll3-knockout B16-F10 cells, rep1


title: RNA-seq of Mll4-knockout B16-F10 cells, rep2


title: A673 cells with CRISPR sgETV6-2 KO at 3 days - replicate A

tag: modification type


title: F-etv6

value: F


title: RNA-seq of wild-type B16-F10 cells, rep4

value: wild-type


title: PBMCs, TSLP_CCL3, Hashtag

city: Chicago

first: Nicolas

last: Chevrier

state: Illinois

address: 5640 South Ellis Avenue

department: Pritzker School of Molecular Engineering

institute: The University of Chicago

description:
whole_cyto_normalized.h5ad
whole_cyto_raw.h5ad

library_source: other

data_processing:
Raw sequencing data were processed by the Cell Ranger pipeline to produce the cell by gene matrix of UMI counts.
Alignments were demultiplexed with a custom script and hashtag indexes.
Quality control was performed to filter out cells with too low (< 400) or high (> 22,000) counts and cells with a large fraction of mitchondrial counts (> 20%), and filter out genes expressed in fewer than 20 cells.
Cells were clustered into different cell types based on transcriptional profiles using the Louvain algorithm.
Based on known marker genes, we annotated 8 major cell types: B cells (Cd19, Cd79a, Cd79b), CD4+ T cells (Cd3d, Cd3e, Thy1, Cd4), CD8+ T cells (Cd3d, Cd3e, Thy1, Cd8a), dendritic cells (Flt3), Ly6C- monocytes (Nr4a1, Pparg), Ly6C+ monocytes (Ly6c2, F13a1), neutrophils (S100a8, S100a9), and NK cells (Ncr1).
Assembly: mm10
Supplementary files format and content: h5ad files; data matrix of shape, annotation of variables/features, and annotation of observations
Supplementary files format and content: whole_cyto_raw.h5ad (the filtered counts data for GEX and Hashtag samples)
Supplementary files format and content: whole_cyto_normalized.h5ad (normalized, log-transformed data for GEX and Hashtag samples)
Supplementary files format and content: whole_cyto_annot.csv (Annotations for each of the cells (rows) in the table. Notable columns are the sample/cytokine they came from, and the assigned celltype.)

molecule: protein

source_name: PBMCs, TSLP_CCL3, 12 hours

extract_protocol:
Samples were immediately run on the 10X Chromium (10X Genomics)
Samples were processed through library preparation following the recommended protocol (CG000186 Rev A) for the Chromium Single Cell V(D)J Reagent Kit.

treatment_protocol: Mice were intravenously injected with 2.5 µg of 48 recombinant cytokines. Cytokine-injected mice were anesthetized with avertin (250-500 mg/kg) 12 hours after cytokine injection and whole blood was collected from the left ventricle of the heart into the tubes containing ice-cold buffer (PBS plus 0.5% FCS and 2 mM EDTA). Red blood cells were lysed in ACK Red blood cell lysis buffer (Lonza, BW10548E) for 3 min and then three biological replicates were pooled into a tube. After pooling samples, the cells were washed by the buffer. We next used anti-Ter119 MicroBeads (Miltenyi Biotec, 130-049-901) to deplete Ter119+ cells thoroughly. Cells were then labelled with the TotalSeqTM-C0301 anti-mouse Hashtag 1 antibody (BioLegend, 155861) and TotalSeqTM-C0302 anti-mouse Hashtag 2 antibody (BioLegend, 155863) at 0.25 µg/sample for 15 min at 4°C. After staining, cells were washed with PBS, and resuspended in PBS + 0.04% BSA. Cells were counted and resuspended at a density of 1000 cells/µl.

value: blood

value: Peripheral blood mononuclear cells

value: TSLP, CCL3


title: RNA-seq of Mll4-knockout B16-F10 cells, rep1


title: A673 cells with CRISPR sgLacZ KO control at 3 days - replicate B

tag: modification

value: sgLacZ


title: A673 cells with CRISPR sgLacZ KO control at 3 days - replicate A

value: CRISPR

tag: time


title: PBMCs, TGFb_CCL2, Hashtag

source_name: PBMCs, TGFb_CCL2, 12 hours

tag: treatment

value: TGF-β, CCL2


title: E-etv6

value: E


title: RNA-seq of wild-type B16-F10 cells, rep3


title: F-ctrl


title: A673 cells with CRISPR sgChr2-2 KO control at 3 days - replicate B

value: day 3


title: PBMCs, IL4_IL6, Hashtag

source_name: PBMCs, IL4_IL6, 12 hours

tag: tissue


title: PBMCs, IL9_IL11, Hashtag

source_name: PBMCs, IL9_IL11, 12 hours


title: E-etv3


title: RNA-seq of wild-type B16-F10 cells, rep2


title: A673 cells with CRISPR sgChr2-2 KO control at 3 days - replicate A

source_name: A673 Ewing sarcoma cell line


title: E-ctrl


title: BM2 [VDJ]

city: Atlanta

first: Eliver

last: Ghosn

state: GA

address: 1760 Haygood Dr NE

department: Lowance Center for Human Immunology

institute: Emory University School of Medicine

data_processing:
Gene expression libraries were sequenced together on a NovaSeq 6000 platform (Illumina, San Diego, CA). ADT and V(D)J libraries were sequenced separately on a Next-seq platform (Illumina, San Diego, CA).
Cell Ranger Software (v.3.1.0) was used to perform barcode processing and single-cell 5′ unique molecular identifier (UMI) counting. Reads from GEX and ADT libraries were processed simultaneously using “cellranger count” with "--r2-length=98 --expect-cells=5000", while reads from V(D)J libraries were aligned by running “cellranger vdj”.
Genome_build: GRCh38
Supplementary_files_format_and_content: mtx files are the sparse matrices of the gene expression and surface-protein expression data.

source_name: Bone marrow

extract_protocol:
PBMCs were isolated from whole blood using EasySep™ Direct Human PBMC Isolation Kit (Catalog #19654 Stem Cell Technologies). B cells were enriched from fresh whole bone marrow using EasySep™ B Cell Enrichment: Complete Processing Kit for Whole Blood (Catalog # 19954 Stem Cell Technologies)
Libraries were prepared according to Chromium Single Cell V(D)J Reagent Kit (v1 Chemistry) with Feature Barcoding technology for Cell Surface Protein User Guide.

value: Bone marrow

value: B-cell enriched

tag: disease status

value: Healthy donor


title: RNA-seq of wild-type B16-F10 cells, rep1


title: BM1 [VDJ]


title: PBMCs, IL36a_Ctrl2, Hashtag

source_name: PBMCs, IL36a_Ctrl2, 12 hours

value: IL-36α, Control2


title: PBMC3 [VDJ]

source_name: Blood

value: Blood

value: PBMC


title: WT_BL6J_ 23M_259_M

city: Bonn

first: Dan

last: Ehninger

state: NRW

address: Venusberg-Campus 1/99

department: AG Ehninger

country: Germany

institute: DZNE

data_processing:
Demultiplexing and data transformation to generate fastq files was done using bcl2fastq2 (v2.20).
Sequencing reads were trimmed using CutAdapt (https://usegalaxy.org/) to remove adapter sequences. Trimmed reads were mapped to the mouse transcriptome (GRCm38, mm10) using HISAT2 (v2.1.0).
Bam files were indexed using Samtools and count matrices generated by Genomic Alignments in R. Gene count matrices were generated using annotation information from a Mus_musculus.GRCm38.102.chr.gtf file imported with the rtracklayer (Lawrence et al., 2009) package into R. All downstream analyses were performed using R (Version 3.5.1, https://cran.r-project.org/). Library normalization and expression differences between samples were quantified using the DESeq2 package (Love et al., 2014). A false discovery rate (FDR) < 0.05 was used as a cutoff in differential expression analyses.
3  and 5 months old mice were used as the "young adult baseline" for Ageing-Brain, Ageing-Spleen and Ageing-mTOR-Spleen datasets, respectively
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with normalized gene counts for every gene and every sample

