title: MEL624, cytokine-treated, LP1-HA_PD, rep2

city: Amsterdam

first: William

last: Faller

address: Plesmanlaan 121

department: Oncogenomics

institute: Netherlands Cancer Institute

data_processing:
Sequencing data from Ribo-seq experiments was first adapter-trimmed using the cutadapt tool (--action=trim -m 18 -a AGATCGGAAGAGCACACGTCT -a CTGTAGGCACCATCAATATCTCGTATGCCGTCTTCTGCTTG --overlap=15 --error-rate=0.1).
Fastq files were further cleaned  from rRNA & tRNA fragments using tophat.
Remaining reads were mapped to hg38 genome using STAR aligner.
Translated ORF predictions were performed with RiboCode using the gencode v34 annotation.
ORF abundances were calculated using the featureCount function from subread package.
Assembly: hg38
Supplementary files format and content: Tab-seperated ORF abundance file with the columns; GeneId, Length, LP1_1, LP1_2, L22_1, L22_2
Library strategy: Ribo-seq

source_name: skin

growth_protocol: Tumor cells expressing eL22-HA and HA-P1 were grown in 4x15cm dishes per condition. Cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% FBS and 100 U/ml Penicillin- 100ug/ml Streptomycin (Life Technologies 15140-122).

extract_protocol:
Cells were treated with 200 μg/ml cycloheximide for 3-5 minutes at 37 °C and cell pellets were washed with ice-cold PBS containing 200 μg/ml cycloheximide. Subsequently, pellets were lysed for 30 minutes in ice-cold lysis buffer (20 mM Tris HCl pH 7.4, 10 mM MgCl2, 150 mM KCl, 1% NP-40, 200 µg/mL cycloheximide and 1x EDTA-free proteinase inhibitor cocktail (Sigma 5892791001). Lysates were centrifuged at 12.000 x g for 20 minutes at 4 °C and the supernatants were collected for RNA digestion using RNaseI (Thermo Scientific AM2294) for 40 minutes at 25 °C. RNA digestion was stopped using SUPERase (Thermo Scientific AM2694). Digested lysates were incubated with Pierce™ Control Agarose Matrix (Thermo Scientific 26150) for 15 minutes at 4°C followed by incubation with AntiHA.11 Epitope Tag Affinity Matrix (BioLegend 900801) for 4 hours at 4°C under constant rotation. Supsequely, tagged ribosomes were eluted with 1mg/ml HA peptide (Thermo Scientific 26184) for 15 minutes at 30°C. Finally, ribosome protected fragments (RPFs) were purified using miRNeasy minikit (Qiagen) according to manufacturer’s instructions and RNA concentrations were measured with the Agilent 2100 bioanalyzer using a Small RNA Chip (Agilent 5067-1548).
Briefly, RPFs were run on a 15% TBE-urea polyacrylamide gel and size-selected between 26nt and 32nt using RNA markers. RNA was extracted using RNA gel extraction buffer (300 mM NaOAc pH 5.5, 1.0 mM EDTA, 0.25% SDS) and precipitation for 30 minutes on dry ice. After precipitation, samples were incubated overnight at 25°C. End dephosphorylation was performed using T4 polynucleotide kinase (PNK) (NEB M0201) for 1 hour at 37°C and ligation was performed using the T4 RNA ligase I (NEB M0204) for 2 hours at 25°C. Reverse transcription was performed using the SuperScript III reverse transcriptase (Thermo Scientific 18080051) using the oCJ485 RT primer for 30 minutes at 50°C. cDNA was then size-selected at 110bp using a 10% TBE-urea polyacrylamide gel. DNA was extracted using DNA gel extraction buffer (300 mM NaCl, 10 mM Tris pH 8, 1 mM EDTA) and precipitation for 30 minutes on dry ice. After precipitation, samples were incubated overnight at 25°C. Circular ligation was performed using CircLigase II ssDNA Ligase (Epicentre CL4111K) for 1,5 hours at 60°C. cDNA amplification was performed for 15 cycles with the Phusion High-Fidelty DNA polymerase (Thermo Scienfific F530) and primers containing different indexes for sequencing. The amplification product was size-selected at 180bp using a 8% TBE polyacrylamide gel. Samples were measured with the Agilent 2100 bioanalyzer using a DNA chip (Agilent 5067-1506) to assure high quality followed by molarity quantification. Sequencing was performed on the Illumina HiSeq2500.

treatment_protocol: Cytokine-treated HA tagged tumor cells were treated with 50ng/ml IFNγ and TNFα for 24 hours.

value: skin

value: melanoma

value: cytokines


title: HL-7702 cells, KO, 2

status: Public on Oct 23 2024

type: SRA

city: 南京市

first: Jing

last: Jin

state: 江苏省

address: 南京市江宁区龙眠大道639号中国药科大学

country: China

institute: 中国药科大学

library_source: transcriptomic

data_processing:
Fqtools plus was applied to remove the adaptors and low-quality sequencing reads. Clean reads were aligned to the hg38 human genome by HISAT2 (Version 2.2.1)
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

molecule: total RNA

organism: Homo sapiens

growth_protocol: HL-7702 cells were cultured in DMEM supplemented with 10% fetal bovine serum at 37 °C and 5% CO2.

extract_protocol:
Total cellular RNA was extracted using RNA-easy isolated reagent (Vazyme, R701) according to the manufacturer’s instructions.
RNA quantification was detected using NanoPhotometer (Thermo Fisher), followed by examination of RNA integrity and concentration with Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies). mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads. Poly A enriched mRNA was fragmented and ﬁrst and second-strand cDNA was synthesized. The purified double-stranded cDNA was subjected to end repair, addition of base A, addition of sequencing junctions, and fragment screening to recover 350 bp cDNA. PCR enrichment was performed to obtain the cDNA library. After the constructed library was qualified by Qubit3.0 (Thermo Fisher) and Agilent 2100 bioanalyzer (Agilent Technologies), it was sequenced on the MGI DNBSEQ-T7 platform.

treatment_protocol: The cells were incubated with PA (200 μM)) and OA (400 μM) for 24 h.