source_name: spleen

extract_protocol:
Mouse tissues were harvested, flash frozen on dry ice and total RNA isolated from the tissues with TRI-Reagent. Total RNA was purified with the Monarch RNA Cleanup kit.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using a ligation mediated RNA sequencing protocol published by Huo et al. 2015

value: spleen

value: WT

tag: age

value: 23 months

tag: Sex

value: male


title: PBMCs, IL25_IL33, Hashtag

source_name: PBMCs, IL25_IL33, 12 hours

value: blood

value: Peripheral blood mononuclear cells

value: wild-type


title: C-ctrl

value: C

value: ctrl


title: C-etv6


title: WT_BL6J_ 23M_278_M


title: PBMC2 [VDJ]


title: PBMCs, IL21_IL23, Hashtag

source_name: PBMCs, IL21_IL23, 12 hours


title: B-etv6

value: B


title: WT_BL6J_ 21M_269_M

value: 21 months


title: B-etv3


title: PBMC1 [VDJ]


title: BM2 [ADT]

value: Bone marrow


title: mTOR_BL6J_ 23M_262_M

value: mTOR


title: PBMCs, IL5_IL7, Hashtag

source_name: PBMCs, IL5_IL7, 12 hours


title: mTOR_BL6J_ 5M_2795_M

value: 5 months


title: B-ctrl


title: BM1 [ADT]

value: B-cell enriched

value: Healthy donor


title: mTOR_BL6J_ 21M_271_M


title: A-etv6

value: A


title: PBMCs, IL18_IL22, Hashtag

source_name: PBMCs, IL18_IL22, 12 hours


title: PBMC3 [ADT]

value: Blood

value: PBMC


title: PBMCs, IL27_IL34, Hashtag

source_name: PBMCs, IL27_IL34, 12 hours


title: PBMCs, IL15_IL17f, Hashtag

source_name: PBMCs, IL15_IL17f, 12 hours


title: C-etv3


title: A-etv3


title: mTOR_BL6J_23M_280_M

value: spleen

value: 23 months


title: PBMC2 [ADT]


title: WT_BL6J_ 5M_2826_M

value: WT

value: male


title: PBMCs, IL13_IL17a, Hashtag

source_name: PBMCs, IL13_IL17a, 12 hours

value: blood

value: Peripheral blood mononuclear cells

value: wild-type


title: A-ctrl

source_name: human monocytes

value: ctrl


title: mTOR_BL6J_5M_3007_M


title: PBMCs, IL1b_IL3, Hashtag

source_name: PBMCs, IL1b_IL3, 12 hours

value: IL-1β, IL-3


title: PBMCs, IL10_IL12p70, Hashtag

source_name: PBMCs, IL10_IL12p70, 12 hours


title: PBMC1 [ADT]


title: PBMCs, IL1a_IL2, Hashtag

source_name: PBMCs, IL1a_IL2, 12 hours

value: IL-1α, IL-2


title: mTOR_BL6J_5M_2825_M

value: mTOR


title: SE5_ER2

city: Isehara-shi

first: Atsushi

last: Fukuda

institute: Tokai University

data_processing:
RNA sample prepared stranded library with polyA selection for DNBSEQ.
Sequencing were performed on the DNBSEQ platform, in a 2x150bp, paired-end (PE) configuration, per lane, ~350M pair-end read/lane, per lane.
Genome_build: hg38

source_name: human embryonic stem cells

growth_protocol: The hPSCs were cultured in StemFlex (Thermo Fisher Scientific) on a plate coated with Matrigel (Corning  ). For passaging hPSCs, 1mM EDTA and 10 mM Y-27632 (StemCell Technologies) were added to the culture  medium and maintained 24 h.

extract_protocol:
Total RNA is extracted using Rneasy plus micro kit (Qiagen) with manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols by Genewiz.

treatment_protocol: Gene manupulated cell lines were generated by CRISPR-Cas9 system.

tag: gender

value: female

value: ES cells


title: PBMCs, IFNg_GMCSF, Hashtag

source_name: PBMCs, IFNg_GMCSF, 12 hours

value: IFN-γ, GM-CSF


title: PBMCs, IFNa_IFNb, Hashtag

source_name: PBMCs, IFNa_IFNb, 12 hours

value: IFN-α, IFN-β


title: MP41_miRNA-16_48h

city: Valbonne - Sophia-Antipolis

first: Kevin

last: Lebrigand

address: 660 route des lucioles

institute: IPMC/CNRS

data_processing:
(i) Reads quality control using fastQC and Fastq-scren
(ii) mapping with STAR_2.4.0a versus hg38 following ENCODE RNA-seq options
(iii) features quantification using featureCounts (subread-1.5.0-p3-Linux-x86_64) with "--primary -g gene_name -p -s 1 -C" options using Ensembl GRCh38.76 release.
Genome_build: hg38
Supplementary_files_format_and_content: Normalized_Data.txt

source_name: uveal melanoma cell line

growth_protocol: MP41 cell line were maintained in RPMI-1640 medium supplemented with 20% Fetal Bovine Serum (FBS) and 1% Penicillin-Streptomycin antibiotics

extract_protocol:
RNA was isolated from cell samples using NucleoSpin RNA Plus kit (Macherey-Nagel) and quantified using a NanoDrop 1000 Spectrophotometer (ThermoFisher Scientific).
cDNA

treatment_protocol: All siRNAs and synthetic miRNAs were transfected at 66nM using Lipofectamine RNAiMAX (ThermoFisher Scientific) according to manufacturer’s instructions.  For RNA and proteins analysis, 250,000 cells were seeded in 6-well plates.

value: mimic 16


title: WT_BL6J_5M_3006_M

value: 5 months


title: SE5_NE2


title: WT_BL6J_5M_2793_M

value: spleen


title: PBMCs, GCSF_MCSF, Hashtag

source_name: PBMCs, GCSF_MCSF, 12 hours

value: GCSF, MCSF


title: MP41_miRNA-CTRL_24h

value: mimic CTRL


title: GMC_BL6J_ 14M_ET0_c2626_spleen

source_name: spleen

value: WT

value: 14 months

value: male


title: PBMCs, CXCL9_CXCL12, Hashtag

source_name: PBMCs, CXCL9_CXCL12, 12 hours

value: blood

value: Peripheral blood mononuclear cells

value: wild-type

value: CXCL9, CXCL12


title: MP41_miRNA-16_24h


title: MP41_miRNA-CTRL_12h


title: GMC_BL6J_ 8M_ET1_c1457_spleen

value: 8 months


title: 3A3B_dKO_SE5_ER1

description: Female hES cells with null DNMT3A/3B deletion using the CRISPR-Cas9 system.

value: female

value: DNMT3A/3B deletion


title: GMC_BL6J_ 5m_ET82_c2349_spleen


title: 3A3B_dKO_SE5_NE2

value: ES cells


title: 3A3B_dKO_SE5_ER2


title: PBMCs, Ctrl_TNF, Hashtag

source_name: PBMCs, Control_TNF, 12 hours

value: Control, TNF


title: SE5_ER1


title: GMC_BL6J_ 20M_ET0_c3580_spleen

value: 20 months


title: 3A3B_dKO_SE5_NE1


title: PBMCs, CCL5_CCL17, Hashtag

source_name: PBMCs, CCL5_CCL17, 12 hours

value: CCL5, CCL17


title: MP41_miRNA-CTRL_6h


title: MP41_miRNA-16_6h

value: mimic 16


title: PBMCs, CCL4_CCL11, Hashtag

source_name: PBMCs, CCL4_CCL11, 12 hours

value: CCL4, CCL11


title: GMC_BL6J_14M_ET20_c3841_spleen

value: spleen


title: GMC_BL6J_ 8M_ET2_c1383_spleen

value: WT


title: MP41_miRNA-CTRL_0h

value: mimic CTRL


title: EW8 ETV6 dTAG cells - 72 hour DMSO treated - replicate 3

source_name: EW8 Ewing sarcoma cell line

value: dTAG

value: ETV6 dTAG

value: 72 hours

value: DMSO


title: GMC_BL6J_ 5M_ET32_c2346_spleen

value: 5 months

value: male


title: SE5_NE1

value: female


title: EW8 ETV6 dTAG cells - 72 hour DMSO treated - replicate 2


title: PBMCs, CCL20_CXCL1, Hashtag

source_name: PBMCs, CCL20_CXCL1, 12 hours

value: blood

value: Peripheral blood mononuclear cells

value: wild-type

value: CCL20, CXCL1


title: Down syndrome CPCs_DIV24

city: Pune

first: Nishant

last: Singhal

state: Maharashtra

address: Ganeskhind Road

country: India

institute: National Centre for Cell Science

data_processing:
Reads were aligned to human genome assembly hg19 using Bowtie for illumina (Galaxy version 1.12)
Binding sites were identified with MACS2 (Galaxy version 2.1.0.2015222.0)
Assigned to the nearest RefSeq transcription start site within 3kn using R package ChIPpeak Anno
ChIP peak comparision and visualization were done using R package ChIPseeker

source_name: Down syndrome human iPSCs

extract_protocol:
Down syndrome and isogenic normal human iPSCs were differentiated for 24 days in vitro. Subconfluent DIV24 cells were dual crosslinked using DSG and formaldehyde. ChIP was carried out using PAX6 antibody. Purified DNA was isolated after ChIP using the PCR Purification kit (Qiagen) following the manufacturer’s instructions.
Libraries were prepared using the NEBNext Ultra II DNA library Prep Kit for Illumina from NEB according to the manufacturers instructions. Briefly, DNA was end-repaired, phosporylated and dA tailed prior to adaptor ligation with NEBNext adaptors. After adapter ligation DNA was PCR amplified with NEBNext primers for Illumina for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were size selected using Ampure Beads (Becton Dickinson) followed by DNA cleanup using standard magnetic bead based DNA purification protocols. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the NextSeq500 following the manufacturer's protocols.

value: cortical progenitor cells (CPCs)

value: in vitro differentiated cells


title: GMC_BL6J_ 3M_ET8_c1190 _spleen

value: 3 months


title: EW8 ETV6 dTAG cells - 72 hour DMSO treated - replicate 1


title: MP41_miRNA-16_12h

value: mimic 16


title: EW8 ETV6 dTAG cells - 72 hour dTAGV-1 treated - replicate 3


title: PBMCs, TSLP_CCL3, GEX

library_source: transcriptomic single cell

source_name: PBMCs, TSLP_CCL3, 12 hours

value: TSLP, CCL3


title: MP41_miRNA-CTRL_48h

value: mimic CTRL


title: PBMCs, CXCL10_CXCL13, Hashtag

source_name: PBMCs, CXCL10_CXCL13, 12 hours

value: CXCL10, CXCL13


title: BC16_HeLa_MP_rep2

city: Beijing

first: Yan

last: Zhang

state: Not Applicable

address: Dongdajie street

institute: Beijing institute of Biotechnology

description: chromatin RNA

data_processing:
Signal processing, mapping and quality control were performed with Torrent Suite v.3.4.2 (Life Technologies).
Preliminary RNA-seq data processing were done by Ion Torrent server with RNA-seq plugin (Life Technology).
Briefly, after filtering out polyclonal Ion Sphere™ Particle (ISP) (ISPs carrying clones from two or more templates), low quality (ISPs with a low or unrecognizable signal), and usable reads (ISPs that pass the polyclonal, low quality, and primer dimer filters), reads are aligned to the human reference genome build 19 (hg19) using STAR and bowtie2 aligners to find full and partial mappings.
Reads were mapped to hg38 (GRCh38.p13) using hisat2.
Stringtie was used with gencode.v33.chr_patch_hapl_scaff.annotation.gtf (https://www.gencodegenes.org/human/release_33.html) to evaluate abundance of transcripts and genes.
Genome_build: Reads are aligned to the human reference genome build GRCh38.p13.
Supplementary_files_format_and_content: gene_info.tsv: Tab-delimited text file includes gene level read count table.

growth_protocol: A549 (ATCC CCL-185) and HeLa-S3 (ATCC CCL-2.2) Cells were grown in standard DME/F12 1:1 media (HyClone #SH30023.01) with 10% Bovine serum (Gibco #16170078), 1% PenStrep (Gibco #15140).

extract_protocol:
Cell pellets were resuspended in 2.5 x volumes of Buffer A (10 mM HEPES pH 7.5, 10 mM KCl, 10% glycerol, 340 mM sucrose, 4mM MgCl2, 1 mM DTT,1 x Protease Inhibitor Cocktail [1 mM PMSF, 1mM ABESF, 0.8 μM aprotinin, 20 μM leupeptin, 15 μM pepstatin A, 40 μM bestatin, 15 μM E-64]), and then an equal volume of Buffer A with 0.2% (v/v) Triton X-100 was added and the mixture incubated on ice for 12 minutes to lyse cells, followed by centrifugation (1,200 x g, 5 min, 4°C). The crude nuclear pellet was resuspended in 250 μl NRB (20 mM HEPES pH 7.5, 50% Glycerol, 75 mM NaCl, 1 mM DTT, 1 x protease inhibitor cocktail), transferred to a microcentrifuge tube and centrifuged (500 x g, 5 min, 4°C) to wash. The pellet was resuspended in 250 μl NRB, and then an equal volume of NUN buffer (20 mM HEPES, 300 mM NaCl, 1M Urea, 1% NP-40 Substitute, 10 mM MgCl2, 1 mM DTT) was added and incubated 5 minutes on ice, then centrifuged (1,200 x g, 5 min, 4°C). The soluble nuclear extract supernatant was transferred to another tube, and the depleted nuclear pellet was resuspended in 1 ml Buffer A to wash, transferred to another microcentrifuge tube, and centrifuged (1,200 x g, 5 min, 4°C). Resulting purified chromatin pellets were resuspended in 50 μl Buffer A.
5 μg of total RNA was subjected to rRNA removal using  RiboMinus™ Eukaryote System v2 (Life Technologies). Then The RNA-seq library preparation was performed using the Ion Total RNA-Seq Kit v.2 following standard protocols (Life Technologies). Templates were prepared using the ION PI Template OT2 200 Prep Kit and the One Touch 2 System (Life Technologies). RNA Sequencing was performed on a PI chip (ION PI Sequencing 200 Kit v.2; Life Technologies). Signal processing, mapping and quality control was performed with Torrent Suite v.3.4.2 (Life Technologies). library synthesis using the TruSeq V2 RNA-Seq kit.

treatment_protocol: 48 hours prior to synchronization, cells were plated on 15 cm plates at 50% confluence. First, cells were incubated with media containing 2 mM Thymidine (Sigma T1895-10G) for 24 hours, washed twice with 10 ml 1x PBS and released into standard media for 3 hours. Media were then substituted with media containing 100ng/ml nocodazole (Sigma #M1404) for 12h. At the end of the incubation, media with floating mitotic cells was collected.