tag: cell line

tag: cell type

value: hepatocyte

tag: genotype

value: GCN5 KO

tag: treatment

value: free fatty acid


title: HL-7702 cells, WT, 2

address: 南京市江宁区龙眠大道639号中国药科大学

value: WT


title: CN_Untreated_TERT_Parent_Untreated_3

city: College Station

first: Ivan

last: Rusyn

state: TX

address: VIDI(Veterinary Medicine 2), 2, 402 Raymond Stotzer Pkwy

department: Interdisciplinary Faculty of Toxicology

country: USA

institute: Texas A&M University

data_processing:
The gene count matrices were generated from single-end reads with four lanes per sample with 76 base pairs (bp).
Reads were quality trimmed using Fastp (version 0.21.0) approach using the default settings with the exceptions of adapter trimming being excluded and the reads being trimmed to 50 bp (Chen et al., 2018).
The reads from the four lanes for each sample were combined to generate a single fastq file.
These files were used as input to the TempO-seq analysis pipeline (House et al., 2017) with the human S1500+ probe manifest file to generate a gene count matrix.
Quality control steps were applied to filter the raw counts: (i) exclusion of samples with fewer than 200,000 counts and (ii) removal of genes with average counts lower than 5% of the number in the remaining samples, except for the genes listed in Supplemental Table 2 that were retained for subsequent analyses. For further analyses, a total of 2,311 genes were evaluated. The Bioconductor's DESeq2 package (Love et al., 2014) was utilized to perform differential expression analysis and generate the complete normalized count matrix for all experimental conditions.
Assembly: S1500+ Gene Set
Supplementary files format and content: normcounts.csv file with normalized count data using DESeq2 R package (Love et al., 2014)
Supplementary files format and content: hash.csv file with meta data of the samples

extract_protocol:
Cell lysates were used for the Templated Oligonucleotide Sequencing Assay (TempO-Seq™, BioSpyder Technologies) assay as mRNA quantitation technology of choice (House et al., 2017). Detailed protocols for TempO-seq are provided by the manufacturer and were previously reported detailed elsewhere (House et al., 2022).
TempO-seq libraries were prepared using the human S1500+ targeted transcriptome panel (Mav et al., 2018) consisting of 2,982 transcripts according to the manufacturer’s instructions. Briefly, hybridization of the mRNA content of cell lysates was achieved by incubation of 2 μL of the lysate with 2 μL hybridization mix as follows: 10 min at 70°C, cooling ramp from 70°C to 45°C for 49 min, and 1 min at 45°C. Excess oligonucleotides were then digested in a nuclease catalyzed reaction for 90 min at 37°C. Next, hybridization products were incubated with DNA ligase for 60 min at 37°C. Nuclease and ligase were then denatured using a heat denaturation step (80°C for 30 min). A total of 10 μl of each ligation product were then mixed with an equal volume of PCR amplification mix and amplified in a LightCycler 96 (Roche, Basel, Switzerland) using the manufacturer recommended settings. Amplicon samples (5 μl) were then pooled and purified using a commercial PCR clean-up kit (Clontech, Mountain View, CA). Pooled libraries were sequenced in 75 single-end read mode dual index run with custom primers using NextSeq 550 sequencing (Illumina, San Diego, CA).

value: Untreated


title: ILD366

type: RNA

city: VANCOUVER

first: Daniel

last: He

state: BC

address: 1081 Burrard St Room 166

country: Canada

institute: University Of British Columbia

scan_protocol: Nano string

data_processing: Sample quality was confirmed via manufacturer recommended quality control assessments, then normalized according to housekeeping genes

source_name: Whole Blood

extract_protocol: RNA was extracted from PAXgene samples using the PAXgene Blood miRNA Kit (PreAnalytiX, Hombrechtikon, Switzerland), and RNA quality was confirmed by the RNA 6000 Nano Kit (Agilent, Santa Clara, California, USA) via RNA integrity numbers obtained from Bioanalyzer analysis. Blood gene expression was profiled using 100 ng of purified RNA with a custom NanoString nCounter Elements assay (NanoString Technologies, Seattle, WA) that measures 166 transcripts.

tag: diagnosis

value: SSc-ILD

tag: age

tag: Sex

value: F

tag: fvc

tag: dlco

tag: race

value: White


title: HL-7702 cells, WT, 3

address: 南京市江宁区龙眠大道639号中国药科大学


title: HL-7702 cells, KO, 3

address: 南京市江宁区龙眠大道639号中国药科大学


title: HL-7702 cells, KO, 1

address: 南京市江宁区龙眠大道639号中国药科大学


title: ILD362

value: HP

value: AntiInflammatory


title: CN_Untreated_TERT_Parent_Untreated_2


title: ILD360

value: Asian


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_32_D07_CH03]

city: Duluth

middle: L.

last: Villeneuve

state: MN

address: 6201 Congdon Blvd

department: Mid-Continent Ecology Division

institute: US EPA

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF01_PFOS_FHM.txt

data_processing:
Sequence reads were demultiplexed based on sample-specific bar codes and a FASTQ file was generated for each sample using Illumina’s bcl2fastq conversion software.
Resulting TempO-Seq data were analyzed by Biosypder using TempO-SeqR software implemented in R. FASTQ files are aligned to the known transcript composition of the reduced transcriptome and a count table (columns = samples, genes = rows) was generated.
The single count table for the entire project was parsed into chemical-specific sample sets (with plate matched controls), a pseudo-count of 1 was added, then data were log-base 2 transformed for use in the data analysis.
Assembly: Pimephales promelas genome assembly GCA_016745375.1
Supplementary files format and content: processed data file_all samples:  Count table for all samples, prior to chemical-specific parsing, pseudo count (+1), and log2 normalization
Supplementary files format and content: processed data file_chem specific: Chemical-specific count table with pseudo count (+1) added, followed by log2 normalization; control samples correspond to two different chemicals, thus two columns of chemical-specific processed data files are provided. These are the original files before curation to remove samples corresponding to mortalities.
Supplementary files format and content: processed data file_curated:  Chemical-specific count tables, with columns removed or re-grouped (into treatment groups), based on mortality data and analytical exposure verification results (data curation).