tag: cell phase

value: M-phase

tag: nuclear fraction

value: chromatin pellet


title: GMC_BL6J_ 20M_ET9_c1315_spleen

value: spleen

value: WT

value: 20 months


title: PBMCs, IL9_IL11, GEX

source_name: PBMCs, IL9_IL11, 12 hours

tag: cell type


title: BC14_HeLa_IP_rep2

description: chromatin RNA

value: interphase


title: EW8 ETV6 dTAG cells - 72 hour dTAGV-1 treated - replicate 2

value: dTAG

value: ETV6 dTAG

value: 72 hours


title: GMC_BL6J_ 8M_ET0_c3663_spleen

value: 8 months

value: male


title: PBMCs, IL5_IL7, GEX

source_name: PBMCs, IL5_IL7, 12 hours

value: blood

value: Peripheral blood mononuclear cells

value: wild-type


title: GMC_BL6J_ 14M_ET30_c3840_spleen

value: 14 months


title: GMC_BL6J_ 5M_ET20_c2318_spleen

value: 5 months


title: EW8 ETV6 dTAG cells - 24 hour DMSO treated - replicate 3

value: 24 hours

value: DMSO


title: PBMCs, IL4_IL6, GEX

source_name: PBMCs, IL4_IL6, 12 hours


title: EW8 ETV6 dTAG cells - 72 hour dTAGV-1 treated - replicate 1


title: PBMCs, CCL22_CXCL5, Hashtag

source_name: PBMCs, CCL22_CXCL5, 12 hours

value: CCL22, CXCL5


title: BC13_HeLa_IS_rep2

description: nuclear RNA

value: soluble nuclear extract


title: EW8 ETV6 dTAG cells - 24 hour DMSO treated - replicate 2


title: BC12_A549_MP_rep2

description: chromatin RNA

value: M-phase

value: chromatin pellet


title: Isogenic Normal CPCs_DIV24

source_name: Isogenic Normal human iPSCs

value: cortical progenitor cells (CPCs)

value: in vitro differentiated cells


title: GMC_BL6J_ 3M_ET30_c1164 _spleen

value: spleen

value: WT

value: 3 months


title: PBMCs, IL36a_Ctrl2, GEX

source_name: PBMCs, IL36a_Ctrl2, 12 hours

value: IL-36α, Control2


title: GMC_BL6J_ 26M_ET30_c620_spleen

value: 26 months

value: male


title: BC11_A549_MS_rep2

description: nuclear RNA


title: PBMCs, IL27_IL34, GEX

source_name: PBMCs, IL27_IL34, 12 hours

value: blood

value: Peripheral blood mononuclear cells

value: wild-type


title: EW8 ETV6 dTAG cells - 24 hour dTAGV-1 treated - replicate 3

value: dTAG

value: ETV6 dTAG

value: 24 hours


title: BC10_A549_IP_rep2

description: chromatin RNA

value: interphase


title: GMC_BL6J_ 20M_ET3_c1312_spleen

source_name: spleen

value: 20 months


title: PBMCs, IL25_IL33, GEX

source_name: PBMCs, IL25_IL33, 12 hours


title: PBMCs, TGFb_CCL2, GEX

source_name: PBMCs, TGFb_CCL2, 12 hours

value: TGF-β, CCL2


title: BC15_HeLa_MS_rep2

description: nuclear RNA

value: M-phase

value: soluble nuclear extract


title: EW8 ETV6 dTAG cells - 24 hour dTAGV-1 treated - replicate 2


title: GMC_BL6J_ 14M_ET8_c2634_spleen

value: spleen

value: 14 months


title: PBMCs, IL21_IL23, GEX

source_name: PBMCs, IL21_IL23, 12 hours


title: PBMCs, IL1b_IL3, GEX

source_name: PBMCs, IL1b_IL3, 12 hours

value: IL-1β, IL-3


title: BC8_HeLa_MP_rep1

description: chromatin RNA

value: chromatin pellet


title: GMC_BL6J_ 8M_ET35_c1378_spleen

value: WT

value: 8 months


title: BC9_A549_IS_rep2

description: nuclear RNA


title: GMC_BL6J_ 5M_ET0_c3671_spleen

value: 5 months

value: male


title: PBMCs, IL1a_IL2, GEX

source_name: PBMCs, IL1a_IL2, 12 hours

value: blood

value: Peripheral blood mononuclear cells

value: wild-type

value: IL-1α, IL-2


title: EW8 ETV6 dTAG cells - 24 hour DMSO treated - replicate 1

source_name: EW8 Ewing sarcoma cell line

value: dTAG

value: ETV6 dTAG

value: 24 hours

value: DMSO


title: BC7_HeLa_MS_rep1

description: nuclear RNA

value: M-phase

value: soluble nuclear extract


title: GMC_BL6J_ 3M_ET3_c1114 _spleen

value: spleen

value: 3 months


title: EW8 ETV6 dTAG cells - 24 hour dTAGV-1 treated - replicate 1


title: EW8 ETV6 dTAG cells - 6 hour DMSO treated - replicate 3

value: 6 hours


title: BC6_HeLa_IP_rep1

description: chromatin RNA

value: interphase

value: chromatin pellet


title: EW8 ETV6 dTAG cells - 6 hour DMSO treated - replicate 2


title: EW8 ETV6 dTAG cells - 6 hour DMSO treated - replicate 1


title: GMC_BL6J_ 26M_ET5_c2293_spleen

value: WT

value: 26 months


title: PBMCs, IL18_IL22, GEX

source_name: PBMCs, IL18_IL22, 12 hours

value: blood


title: BC5_HeLa_IS_rep1

description: nuclear RNA


title: GMC_BL6J_ 20M_ET66_c3055_spleen

value: 20 months

value: male


title: EW8 ETV6 dTAG cells - 6 hour dTAGV-1 treated - replicate 3


title: BC4_A549_MP_rep1

description: chromatin RNA


title: PBMCs, IL13_IL17a, GEX

source_name: PBMCs, IL13_IL17a, 12 hours

value: Peripheral blood mononuclear cells

value: wild-type


title: EW8 ETV6 dTAG cells - 6 hour dTAGV-1 treated - replicate 2

value: dTAG

value: ETV6 dTAG


title: GMC_BL6J_ 14M_ET3_c847_spleen

value: 14 months


title: EW8 ETV6 dTAG cells - 6 hour dTAGV-1 treated - replicate 1


title: BC2_A549_IP_rep1

description: chromatin RNA


title: PBMCs, IL10_IL12p70, GEX

source_name: PBMCs, IL10_IL12p70, 12 hours


title: GMC_BL6J_ 14M_ET4_c755_spleen


title: PBMCs, IFNg_GMCSF, GEX

source_name: PBMCs, IFNg_GMCSF, 12 hours

value: IFN-γ, GM-CSF


title: A673 ETV6 dTAG cells - 72 hour DMSO treated - replicate 3

source_name: A673 Ewing sarcoma cell line

value: 72 hours

value: DMSO


title: GMC_BL6J_ 8M_ET6_c1364_spleen

value: spleen

value: 8 months


title: BC1_A549_IS_rep1

description: nuclear RNA

extract_protocol:
Cell pellets were resuspended in 2.5 x volumes of Buffer A (10 mM HEPES pH 7.5, 10 mM KCl, 10% glycerol, 340 mM sucrose, 4mM MgCl2, 1 mM DTT,1 x Protease Inhibitor Cocktail [1 mM PMSF, 1mM ABESF, 0.8 μM aprotinin, 20 μM leupeptin, 15 μM pepstatin A, 40 μM bestatin, 15 μM E-64]), and then an equal volume of Buffer A with 0.2% (v/v) Triton X-100 was added and the mixture incubated on ice for 12 minutes to lyse cells, followed by centrifugation (1,200 x g, 5 min, 4°C). The crude nuclear pellet was resuspended in 250 μl NRB (20 mM HEPES pH 7.5, 50% Glycerol, 75 mM NaCl, 1 mM DTT, 1 x protease inhibitor cocktail), transferred to a microcentrifuge tube and centrifuged (500 x g, 5 min, 4°C) to wash. The pellet was resuspended in 250 μl NRB, and then an equal volume of NUN buffer (20 mM HEPES, 300 mM NaCl, 1M Urea, 1% NP-40 Substitute, 10 mM MgCl2, 1 mM DTT) was added and incubated 5 minutes on ice, then centrifuged (1,200 x g, 5 min, 4°C). The soluble nuclear extract supernatant was transferred to another tube, and the depleted nuclear pellet was resuspended in 1 ml Buffer A to wash, transferred to another microcentrifuge tube, and centrifuged (1,200 x g, 5 min, 4°C). Resulting purified chromatin pellets were resuspended in 50 μl Buffer A.
5 μg of total RNA was subjected to rRNA removal using  RiboMinus™ Eukaryote System v2 (Life Technologies). Then The RNA-seq library preparation was performed using the Ion Total RNA-Seq Kit v.2 following standard protocols (Life Technologies). Templates were prepared using the ION PI Template OT2 200 Prep Kit and the One Touch 2 System (Life Technologies). RNA Sequencing was performed on a PI chip (ION PI Sequencing 200 Kit v.2; Life Technologies). Signal processing, mapping and quality control was performed with Torrent Suite v.3.4.2 (Life Technologies).