organism: Pimephales promelas

source_name: whole body

growth_protocol: All larval fathead minnows (Pimephales promelas) used for testing were obtained from an on-site culture facility at the US EPA Great Lakes Toxicology and Ecology Division in Duluth, MN, USA.  Fathead minnow embryos were collected from multiple crosses of at least three females in paired breeding. Fertilized embryos that were attached to polyvinyl chloride breeding tiles were transferred to a bath of aerated Lake Superior water and held at 25 °C.  At five-day post-fertilization, larvae that had hatched and were freely swimming were collected, pooled, and randomly sorted for use.  Vertebrate animal husbandry and use was performed according to an approved animal care and use plan reviewed by a local animal care and use committee in accordance with the Animals in Research Act and Guide for the Care and Use of Laboratory Animals (National Research Council, 2011)

extract_protocol:
For homogenization, 75 µl of Biospyder homogenization buffer and a 2.3 mm stainless steel bead added. The fish were then homogenized in 96 well plate format using a bead mixer mill (Omni-Bead Ruptor; 30 Hz for 2 min). Homogenates corresponding to the same well position on each of two replicate plates (both from the same treatment) were pooled together (except in the case of mortality on one or both plates). This resulted in five replicate pools (independent biological replicates) per treatment, each representing the mean of two individuals. For controls there were eight replicate pools, each representing the mean of two individuals, however, the controls were shared for both PFAS tested on the same plate.
TempO-Seq libraries were prepared by ligating detector oligos to corresponding transcripts present in the whole-body homogenates. Quality control and sample quantification was performed with a DeNovix UV-Vis spectrophotometer (DeNovix Inc.). Ligated transcripts were subjected to PCR amplification which also introduces adaptors for sequencing and a sample-specific barcode. Resulting sample specific TempO-Seq libraries were subsequently pooled together and sequenced on an Illumina sequencer (NextSeq 500), 2x50 bp, single-end reads, NovaSeq X 10B reagent kits.

treatment_protocol: Larval fathead minnows (Pimephales promelas; 5-6 days post-fertilization) were exposed to each of the 20 PFAS, in concentration response, for 24 h in 96-well plate format. For each assay, 30 mM and 9.5 mM stock solutions in DMSO were used to prepare a dilution series spanning from 30 mM to 0.0095 mM (1/2 log spacing between concentrations) in DMSO. Solutions in DMSO were then diluted 300-fold in sand filtered, UV-treated Lake Superior water (LSW) to generate a series of aqueous nominal concentrations ranging from 100 µM to 0.03 µM (1/2 log-spacing between concentrations), each, including control treatments, containing 0.33% DMSO. Larval fathead minnows (five days post fertilization) were transferred to wells of three 96-well (1 ml wells; NEST), one animal per well. The volume (variable from organism loading) in each well of the three plates was reduced to a uniform volume of 50 µl using a Biomek i5 liquid handler (Beckman), and then 550 µl of dosing solution was added to each well, bringing the total volume to 600 µl. On each of the three replicate plates five individual fish were exposed to each concentration of two PFAS test chemicals, eight individuals were exposed to control water, and the remaining eight wells were treated with reference chemicals (150 µg CuSO4/L). In total, 15 fish (distributed across 3 plates) were exposed to each PFAS treatment and 24 fish (distributed across 3 plates) were exposed to control water. Following the addition of the exposure solutions, plates were incubated at 25C for 24 h. At the end of each exposure period, each well was inspected under a dissecting microscope. Mortalities were enumerated wells containing dead animals noted. Any non-lethal phenotypic abnormalities such as edema, spinal malformations, or unusual behaviors were noted. A Biomek i5 liquid handler was used to transfer 100 µl of exposure water from one of the plates (Plate A) to be used for exposure verification (below) to a new 96 well plate. All wells from plates B and C were de-watered and frozen at -80 until homogenized. For homogenization, 75 µl of Biospyder homogenization buffer and a 2.3 mm stainless steel bead added. The fish were then homogenized in 96 well plate format using a bead mixer mill (Omni-Bead Ruptor; 30 Hz for 2 min). Homogenates corresponding to the same well position on each of two replicate plates (both from the same treatment) were pooled together (except in the case of mortality on one or both plates). This resulted in five replicate pools (independent biological replicates) per treatment, each representing the mean of two individuals. For controls there were eight replicate pools, each representing the mean of two individuals, however, the controls were shared for both PFAS tested on the same plate. PFAS concentrations in the exposure medium (collected from plate A) were measured at the end of each 24 h exposure.

tag: tissue

value: whole body

value: US EPA GLTED wild type

value: PFOS (DTXSID8037706)

tag: conc.

tag: conc. units

value: microg/L

tag: exposure duration

value: 5-6 days post fertilization


title: MEL624, cytokine-treated, L22-HA_PD, rep2

country: Netherlands

value: skin

value: melanoma

value: cytokines


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_32_A03_CH03]


title: ILD359


title: HL-7702 cells, WT, 1

address: 南京市江宁区龙眠大道639号中国药科大学

value: hepatocyte

value: free fatty acid


title: RAW264.7, LPS+PBS_Rep4

city: Jinan

first: Yingnan

last: You

address: Jingwuweiliu Road

institute: Shandong provincial hospital

data_processing:
The sequencing data (Raw data) underwent quality control using fastp (v2.0) to remove adapters, trim low-quality reads (score < 20), and discard reads with an N content exceeding 10%. The processed data is termed clean data. Clean reads were aligned to the reference genome with HISAT2 (v2.1.0) and assessed for quality using RSeQC (v3.0.1). Expression quantification was performed with StringTie, and significant differential genes were identified using DESeq2.
Assembly: GRCm39
Supplementary files format and content: file included raw counts for each sample

molecule: polyA RNA

organism: Mus musculus

extract_protocol:
RNA extraction involves adding chloroform and centrifuging to collect the RNA.
Library preparation is simplified with a kit combining double-strand synthesis, end repair, and dA-tailing. mRNA is enriched with VAHTS mRNA Capture Beads, then fragmented, and used for double-stranded cDNA synthesis. The cDNA is then purified, and adapters are ligated. Libraries are quality-checked using the Agilent Bioanalyzer and Qubit. Sequencing is performed on an Illumina Novaseq6000 platform using PE150 (paired-end 150) mode. The process ensures high-quality sequence data suitable for downstream bioinformatic analysis.

value: macrophage

value: LPS+PBS


title: MEL624, cytokine-treated, L22-HA_PD, rep1


title: ILD358

value: IPF

value: M

value: AntiFibrotic


title: ILD351

value: SSc-ILD

value: AntiInflammatory

value: White


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_1_E11_CH03]

value: whole body

value: US EPA GLTED wild type


title: c587ts-STAT-Dam

city: Beijing

first: Ruiyan

last: Kong

address: 105 Xi San Huan Bei Lu, Haidian District, Beijing

institute: Capital Normal University

library_source: genomic

data_processing:
The reads had a quality score > 30, using Trimmomatic v0.38.0, discarding reads left with < 20 bp
Reads were aligned using Bowtie (version 1.1.2) to build version BDGP6 of the D. melanogaster genome.
MACS (version 1.4.1) was used to identify regions of ChIP-seq enrichment.
The density of reads in each region was normalized to reads per million(rpm).
BigWig files were generated for visualization using the Homer package.
Assembly: BDGP6
Supplementary files format and content: bigWig

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: testis

growth_protocol: The crosses were raised at 18°C and the desired adult flies were picked up and transferred to new vials with fresh food 1 days at 29°C and dissected the testes.

extract_protocol:
Testes from esg-Dam, Stat92E-Dam and UAS-Dam (control) were dissected in cold 1XPBS and immediately preserved on dry ice and kept at -80°C. Genomic DNA was then isolated.
Genomic DNA was treated by DpnII and alkaline phosphatase.The treated samples were digested with DpnI and ligated with adaptor for ligation-mediated polymerase chain reaction (LM-PCR). Following PCR, the amplified DNAs were treated with T7 exonuclease and purified for sequencing following fragmentation.

value: testis

tag: antibody

value: DamID

value: 1 days at 29 degreeC


title: RAW264.7, LPS+PBS_Rep3


title: MEL624, cytokine-treated, LP1-HA_PD, rep1

value: skin

value: melanoma


title: c587ts-UAS-Dam


title: RAW264.7, LPS+PBS_Rep2


title: ILD349

value: F

value: Asian


title: RAW264.7, LPS+PBS_Rep1

value: macrophage


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_32_B01_CH03]

value: PFOS (DTXSID8037706)

value: microg/L

value: 5-6 days post fertilization


title: c587ts-esg-Dam


title: ILD348

value: HP


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_1_B11_CH03]


title: RAW264.7, LPS+EVLPS_Rep4

value: LPS+EVLPS


title: ILD347

value: IPF

value: M

value: AntiFibrotic


title: RAW264.7, LPS+EVLPS_Rep3


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_1_E07_CH03]

value: whole body

value: US EPA GLTED wild type


title: GS cell diff2-2

city: Houston

first: jerry

last: yang

address: 1 Baylor Plaza

institute: Baylor College of Medicine

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Rnor_6.0
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: heart

growth_protocol: rat cardiac fibroblasts cultured

extract_protocol:
Total RNA was prepared using RNeasy Mini kit (Qiagen), 0.2μg RNA was used for construction of sequencing libraries
Using the Ovation RNA-seq System v2 Kit (NuGEN),

treatment_protocol: viral overexpression of Sall4 Gata4

value: heart

value: primarily cultured cells

value: cardiac fibroblast

value: GS cells, immortalized


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_10_F06_CH03]


title: GS cell diff2-3


title: ILD344

value: F

value: White


title: ILD337

value: SSc-ILD

value: AntiInflammatory


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_10_C08_CH03]

value: PFOS (DTXSID8037706)

value: microg/L


title: RAW264.7, LPS+EVLPS_Rep1

value: macrophage


title: ILD336


title: RAW264.7, LPS+EVLPS_Rep2

value: LPS+EVLPS


title: ILD315

value: HP


title: GS cell diff1-3

value: cardiomyocyte differentiation


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_10_C01_CH03]

value: 5-6 days post fertilization


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_10_B05_CH03]

value: whole body


title: GS cell diff2-1


title: TempO-Seq larval whole body after 24 h exposure to PFTrDA (DTXSID90868151) [AF02_0_32_A07_CH06]

description:
SP0301_gene_counts_GEO.csv
Normalized+1_AF02_PFTrDA_FHM.txt
Normalized+1_AF02_PFTrDA_FHM_regrouped.txt

value: US EPA GLTED wild type

value: PFTrDA (DTXSID90868151)


title: LKR13-H tumor, acquired resistance to anti-PD-1 and anti-CTLA-4

city: New Haven

first: Camila

last: Robles-Oteiza

state: CT

address: 333 Cedar St

department: Yale Cancer Center

institute: Yale University

description:
5
LKR13-H  Acquired Resistance to anti-PD-1+anti-CTLA-4

library_source: transcriptomic single cell

data_processing:
Cell Ranger was used to generate fastq files from raw call files, align reads to the mm10 reference genome, filter reads, and aggregate the cell-by-gene matrices for each individual sample. Seurat (v4.0.3) was used to process, analyze, and visualize the data
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
Tumor tissue was minced in RPMI1640 with 2% FBS, 200U/ml collagenase IV, and 1 µg/ml DNase and digested at 37°C for 30 min. Samples were filtered through a 70µm cell strainer, incubated with ammonium-chloride-potassium lysing buffer for 3 min, washed with PBS, and resuspended in RPMI1640 with 2% FBS. The resulting single cell suspension was stained with the following antibodies: CD45:PacificBlue (1:500; BioLegend #103126), CD8:PE (1:100; BioLegend #100512), CD4:PE (1:100; BioLegend #100708), and CD3:APC-Cy7 (1:50). Dead cells were excluded using Live/Dead Red Fixable Viability Dye (1:500). CD45+CD3+CD4/8+ T cells, CD45+CD3-CD4/8- other immune cells, and CD45- cancer (and stromal) cells were sorted on a FACSAria (BD) into RPMI-1640 supplemented with 2% FBS. For each individual tumor, the three sorted cell populations – T cells, other immune cells, and CD45- cancer (and stromal) cells – were combined at a 2:1:1 ratio.
Library construction was performed using 10x Genomics reagents according to the manufacturer’s instructions (3’ library prep kit)

treatment_protocol: Mice were treated with isotype control, anti-PD-1, and/or anti-CTLA-4 starting on day 10 after tumor inoculation.

value: tumor

value: anti-PD-1 and anti-CTLA-4


title: mouse_6mth_FMC_ON2

city: Saint Louis

first: David

last: Gutmann

address: 660 S. Euclid Ave

institute: Washington University in St. Louis School of Medicine

description: 10x Genomics

data_processing:
chemistry: Single Cell 5' PE
The demultiplexing, barcode processing, gene couning and aggregation were made using the cellranger pipline v6.1.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
genome build: mm10-2020-A for mus musculus , GRCh38-2020-A for homo sapiens
single cell data were processed using Partek® Flow® (Version 10.0) https://www.partek.com/partek-flow/. Gene expression and TCR V(D)J data were overlaid by R scRepertoire package.
Cell quality was evaluated by number of reads, detected gene count, and percentage of mitochondrial read, followed by CPM (counts per million) normalization. To account for library chemistry, and other possible unknown differences between experiments, cells were integrated using the Seurat3 integration method to produce batch-corrected data. PCA analysis followed by graph-based clustering using Louvain algorithm, and t-SNE/ UMAP generation employing Euclidean distance, were conducted on the first 20 principal components of the integrated expression data. Differential analyses were performed using gene specific analysis (GSA). Pathway analyses were performed using DAVID Bioinformatics platform.
Assembly: mm10-2020-A for mus musculus, GRCh38-2020-A for homo sapines
Supplementary files format and content: sequences corresponding to every barcode in the matrix table
Supplementary files format and content: sequences corresponding to every feature in the matrix table
Supplementary files format and content: matrix table with the number of unique molecular identifiers for every feature by row and every barcode by column