value: interphase

value: soluble nuclear extract


title: A673 ETV6 dTAG cells - 72 hour DMSO treated - replicate 2


title: B16 cells, Blebbistatin treated, Parallel experiment 3

city: Xi'an

first: Yingjun

last: Yang

state: Shaanxi

address: Weiyang University Park

institute: Shaanxi University of Science and Technology

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38.90 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: B16 melanoma cells were cultured in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics on PDMS film in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Trizol. More than 1 milion cells were used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Cyclic straining were applied from PDMS tensile for 72h.
100 ng/mL blebbistatin in DMEM supplied with 10% FBS and antibiotic were applied on cells for 72h.

value: melanoma cells

value: WT

value: Blebbistatin treated

value: Day 3


title: PBMCs, GCSF_MCSF, GEX

source_name: PBMCs, GCSF_MCSF, 12 hours

value: blood

value: GCSF, MCSF


title: B16 cells, Blebbistatin treated, Parallel experiment 2


title: A673 ETV6 dTAG cells - 72 hour DMSO treated - replicate 1

city: Boston

first: Kenneth

last: Ross

institute: Dana-Farber Cancer Institute


title: GMC_BL6J_ 5m_ET66, c2287_spleen

value: 5 months

value: male


title: GMC_BL6J_ 5M_ET30_c2254_spleen


title: A673 ETV6 dTAG cells - 72 hour dTAGV-1 treated - replicate 3

value: dTAG

value: ETV6 dTAG


title: PBMCs, CXCL9_CXCL12, GEX

source_name: PBMCs, CXCL9_CXCL12, 12 hours

value: Peripheral blood mononuclear cells

value: wild-type

value: CXCL9, CXCL12


title: B16 cells, Blebbistatin treated, Parallel experiment 1


title: GMC_BL6J_ 3M_ET0_c2908_spleen

value: spleen

value: 3 months


title: PBMCs, IL15_IL17f, GEX

source_name: PBMCs, IL15_IL17f, 12 hours


title: PBMCs, CXCL10_CXCL13, GEX

source_name: PBMCs, CXCL10_CXCL13, 12 hours

value: CXCL10, CXCL13


title: BC3_A549_MS_rep1

description: nuclear RNA

value: M-phase

value: soluble nuclear extract


title: A673 ETV6 dTAG cells - 72 hour dTAGV-1 treated - replicate 2

value: 72 hours


title: B16 cells, Cyclic straining treated, Parallel experiment 3

value: melanoma cells

value: WT

value: cyclic straining


title: GMC_BL6J_ 26M_ET0_c3668_spleen

value: 26 months


title: A673 ETV6 dTAG cells - 72 hour dTAGV-1 treated - replicate 1


title: PBMCs, Ctrl_TNF, GEX

source_name: PBMCs, Control_TNF, 12 hours

value: blood

value: Control, TNF


title: B16 cells, Cyclic straining treated, Parallel experiment 2

value: Day 3


title: GMC_BL6J_ 20M_ET60_c1300_spleen

source_name: spleen

value: 20 months

value: male


title: PBMCs, CCL5_CCL17, GEX

source_name: PBMCs, CCL5_CCL17, 12 hours

value: Peripheral blood mononuclear cells

value: wild-type

value: CCL5, CCL17


title: A673 ETV6 dTAG cells - 24 hour DMSO treated - replicate 3

value: dTAG

value: ETV6 dTAG

value: 24 hours

value: DMSO


title: B16 cells, Cyclic straining treated, Parallel experiment 1


title: GMC_BL6J_14M_ET20_c636_spleen

value: spleen

value: 14 months


title: PBMCs, IFNa_IFNb, GEX

source_name: PBMCs, IFNa_IFNb, 12 hours

value: IFN-α, IFN-β


title: PBMCs, CCL4_CCL11, GEX

source_name: PBMCs, CCL4_CCL11, 12 hours

value: CCL4, CCL11


title: GMC_BL6J_ 8M_ET2_c1358_spleen

value: WT

value: 8 months


title: PBMCs, CCL22_CXCL5, GEX

source_name: PBMCs, CCL22_CXCL5, 12 hours

value: blood

value: CCL22, CXCL5


title: B16 cells, Control, Parallel experiment 3

value: melanoma cells

value: control

value: Day 3


title: A673 ETV6 dTAG cells - 24 hour DMSO treated - replicate 2


title: B16 cells, Control, Parallel experiment 2


title: PBMCs, CCL20_CXCL1, GEX

source_name: PBMCs, CCL20_CXCL1, 12 hours

value: Peripheral blood mononuclear cells

value: wild-type

value: CCL20, CXCL1


title: GMC_BL6J_ 5M_ET24_c2275_spleen

value: 5 months

value: male


title: A673 ETV6 dTAG cells - 24 hour dTAGV-1 treated - replicate 3

value: dTAG

value: ETV6 dTAG

value: 24 hours


title: GMC_BL6J_ 3M_ET55_c1030_spleen

value: spleen

value: 3 months


title: A673 ETV6 dTAG cells - 24 hour DMSO treated - replicate 1

value: DMSO


title: 12 hour lighting rep3

city: Hong Kong

first: Zizhen

last: Liang

address: The Chinese University of Hong Kong

institute: The Chinese University of Hong Kong

data_processing:
We use Agilent 2100 Bio analyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample
Raw reads were filtered by SOAPnuke software
The transcript expression level was then calculated and normalized to FPKM using RSEM software
We mapped clean reads to reference using Bowtie2\[3\], and then calculate gene expressionlevelwithRSEM
Genome_build: We use HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) to do the mapping step.

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: seeds were geminated in MS medium for 7 days to induce etiolation

extract_protocol:
Qiagen Plant RNA extraction kit (Qiagen; catalog no. 74904)
BGISEQ-500 RNA-Seq  Library P reparation Protocol

treatment_protocol: etiolated seedlings were treated with light to induce de-etiolation

value: seedling

tag: growth condition

value: grow in dark for 7 days

tag: light treatment

value: 12 hour after light treatment

value: wild type


title: MR_PDL3

first: Taohua

last: Yue

address: 8 Xi Shiku Street, Beijing

institute: Peking university first hospital

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.