source_name: optic nerve

extract_protocol:
De-identified human PA samples (4 female sporadic PAs and 1 female NF1-PA; clinical information in Supplemental Table 3) were obtained under an approved Human Studies Protocol as dissociated frozen tumor single cells from the St. Louis Children’s Hospital Pediatric Tumor Bank. The frozen dissociated tumor single cells were thawed and resuspended in DMEM.The cells were then stained with 7-Aminoactinomycin D (7-AAD) (Fisher Scientific, A1310) for sorting using the MoFlo (Siteman Flow Cytometry Core at the Washington University in St Louis). Live cells were collected and submitted for single cell RNA sequencing (scRNA-seq).  Nf1-OPG optic nerves and meningeal duras were collected separately from ten 12-week old mice, and pooled to prepare a single-cell suspension. Optic nerves were collected and dissociated using the neural dissociation kit (Miltenyi Biotec, 130-095-942) followed by debris (Miltenyi Biotec, 130-107-677) and myelin (Miltenyi Biotec, 130-096-733) removal. Single cell supensions from meningeal duras were prepared as described above, stained with 7-AAD, and sorted using MoFlo. Live cells were collected and sent for scRNA sequencing with TCR V(D)J enrichment.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  Gene Expression libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 5’ Reagent Kit (v2 Chemistry Dual Index) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286) and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library.

value: optic nerve


title: GS cell diff1-2

value: heart

value: primarily cultured cells

value: cardiac fibroblast

value: GS cells, immortalized


title: GS cell diff1-1


title: ILD314

value: M

value: AntiInflammatory

value: White


title: LKR13-H tumor, acquired resistance to anti-PD-1

description:
4
LKR13-H Acquired Resistance to anti-PD-1


title: ILD312

value: SSc-ILD

value: F


title: ILD303

value: IPF


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_100_F09_CH03]

value: PFOS (DTXSID8037706)

value: microg/L

value: 5-6 days post fertilization


title: ILD302

value: HP


title: RCF-3 (control)

value: WT

value: non treated


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_1_A06_CH03]

value: whole body

value: US EPA GLTED wild type


title: RCF-1 (control)

value: heart

value: primarily cultured cells


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_100_F02_CH03]


title: RCF-2 (control)

value: cardiac fibroblast


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_100_A02_CH03]


title: ILD270


title: LKR13-H tumor, isotype

description:
1
LKR13-H Isotype

value: tumor

value: Isotype


title: retina, scRNA-seq

first: Joseph

middle: C.

last: Corbo

state: MO

address: 660 S. Euclid

department: Pathology and Immunology

institute: Washington University School of Medicine

description: 10x Genomics

data_processing:
Read alignment and initial quality control were performed using Cell Ranger software (version 7.0.0, 10X Genomics).
Assembly: GRCz11
Supplementary files format and content: Tab-separated value file and matrix file

organism: Danio rerio

source_name: retina

extract_protocol:
Fifty heads were dissected from 4-dpf heterozygous Tg(crx:GFP)stl887Tg larvae. Following dissection, eyes were stored in ice-cold Hanks’ Balanced Salt Solution (HBSS) until all eyes were harvested. Once the eyes were collected, HBSS was removed and the eyes were incubated in 400 µl of calcium/magnesium-free HBSS containing 0.4 mg papain (Worthington Biochem) for 15 min at 37°C. 800 µl of 10% fetal bovine serum (FBS) in Dulbecco's Modified Eagle Medium (DMEM) containing 5mM MgCl2 and 120 units DNaseI (Roche) were added to the mixture and incubated for 5 min at 37°C. Cells were then resuspended in 300 µl of sorting buffer (2.5 mM EDTA, 25 mM HEPES, 1% bovine serum albumin (BSA) in calcium/magnesium-free HBSS). Cells were sorted on an Aria II FACS machine (BD biosciences) with gating based on forward scatter, side scatter, and GFP fluorescence and collected in 700 μl of D-PBS without Ca2+ and Mg2+  supplemented with 0.4 % BSA (D-PBS-CMF) in 1.5 ml microcentrifuge tubes. The collected cells were then centrifuged at 300×g for 5 min, washed with D-PBS-CMF, centrifuged, and supernatant reduced to ~80 µl. Cell density was quantified on a hemocytometer, and ~ 5000 cells were used for single-cell library preparation.
A library for single-cell RNA-seq was constructed with the Chromium v3  platform  (10X  Genomics,  Pleasanton,  CA) according to the manufacturer protocol.

value: retina

tag: developmental stage

value: 4 dpf


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_10_A04_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_100_D02_CH03]


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_1_E01_CH03]


title: ILD265

value: M

value: White


title: ILD301

value: F

value: AntiInflammatory


title: GS cell-3 (undifferentiated)

value: GS cells, immortalized


title: C6WT

city: Madison

first: Jun

last: Dai

state: WI

address: 777 Highland Avenue

department: The School of Pharmacy

institute: University of Wisconsin-Madison

data_processing:
Illumina bcl2fastq v2.20.0.422
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculate-expression v1.2.31 --alignments --no-bam-output
Differential expression estimation with edgeR v3.28.0
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files includes raw gene expression matrix for each sample

source_name: Epidermis

extract_protocol:
Total RNA was extracted using the manufacturers recommendations for the Rneasy protocol
RNA libraries were prepared for sequencing using standard Truseq Illumina protocols

value: Epidermis

value: postnatal day 4


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_100_A01_CH03]

value: PFOS (DTXSID8037706)

value: microg/L

value: 5-6 days post fertilization


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_32_F01_CH03]

value: whole body

value: US EPA GLTED wild type


title: ILD254

value: IPF


title: C3MT

value: epidermis Rora knockout


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_32_G06_CH03]


title: GS cell-2 (undifferentiated)

value: heart

value: primarily cultured cells

value: cardiac fibroblast

value: non treated


title: C2MT


title: LKR13-H tumor, response to anti-PD-1

description:
2
LKR13-H Responding to anti-PD-1

value: tumor


title: GS cell-1 (undifferentiated)


title: LKR13-H tumor, response to anti-PD-1 and anti-CTLA-4

description:
3
LKR13-H Responding to anti-PD-1+anti-CTLA-4

value: anti-PD-1 and anti-CTLA-4


title: Serum6

city: chengdu

first: yu

last: liu

address: shier

institute: chengdu university of traditional Chinese medicine

data_processing:
1. Data quality control and filtering The quality information of raw data in FASTQ format was calculated and then the raw data was filtered using the Personalbio company's self developed script, clean data was obtained by removing adapter and Low quality sequence. Filter Clean Reads from 18 nt to 36 nt in length and perform deduplicatio n to obtain Unique Reads for subsequent analysis.
2. Data mapping analysis Reference genome index was built by Bowtie2 v 2.2.6) and the de duplicated Clean Reads were mapping to the reference genome using the miRDeep 2( v 2.0.0.8 )software.
3. Small RNA classification notes  Unique Reads is annotated with known miRNAs first in the miRBase database http://www.mirbase.org/ and then annotated with other non coding RNAs. Sequences that are not annotated with any information use mireap v 2.0 for new miRNA prediction analysis. Organize the existing annotation results according to the known miRNA >piRNA> rRNA > tRNA > snRNA > sno RNA > novel miRNA priority to ensure that each small RNA has a unique annotation.
4.Expression level analysis The Reads Count value of the miRNA is counted based on the number of sequences aligned to the mature miRNA. The first abundance in the miRNA of the same name was chosen as the abundance of the miRNA for subsequent analysis.
5.Differential expression analysis DESeq v 1.30.0) was condu cted to analyze the differential expressed miRNAs, tr anscripts with  P value<0.05 were considered as differentially expressed miRNAs.
Assembly: mRatBN7.2
Supplementary files format and content: xlsx

source_name: Serum

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific）
Small RNA libraries were constructed using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Inc.) according to the manufacturer’s instructions.

value: Serum

value: SD rat


title: B4MT

value: Epidermis


title: Serum5


title: ILD250

value: F

value: White


title: C1WT

value: WT

value: postnatal day 4


title: ILD253

value: M

value: AntiFibrotic


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_32_D10_CH03]

value: whole body

value: US EPA GLTED wild type

value: PFOS (DTXSID8037706)

value: microg/L

value: 5-6 days post fertilization


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_32_C07_CH03]


title: B1WT


title: Serum3


title: Serum4


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_32_A07_CH03]


title: ILD244

value: HP

value: Asian


title: A1WT


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_1_G01_CH03]


title: Serum2


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_1_F05_CH03]


title: ILD204

value: IPF


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_1_C03_CH03]


title: Npm1_KO_2

first: xin

last: wang

address: No.5 DongdanSantiao Road, Dongcheng District

institute: Chinese Academy of Medical Sciences

data_processing:
Illumina CASAVA 1.8 software was used forbasecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse genome (GRCm38/mm10).
Paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two groups was performed using the DESeq2 R package (1.20.0).
Assembly: GRCm38/mm10
Supplementary files format and content: gene fpkm xls

source_name: MC38 tumors

growth_protocol: MC38 tumor cells were subcutaneously inoculated into wild type C57BL/6 mice. Tumor tissues were collected and CD45- tumor cells were isolated  using CD45 mouse microbeads.

extract_protocol:
Total RNA was extracted by TRIzol reagent. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: MC38 tumors

value: murine colon cancer cells

value: Npm1 knockout by CRISPR/Cas9


title: ILD235

value: F


title: Serum1

value: Serum

value: SD rat


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_1_B06_CH03]


title: ILD203

value: White


title: Npm1_KO_3


title: heart6

value: heart


title: Npm1_KO_1


title: ILD245

value: SSc-ILD


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_1_A08_CH03]

value: whole body


title: heart4


title: WT_3

value: Wide type


title: ILD187


title: heart5


title: ILD179

value: AntiInflammatory


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_032_F04_CH03]

value: US EPA GLTED wild type

value: PFOS (DTXSID8037706)

value: microg/L


title: ILD198

value: M

value: AntiFibrotic

value: Asian


title: WT_1

value: MC38 tumors

value: murine colon cancer cells


title: heart3


title: A3MT

value: Epidermis

value: epidermis Rora knockout

value: postnatal day 4


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_032_D05_CH03]

value: 5-6 days post fertilization


title: heart2

value: heart

value: SD rat


title: ILD163

value: IPF

value: F

value: Native Hawaiian or Other Pacific Islander


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_032_B03_CH03]

value: whole body

value: US EPA GLTED wild type


title: heart1


title: mixture of KR158 reprogrammed by dP-mF3 vector,KR158 treated with empty vector, 4T1 cells (scRNA-seq)

city: Los Angeles

last: Tran

state: CA

address: 1441 Eastlake Ave

department: Department of Neurological Surgery

institute: University of Southern California

description:
mF4-2nd
mF4-2nd contains:  1000 cells from empty vetor ( EV-EV) reprogrammed cells,  2595 CD45+MHCII+ FACS sorted cells from dP-mF3 reprogrammed cells,  7433 CD45+MHCII- FACS sorted cells from dP-mF3 reprogrammed cells,  2869 CD45-MHCII+ FACS sorted cells from dP-mF3 reprogrammed cells,  1000 CD45-MHCII- FACS sorted cells from dP-mF3 reprogrammed cells,  600 4T1 GFP-Luc cells as internal control
barcodes.tsv.gz (barcode-3), features.tsv.gz, matrix.mtx.gz

data_processing:
Conversion of the raw sequencing data from the bcl to fastq format and the subsequent alignment to the reference genome GRCm39 (GENCODE v.24) and gene count were performed using the cellranger software (10x Genomics, version 4.0.0) with the command cellranger mkfastq, the STAR aligner, and the command cellranger count, respectively.
Results from all libraries and batches were pooled together using the command cellranger aggr without normalization for dead cells as it will be handled downstream.
UMAP coordinates calculations were performed by using Seurat package (3.2.2), using top 75 PCA principle components as input features.
Cell clustering was  done using graph-based clustering approach implemented in the Seurat package(3.2.2) with command FindClusters
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: KR158 cell/4T1

growth_protocol: cells lines  were cultured in DMEM media with 10% FBS and 1% pen/strep

extract_protocol:
Cells were  counted 1.2e4 cells putting on a 10x Chromium instrument (10x Genomics) to export labeled RNA fragments using Chromium Single Cell 3′ v3 Reagent Kit (PN-1000075).
Single-cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ v3 library construction Kit (PN-1000075)
End repair, A-tailing, adaptor ligation

treatment_protocol: For transduction of CFD-containing lentiviruses, GBM cells in baseline DMEM media were incubated with indicated lentiviral constructs for 24hrs., followed by media replacement to RPMI 1640 supplemented with 10% FBS, 1% pen/strep and 3µg/µl puromycin for selection of transduced cells.  On day 5 after transduction, cells were passaged into RPMI 1640 media supplemented with 10% FBS and 1% pen/strep without puromycin until lib preparation.