source_name: cecum orthotopic CT26 tumors treated with amino acid restriction diet (SARD) and anti-PD-L1

growth_protocol: CT26 cells were maintained in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Balb/c mouse colon cancer cell line

tag: genotype

value: WT

value: SARD + anti-PD-L1


title: B16 cells, Control, Parallel experiment 1

tag: cell line

value: melanoma cells

value: control

value: Day 3


title: GMC_BL6J_ 26M_ET0_c3667_spleen

value: 26 months

value: male


title: A673 ETV6 dTAG cells - 24 hour dTAGV-1 treated - replicate 2

address: 450 Brookline Ave., Room LC6115

value: dTAG

value: ETV6 dTAG


title: A673 ETV6 dTAG cells - 24 hour dTAGV-1 treated - replicate 1

value: 24 hours


title: GMC_BL6J_20M_ET5_c3054_spleen

value: spleen

value: 20 months


title: 12 hour lighting rep1

value: seedling


title: A673 ETV6 dTAG cells - 6 hour DMSO treated - replicate 3

value: 6 hours

value: DMSO


title: MR_PDL2


title: GMC_BL6J_14M_ET2_c568_spleen

value: 14 months


title: 8 hour lighting rep3

value: grow in dark for 7 days

value: 8 hour after light treatment

value: wild type


title: A673 ETV6 dTAG cells - 6 hour DMSO treated - replicate 2


title: MR_IgG3

source_name: cecum orthotopic CT26 tumors treated with amino acid restriction diet (SARD) and IgG

value: Balb/c mouse colon cancer cell line

value: WT

value: ND + anti-PD-L1


title: GMC_BL6J_ 8M_ET66_c2295_spleen

value: 8 months


title: 8 hour lighting rep2


title: A673 ETV6 dTAG cells - 6 hour DMSO treated - replicate 1


title: MR_IgG2


title: GMC_BL6J_5M_ET80_c2231_spleen

value: 5 months

value: male


title: MR_IgG1


title: GMC_BL6J_3M_ET2_c953_spleen

value: 3 months


title: ND_PDL3

source_name: cecum orthotopic CT26 tumors treated with normal diet (ND) and anti-PD-L1

value: SARD + IgG


title: A673 ETV6 dTAG cells - 6 hour dTAGV-1 treated - replicate 2

value: dTAG

value: ETV6 dTAG


title: 12 hour lighting rep2

value: seedling

value: 12 hour after light treatment


title: 4 hour lighting rep2

value: 4 hour after light treatment


title: GMC_BL6J_26M_ET65_c3775_spleen

value: spleen

value: 26 months


title: A673 ETV6 dTAG cells - 6 hour dTAGV-1 treated - replicate 1

value: 6 hours


title: ND_PDL2


title: MR_PDL1

value: SARD + anti-PD-L1


title: GMC_BL6J_20M_ET0_c2140_spleen

value: 20 months


title: ND_PDL1

value: Balb/c mouse colon cancer cell line

value: WT


title: 2 hour lighting rep3

value: grow in dark for 7 days

value: 2 hour after light treatment

value: wild type


title: 4 hour lighting rep1


title: GMC_BL6J_8M_ET0_c3662_spleen

value: 8 months

value: male


title: ND_IgG3

source_name: cecum orthotopic CT26 tumors treated with normal diet (ND) and IgG

value: ND + IgG


title: BM1 [GEX]

description: 20A0000285-Ssq_5GEX_BM-BCell_3031489_20yoM_B2_L004

source_name: Bone marrow

value: Bone marrow

value: B-cell enriched

value: Healthy donor


title: 2 hour lighting rep2

value: seedling


title: GMC_BL6J_5M_ET6_c3670_spleen

value: spleen

value: 5 months


title: 2 hour lighting rep1


title: PBMC3 [GEX]

source_name: Blood

value: Blood

value: PBMC


title: 8 hour lighting rep1

value: 8 hour after light treatment


title: A673 ETV6 dTAG cells - 6 hour dTAGV-1 treated - replicate 3

source_name: A673 Ewing sarcoma cell line

value: dTAG

value: ETV6 dTAG

value: 6 hours


title: ND_IgG2

value: Balb/c mouse colon cancer cell line

value: WT


title: ND_IgG1


title: PBMC2 [GEX]


title: 1 hour lighting rep3

value: grow in dark for 7 days

value: 1 hour after light treatment

value: wild type


title: GMC_BL6J_3M_ET4_c940_spleen

value: 3 months

value: male


title: 4 hour lighting rep3

value: 4 hour after light treatment


title: PBMC1 [GEX]

value: Healthy donor


title: RNASeq-4-cell-FK866-rep2

city: Harbin

first: Hou

middle: wei

last: bo

state: Heilongjiang

address: Xiangfang District

institute: College of Life Science,Northeast Agricultural University

data_processing:
Basecalls performed using CASAVA version 1.4
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Fragments per kilobase of exon per million mapped fragments (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript.
Assembly: mm10
Supplementary files format and content: RNASeq_counts.txt

source_name: mouse embryos

extract_protocol:
After the embryonic blastomere was treated with an acidic manipulation solution to remove the zona pellucida, we transferred it to the lysis solution for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: developmental stage

value: mouse 4-cell

value: mouse embryos

value: treated with FK866


title: GMC_BL6J_ 8M_ET1_c1457_brain

source_name: brain

value: brain

value: 8 months


title: 1 hour lighting rep2

value: seedling


title: RNASeq-4-cell-FK866-rep1


title: GMC_BL6J_ 14M_ET0_c2626_brain

value: 14 months


title: GMC_BL6J_14M_ET0_c2600_spleen

value: spleen


title: BM2 [GEX]

description: 20A0000285-Ssq_5GEX_BM-BCell_630-2551_31yoF_C2_L004

value: Bone marrow

value: B-cell enriched


title: GMC_BL6J_ 5m_ET82_c2349_brain

value: WT

value: 5 months


title: 1 hour lighting rep1

value: grow in dark for 7 days

value: 1 hour after light treatment

value: wild type


title: GMC_BL6J_ 20M_ET0_c3580_brain

value: 20 months

value: male


title: RNASeq-4-cell-FK866-NMN-rep2

value: mouse 4-cell

value: treated with FK866-NMN


title: RNASeq-4-cell-FK866-NMN-rep1

value: mouse embryos


title: NS-SV-AC RES poly I:C transfection replicate 1

city: Daejeon

first: Yoosik

last: Kim

address: 291 Daehak-ro

department: Department of Chemical and Biomolecular Engineering

country: South Korea

institute: KAIST

data_processing:
Basecalls performed using bcl2fastq (Version 2.20)
Raw paired-end sequencing reads were mapped to the human genome (build hg38) with Hisat2 (ver 2.1.0).
Stringtie was used to quantify the expression of genes and transcripts by employing human gene annotation file version 32 from Gencode as the index.
Differentially expressed genes were searched with DESeq2.
Genome_build: hg38

source_name: NS-SV-AC

growth_protocol: NS-SV-AC cells were grown under indicated conditions in the original paper for 48 h.

extract_protocol:
Total RNA was extracted from cell lysate using TRIzol after centrifugation at 10,000 g for 30 sec. After precipitation of the extracted nucleic acids, DNAse I was treated to remove DNA.
2x101 paired-end RNA-seq library was constructed using TruSeq Stranded mRNA Prep Kit and sequenced using the Illumina Novaseq6000 system.

treatment_protocol: 20 μm 2-CM or RES was treated 24 h prior to poly I:C transfection, and simultaneously again with poly I:C transfection. The same volume of DMSo was treated for control.