value: KR158 cell/4T1

tag: disease

value: Glioblastoma


title: ILD161

value: HP

value: M

value: AntiInflammatory

value: White


title: Mixture of KR158 reprogrammed by dP-EV vector, immature DC, mature DC, 4T1 cells (scRNA-seq)

description:
dP-2nd
dP-2nd contains:   936 CD45+MHCII+ FACS sorted cells from dP-EV reprogrammed cells,  935 CD45+MHCII- FACS sorted cells from dP-EV reprogrammed cells,  4271 CD45-MHCII+ FACS sorted cells from dP-EV reprogrammed cells,  1000 CD45-MHCII- FACS sorted cells from dP-EV reprogrammed cells,  600 4T1 GFP-Luc cells as internal control,  600 immature DC from B6 mouse spleen (enriched by negative selection kit),  600 mature DC from B6 mouse spleen ( after enrichment, matured by KR158 lysate and TNFalpha)
barcodes.tsv.gz (barcode-2), features.tsv.gz, matrix.mtx.gz

source_name: KR158 cell/DC/4T1

value: KR158 cell/DC/4T1


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_032_A09_CH03]

tag: cell line

value: PFOS (DTXSID8037706)

value: microg/L


title: ILD153

value: American Indian or Alaska Native


title: TempO-Seq larval whole body after 24 h exposure to PFOS (DTXSID8037706) [AF01_0_032_H01_CH03]

tag: cell type

value: 5-6 days post fertilization


title: ILD158


title: MEC4_S14_RRBS

city: Loma Linda

first: daliao

last: Xiao

state: California

address: 11234 Anderson st

department: center for perinatal biology

institute: Loma Linda University

data_processing:
Raw RNA-seq fastq data was assessed for sequencing quality using FastQC
Adapters and primers were trimmed using Trimmomatic (v0.3.7).
Reads were aligned to the rat reference genome NCBI Rnor6.0, downloaded from iGenome, using Kallisto (v.0.44.0) with the default parameter settings.
The read counts matrix from Kallisto was input to DESeq2 (v.1.38.0) to identify differentially expressed genes (DEG).
The DEGs were identified by DESeq2 with the cutoff of log2FC > +/- 0.2, p-value < 0.005 and padj<0.1.
Assembly: For RRBS analysis, raw fastq reads were trimmed using TrimGalore (v.0.4.5) and Nugen RRBS trimming script (trimRRBSdiversityAdaptCustomers.py). After trimming, reads were aligned to the human reference genome (GRCh38) with Bismark54 by default parameter settings, and PCR duplicates were removed by Nugen script (nudup.py).
Supplementary files format and content: genome NCBI Rnor6.0
Supplementary files format and content: Sequenced approximately 25M reads/each.

source_name: Sprague-Dawley Rat brain

growth_protocol: Housed under a control temperature (22 ºC) and photoperiod (12-h light and 12-h dark cycle) with food and water ad libitum.

extract_protocol:
The genomic DNA and total RNA extraction from the neonatal brain tissues were isolated with the AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, USA).100 ng of total RNA and 100 ng of gDNA for each sample were used for the following sequence analysis.
RNA-seq libraries was constructed using the NuGEN Ovation universal RNA-seq kit (TECAN). RRBS libraries were constructed following standard protocols of the NuGEN Ovation Ultralow Methyl-seq Library Systems.

treatment_protocol: The first group was exposed to e_x0002_cigarette aerosol; and the 2nd group was exposed to air in the same chamber.

tag: strain

value: Sprague-Dawley

value: brain

value: neonatal

value: male

tag: genotype

value: wild-type

value: e-cig aerosol vapor


title: WT_2

value: MC38 tumors

value: murine colon cancer cells

value: Wide type


title: MEC5_S15_RRBS

tag: treatment


title: KR158 transfected with empty vector (scRNA-seq)

description:
Dan_EV
KR158 transfected with empty vector
barcodes.tsv.gz (barcode-1), features.tsv.gz, matrix.mtx.gz

value: KR158 cell/4T1

value: Glioblastoma


title: PCOS,replicate3,scRNAseq

city: Zhengzhou

first: Man

last: Luo

address: 195 Tongbai Road, Zhongyuan District

institute: Zhengzhou Central Hospital Affiliated to Zhengzhou University

description: 10× Genomics

data_processing:
CellRanger was utilized in processing and aligning single-cell data. Quality control included filtering cells based on gene and UMI counts, and mitochondrial DNA content, with doublet removal using DoubletFinder. Normalization, variable gene identification, Principal Component Analysis, and clustering analyses were performed using Seurat. UMAP was used for visualization of cell type distribution and the relationship.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: ovary

extract_protocol:
Ovarian tissues from one side of female mouse was collected and and stored in MACS Tissue Storage Solution. Each overian sample was used in preparation of individual single-cell library using the 10x Genomics platform at 3 samples/group. Initially, tissue samples were carefully processed to yield single-cell suspensions. Subsequently, employing 10× Genomics’ GEMs technology, cells were individually encapsulated with uniquely barcoded gel beads, each bearing a cell-specific barcode and UMI.
Library was performed according to the manufacter's instructions (10×Genomics).  Briefly, Utilizing 10× Genomics’ GEMs technology, individual cells were encapsulated within uniquely barcoded gel beads, each featuring a cell-specific barcode and unique molecular identifier (UMI). Within these GEMs, cellular mRNA was efficiently captured and converted into cDNA via reverse transcription. Each resulting cDNA molecule preserved its corresponding cell’s barcode and UMI information.
Processes were made using the cell ranger software (https://www.10xgenomics.com/support/software/cell-ranger/downloads#download-links)

value: ovary

value: ovarian cell

value: PCOS


title: MEC2_S12_RRBS

tag: age


title: ILD149

tag: diagnosis

value: IPAF

tag: Sex

value: F

value: AntiInflammatory

value: White


title: PCOS,replicate2,scRNAseq

description: 10× Genomics


title: ILD145

value: IPF

value: M

tag: fvc

tag: dlco

value: AntiFibrotic


title: MEC3_S13_RRBS

value: Sprague-Dawley

tag: tissue

value: brain

value: neonatal

value: male

value: wild-type


title: Control,replicate3,scRNAseq

description: 10× Genomics

value: Control


title: ILD143

tag: race


title: BY4741 mock (4)

city: Guildford

first: André

middle: P.