value: NS-SV-AC

value: RES - poly I:C transfection


title: 0 hour lighting rep2

value: seedling

value: 0 hour after light treatment


title: NS-SV-AC RES depc transfection replicate 2

value: RES - depc transfection


title: NS-SV-AC RES poly I:C transfection replicate 2


title: NS-SV-AC RES depc transfection replicate 1


title: RNASeq-4-cell-con-rep2

value: untreated


title: GMC_BL6J_14M_ET20_c3841_brain

value: brain

value: 14 months


title: 0 hour lighting rep1


title: RNASeq-4-cell-con-rep1

value: WT


title: NS-SV-AC 2-CM poly I:C transfection replicate 2

value: 2-CM - poly I:C transfection


title: NS-SV-AC 2-CM poly I:C transfection replicate 1


title: RNASeq-late-2-cell-TSA-rep2

value: mouse late 2-cell

value: treated with TSA


title: GMC_BL6J_ 5M_ET32_c2346_brain

value: 5 months


title: GMC_BL6J_ 3M_ET8_c1190 _brain

value: 3 months

value: male


title: RNASeq-late-2-cell-TSA-rep1


title: RNASeq-late-2-cell-Sirt1-rep2

value: treated with Sirt1


title: GMC_BL6J_ 20M_ET9_c1315_brain

value: 20 months


title: 0 hour lighting rep3

value: grow in dark for 7 days

value: wild type


title: NS-SV-AC DMSO poly I:C transfection replicate 2

value: NS-SV-AC

value: DMSO control - poly I:C transfection


title: GMC_BL6J_ 14M_ET30_c3840_brain


title: GMC_BL6J_ 8M_ET0_c3663_brain

value: 8 months


title: RNASeq-late-2-cell-Sirt1-rep1

value: mouse embryos


title: NS-SV-AC DMSO poly I:C transfection replicate 1


title: RNASeq-late-2-cell-FK866-rep2

value: treated with FK866


title: RNASeq-late-2-cell-FK866-rep1


title: GMC_BL6J_ 8M_ET2_c1383_brain

value: brain


title: monocyte_derived_macrophages3

city: Niigata

first: Itaru

last: Ninomiya

state: Niigata

address: 1-757 Asahimachi-dori, Chuoku

department: Neurology

institute: Brain Research Institute, Niigata University

hyb_protocol: Total RNA was hybridized to Affymetrix Clariom S arrays as described by the manufacturers (Affymetrix/Thermo Fisher Scientific, 168 Third Avenue, Waltham, MA USA 02451).

scan_protocol: Arrays were washed and stained with GeneChip Fluidics Station 450 and scanned with GeneChip Scanner 3000 using the GeneChip Operating Software (Affymetrix).

data_processing: The transcriptomic profiles of the cells were analyzed using Transcript Analysis Console 4.0.2 (TAC) software from Applied Biosystems.

label: Biotin

source_name: monocyte-derived macrophages

label_protocol: RNA quality was determined using a 2200 Bioanalyzer (Agilent Technologies) and was further processed with the Affymetrix GeneChip kit.

extract_protocol: Gene expression analysis was performed on the cultured cells. RNA was purified with the NucleoSpin® RNA Plus kit (Macherey-Nagel) with initial quantitation conducted using a NanoDrop OneC spectrophotometer (Thermo Fisher Scientific). RNA quality was determined using a 2200 Bioanalyzer (Agilent Technologies).

value: Monocyte-derived macrophages


title: GMC_BL6J_ 5M_ET20_c2318_brain

value: WT


title: monocyte_derived_macrophages1


title: RNASeq-late-2-cell-FK866-NMN-rep2

value: mouse late 2-cell

value: treated with FK866-NMN


title: NS-SV-AC DMSO depc transfection replicate 1

value: DMSO control - depc transfection


title: monocyte_derived_macrophages2


title: NS-SV-AC 2-CM depc transfection replicate 2

value: 2-CM - depc transfection


title: HumanCerebralcortex1

source_name: human brain cortex

extract_protocol: Total RNA of the human cerebral cortex was obtained from Clontech (Cat. No. 636561).

value: Cerebral cortex


title: NS-SV-AC 2-CM depc transfection replicate 1


title: GMC_BL6J_ 3M_ET30_c1164 _brain

value: 3 months

value: male


title: HumanCerebralcortex3


title: HumanCerebralcortex2


title: RNASeq-late-2-cell-FK866-NMN-rep1


title: GMC_BL6J_ 26M_ET30_c620_brain

value: 26 months


title: NS-SV-AC DMSO depc transfection replicate 2


title: GMC_BL6J_ 20M_ET3_c1312_brain

value: 20 months


title: RNASeq-late-2-cell-con-rep2

value: untreated


title: RNASeq-late-2-cell-con-rep1


title: macrophage_treatedby_CDFIYB2

description:
Day7CC6cells2
Macrophages treated by CDFIYB (CHIR99021, Dorsomorphin, Forskolin, ISX-9, Y27632, and DB2313).

source_name: induced neuronal cells

value: Macrophages

value: CDFIYB


title: GMC_BL6J_ 14M_ET8_c2634_brain

value: 14 months


title: GMC_BL6J_ 8M_ET35_c1378_brain

value: 8 months


title: GMC_BL6J_ 5M_ET0_c3671_brain

value: brain

value: 5 months


title: RNASeq-early-2-cell-rep1

value: mouse early 2-cell

value: mouse embryos

value: WT


title: RARα TG, 10nM RA (2)

city: Ann Arbor

first: Chang

address: 109 Zina Pitcher

institute: University of Michigan

data_processing:
Reads were quality trimmed and Illumina TruSeq adapter sequences were removed using Trimmomatic v. 0.32 (Bolger, Lohse, & Usadel, 2014).
STAR (Dobin et al., 2013) was used to align reads to the GRCm38.p5 Ensembl mouse genome.
The htseq-count script in HTSeq v.0.6.1 (Anders, Pyl, & Huber, 2015) was run to count the number of reads mapping to each gene. HTSeq used Biopython v.2.7.3 in the analysis.
The Bioconductor package DESeq2 (Love, Huber, & Anders, 2014) was used for differential expression analysis.
Assembly: mm10
Supplementary files format and content: CSV file containing FPKM values for each Sample

source_name: CD4 T cells

growth_protocol: Naïve CD4 T cells (>95% pure) were cultured in cRPMI (w/charcoal-stripped FBS) and activated with anti-CD3 and anti-CD28 in the presence of mIL-6 (20 ng/mL), mIL-1β (10 ng/mL), mIL-21 (10 ng/mL), mIL-23 (10 ng/mL), mTNFα (5 ng/mL), hTGFβ-1 (5 ng/mL), anti-IFNγ (10 μg/mL), and anti-IL-4 (10 μg/mL) for 24h.

extract_protocol:
RNA was extracted from 24h activated naïve CD4+ T cells using Qiagen RNeasy Mini spin kit.
Library preparation was performed using the TruSeq Stranded kit (Illumina, San Diego, CA). The dscDNA quality was checked using an Agilent Bioanalyzer with the High Sensitivity DNA Chip.
RNAseq. 1x100 bp reads were sequenced using the HiSeq2500 on high-throughtput mode.

treatment_protocol: Cells were cultured with or without RA at 10nM for the 24h of culture.

value: CD4 T cells

tag: culture conditions

value: 24h w/ 10nM RA

tag: strain

value: RAR{alpha} TG


title: GMC_BL6J_ 3M_ET3_c1114 _brain

value: 3 months


title: ‘Chayote’,S3-3,30 days after storage

city: Gui Yang

first: Yuting

last: Pu

address: Huaxi District

institute: Guizhou University

data_processing:
Use fastp software to filter offline data to get Clean data, and conduct library quality evaluation such as length test and randomicity test of inserted fragments.
Use Trinity software to assemble the original reads data of RNA seq into Unique sequences, cluster the contigs generated in the previous step, and then build Bruijn diagrams for each class.
Process these Bruijn maps, and find the path according to the reads and paired reads in the map, so as to obtain the full-length transcripts with alternative splicing, and separate the transcripts of the paralogous genes.
Carry out structural level analysis such as alternative splicing analysis, new gene discovery and gene structure optimization.
Carry out differential expression analysis according to the expression amount of genes in different samples or different sample groups, and use GO, Kegg and other software to annotate the function of differentially expressed genes and perform functional enrichment and other expression level analysis.
Assembly: Trinity.fasta provided
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Sicyos edulis

source_name: ‘Chayote’,fruit

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: ‘Chayote’,fruit

value: fruit

value: 30 days after storage


title: GMC_BL6J_ 26M_ET5_c2293_brain

value: 26 months

value: male


title: RARα TG, 10nM RA (1)


title: ‘Chayote’,S3-2,30 days after storage


title: ‘Chayote’,S3-1,30 days after storage


title: RARα TG, 0nM RA (2)

value: 24h w/o RA


title: GMC_BL6J_ 20M_ET66_c3055_brain

value: 20 months


title: ‘Chayote’,S2-3,15 days after storage

value: 15 days after storage


title: RARα TG, 0nM RA (1)


title: macrophage_treatedby_CDFIYB1

description:
Day7CC6cells1
Macrophages treated by CDFIYB (CHIR99021, Dorsomorphin, Forskolin, ISX-9, Y27632, and DB2313).

value: Macrophages

value: CDFIYB


title: RNASeq-early-2-cell-rep2

value: mouse early 2-cell

value: untreated


title: GMC_BL6J_ 14M_ET3_c847_brain

value: brain

value: WT

value: 14 months


title: macrophage_treatedby_CDFIYB3

description:
Day7CC6cells3
Macrophages treated by CDFIYB (CHIR99021, Dorsomorphin, Forskolin, ISX-9, Y27632, and DB2313).


title: ‘Chayote’,S2-2,15 days after storage


title: GMC_BL6J_ 14M_ET4_c755_brain


title: RARα KO, 10nM RA (2)

value: CD4 T cells

value: 24h w/ 10nM RA

value: RAR{alpha} KO


title: ‘Chayote’,S2-1,15 days after storage

value: ‘Chayote’,fruit

value: fruit


title: RARα KO, 10nM RA (1)


title: GMC_BL6J_ 8M_ET6_c1364_brain

value: 8 months


title: macrophage_treatedby_CDFIY2

description:
Day7CC5cells2
Macrophages treated by CDFIY (CHIR99021, Dorsomorphin, Forskolin, ISX-9, and Y27632).

source_name: failed to induce neuronal cells

value: CDFIY


title: ‘Chayote’,S1-3,optimal harvest stage

value: optimal harvest stage


title: RARα KO, 0nM RA (2)

value: 24h w/o RA


title: ‘Chayote’,S1-2,optimal harvest stage


title: GMC_BL6J_ 5m_ET66, c2287_brain

value: 5 months

value: male


title: macrophage_treatedby_CDFIY3

description:
Day7CC5cells3
Macrophages treated by CDFIY (CHIR99021, Dorsomorphin, Forskolin, ISX-9, and Y27632).

value: Macrophages


title: GMC_BL6J_ 5M_ET30_c2254_brain


title: macrophage_treatedby_CDFIY1

description:
Day7CC5cells1
Macrophages treated by CDFIY (CHIR99021, Dorsomorphin, Forskolin, ISX-9, and Y27632).


title: ‘Chayote’,S1-1,optimal harvest stage


title: RARα KO, 0nM RA (1)


title: WT, 10nM RA (2)


title: WT, 10nM RA (1)


title: GMC_BL6J_ 20M_ET60_c1300_brain

value: 20 months


title: GMC_BL6J_ 26M_ET0_c3668_brain

value: 26 months


title: GMC_BL6J_ 3M_ET0_c2908_brain

value: brain

value: 3 months


title: BAA672 HP rep2

city: Seoul

first: JIEUN

last: KANG

institute: Korea university

description: Sample 4

data_processing:
The Illumina sequencer generates raw images utilizing sequencing control software for system control and base calling through an integrated primary analysis software called RTA (Real Time Analysis).
The BCL (base calls) binary is converted into FASTQ utilizing illumina package bcl2fastq. Adapters are not trimmed away from the reads.
The sequencing artifacts and contamination of raw sequencing reads were assessed by FastQC v.0.11.7 and further adapter, poor-quality or short reads (< 10 bp) were trimmed by Cutadapt v.1.18.
The number of reads mapped to each transcript was counted by HTSeq v.0.11.0
Genome_build: The preprocessed reads were aligned to the reference genome of GCF_000011605.1_ASM1160v1_genomic.gff by Bowtie2 v.2.3.4.3, followed by sorting and indexing by Samtools v.1.9.
Supplementary_files_format_and_content: DESeq2 v.1.26.0 was used to normalize the read counts and the resulting count matrix contains the raw gene counts for every gene and every sample.

organism: Pectobacterium atrosepticum

source_name: Pectobacterium atrosepticum

extract_protocol:
BAA672 RNA was isolated using RNA prep kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: HP treated


title: BAA672 WT rep2

description: Sample 2

value: untreated


title: WT, 0nM RA (1)

value: CD4 T cells

value: WT


title: WT, 0nM RA (2)


title: GMC_BL6J_14M_ET20_c636_brain

value: 14 months


title: BAA672 HP rep1

description: Sample 3


title: ESD3 Rep3

data_processing:
Basecalling performed with CASAVA ver. 1.8.2
Reads mapped against mouse (mm10) genome using the TopHat application on Illumina BaseSpace
Differential gene analysis performed using CuffLinks application on Illumina BaseSpace.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited textfile, contains differential gene expression analysis from CuffDiff results on normalized gene count values (FPKM)

source_name: ESD3 [D3] (ATCC¨ CRL1934ª)

growth_protocol: Mouse embryos were collected, eviscerated, decapitated and then further treated with trypsin to obtain the MEFs. Retroviral overexpression of Oct4, Sox2, Klf4 and c-Myc was used to generated iPSCs.

extract_protocol:
Subconfluent MEFs were harvested in Trizol lysis buffer (Qiagen RNAeasy). Single cell suspension of mouse iPSCs were prepared and feeder cells were depleted. Total RNA  was collected using the RNAeasy reagent (Qiagen) following the manufacturer’s instructions.
mRNA-seq libraries were prepared from 1 ug of total RNA using the Illumina mRNA-seq Sample Preparation kit following the manufacturer’s instructions

treatment_protocol: MEFs were cultured at least two passages in classical DMEM (Gibco) medium supplemented with antibiotics, glutamine and 10% fetal calf serum. IPSCs were cultured in ES medium in the presence of 2000 unit of LIF.

value: Mouse pluripotent stem cells

value: Passage 30


title: BAA672 WT rep1

description: Sample 1


title: ESD3 Rep2


title: Rego

city: Kumamoto City

first: Takashi

last: Semba

address: 2-2-1 Honjo, Chuo-ku

institute: International Research Center for Medical Sciences, Kumamoto University

description: Gene expression data

data_processing:
Space Ranger software v1.3.1 was used to process raw FASTQ files and histology images.
Using Space Ranger’s count, reads were aligned to the GRCm38 mouse reference genome, and transcript counts quantified for each annotated gene within every spot. Spatial transcriptomic data was analyzed by R version 4.1.1 and Seurat version 4.0.4.
Supplementary_files_format_and_content: Genes by barcode counts matrices in HDF5 binary data format, PNG of all replicate images, JSON file containing scaling factors that converts pixel positions and, text file containing spot barcode position information.
Assembly: GRCm38

source_name: Subcutaneous tumor

extract_protocol:
Tumor samples from a vehicle control- or a regorafenib-treated mouse were embedded in Tissue-Tek optimal cutting temperature (OCT) compound immediately after surgical resection and frozen with isopentane in a liquid nitrogen bath then stored at – 80°C. OCT embedded blocks were cryosectioned at a thickness of 10 µm in a cryostat and tissue sections were placed within the frames on a Visium Spatial Transcriptomic Library Preparation Glass Slides.
Visium spatial gene expression libraries were prepared for sequencing using 10x Genomics protocols. Enzymatic fragmentation and size selection are used to optimize the cDNA amplicon size. P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 (read 2 primer sequence) are added via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in illumina amplification.

value: Subcutaneous tumor

value: GAN-KP

value: gastric cancer

value: Regorafenib


title: GMC_BL6J_ 5M_ET24_c2275_brain

extract_protocol:
Mouse tissues were harvested, flash frozen on dry ice and total RNA isolated from the tissues with TRI-Reagent. Total RNA was purified with the Monarch RNA Cleanup kit.  Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using a ligation mediated RNA sequencing protocol published by Huo et al. 2015

value: 5 months

value: male


title: Ctrl

description: Gene expression data

value: Vehicle control


title: ESD3 Rep1