last: Gerber

state: Surrey

address: Stag Hill Campus

department: Microbial Sciences

country: United Kingdom

institute: University of Surrey

description: BY4741 grown to mid-log phase in YPAD. IgG-binding and TEV elution. N9/oligo dT primed, amino-allyl labeled.

hyb_protocol: annotation not provided

scan_protocol: Scan Power : 100 PMT Volts : 460 Pixel Size : 10 Laser on time : 437350 Laser Power : 1.93 Scan Date : 2003-01-30 Scan Temperature : 37.52 Scan Time : 10:26:50 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000A [47263] Scanning software : AxImageIO Scanning software version : 2.0.2.3 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 3.0.6.73
Datafile type : GenePix Results 1.4
Image Origin : 2000, 17200

organism: Saccharomyces cerevisiae

source_name: BY4741 tot. RNA extract (4)

extract_protocol: annotation not provided

value: yeast cell


title: MC5_S5_RRBS

value: control


title: Control,replicate2,scRNAseq

description: 10× Genomics

value: ovary

value: ovarian cell


title: Treatment 2

city: Taichung

first: Chih-Hsin

last: Tang

address: 91 Xueshi

country: Taiwan

institute: China Medical University

data_processing:
Quality Control: In order to remove technical sequences, pass filter data of fastq format were processed by Trimmomatic (v0.30) to be high quality clean data. Data processing includes the following steps: (1) remove the adapter sequences (2) remove the 5 'or 3' end bases that contains N's or of quality values below 20 (3) remove bases with average quality score below 20 using the sliding window of 4bp (4) remove reads that are less than 18 bp long after trimming
MicroRNA Identify: According to miRDeep2[2], a software that discovering know and novel miRNAs from deep sequencing, we can get all the identified microRNA and their expression data.
Differential Expression Analysis: Differential expression analysis was conducted using the DESeq2 package from Bioconductor. Genes or microRNAs with a fold change ≥ 2 were considered differentially expressed.
GO and KEGG enrichment analysis: GOSeq(v1.34.1) was used identifying Gene Ontology (GO) terms that annotate a list of microRNA target genes with a significant padj less than 0.05. And topGO was used to plot DAG.
Assembly: miRbase (V22)
Supplementary files format and content: excel file include raw reads for each sample
Supplementary files format and content: excel file include TPM value for each sample

source_name: Bone

growth_protocol: The JJ012 cells were cultured 50%/50% in a Dulbecco’s Modified Eagle Medium (DMEM)/alpha-minimum essential medium (α-MEM) medium, 10% fetal bovine serum (FBS) and antibiotics then maintained in a humidified incubator at 37 °C in 5% CO2

extract_protocol:
RNA was haversted using TRIzol reagent
1μg total RNA or 10ng small RNA was used for library preparation. 3 ´SR Adaptor for Illumina was ligated to the small RNA using 3´ Ligation Enzyme. To prevent adaptor-dimer, the excess of 3 ´SR Adaptor were hybrid with SR RT Primer for Illumina. 5 ´SR Adaptor for Illumina was ligated to the small RNA using 5´ Ligation Enzyme and first strand cDNA was synthesized using ProtoScript II Reverse Transcriptase. Each sample was then amplified by PCR using P5 and P7 primers, the PCR product were purified by DNA clean beads. The purified products of 140- 160bp were recovered and cleaned up using PAGE, validated using an Agilent 2100 Bioanalyzer.

treatment_protocol: Chondrosarcoma cell line JJ012 was treated with Ugonin V (10 μM) for 24 h in the culture medium.

value: Bone

value: cancer cell

value: Ugonin V


title: ILD139

value: White


title: Control,replicate1,scRNAseq

description: 10× Genomics


title: BY4741 mock (1)

description: Mock control experiment: BY4741 grown to mid-log phase in YPD. IgG-binding and TEV elution. N9/oligo-dT primed, amino-allyl labeled.

scan_protocol: Scan Power : 100 PMT Volts : 540 Pixel Size : 10 Laser on time : 14626 Laser Power : 3.70 Scan Date : 2002-12-18 Scan Temperature : 32.61 Scan Time : 11:24:15 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [90695] Scanning software : AxImageIO Scanning software version : 2.0.2.3 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 3.0.6.73
Datafile type : GenePix Results 1.4
Image Origin : 2400, 16800

source_name: BY4741 tot. RNA extract (1)

label_protocol: N9/oligo dT primed, amino-allyl labeled.


title: Control 2


title: ILD125

data_processing: Sample quality was confirmed via manufacturer recommended quality control assessments, then normalized according to housekeeping genes

source_name: Whole Blood

value: IPF

value: F


title: ILD113

value: M

value: AntiFibrotic


title: Control 1


title: PCOS,replicate1,scRNAseq

description: 10× Genomics

value: PCOS


title: MC2_S2_RRBS

value: Sprague-Dawley

value: brain

value: neonatal


title: BY4741 mock (2)

scan_protocol: Scan Power : 100 PMT Volts : 480 Pixel Size : 10 Laser on time : 269228 Laser Power : 3.12 Scan Date : 2003-01-08 Scan Temperature : 30.51 Scan Time : 15:57:47 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000B [81971] Scanning software : AxImageIO Scanning software version : 2.0.2.2 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 3.0.6.73
Datafile type : GenePix Results 1.4
Image Origin : 2440, 16280

source_name: BY4741 tot. RNA extract (2)


title: MC1_S1_RRBS

value: male

value: wild-type


title: FEC5_S20_RRBS

value: female

value: e-cig aerosol vapor


title: ILD096

value: SSc-ILD


title: ILD140

value: AntiInflammatory


title: D96F-3-RNAseq

city: New York

first: Dusan

last: Bogunovic

state: NY

address: 650 W 168th Street

department: Pediatrics

institute: Columbia University Medical Center

data_processing:
Heterozygous SNPs
Whole Exome Seq FASTQ files were aligned to the GRCh38 reference genome, and variants were called using GATK-DRAGEN software provided by Illumina (v4.2.4). Variants were then filtered for location, confidence, zygosity, and predicted deleterious effect (QCI Interpret, Qiagen). For our initial aRMAE analysis, we considered only heterozygous variants located within 20bp of an exon that did not confer an amino acid change (‘synonymous’) (Fig.2). Missense and nonsense variants were subsequently included in the set of variants considered for secondary analysis of aRMAE (Extended Data Fig.5).
Allele-Specific Expression
Bulk RNA-sequencing reads were mapped to the hg38 (GRCh38 release 100) human reference genome using STAR v2.7.5b. STAR was run with the parameter --waspOutputMode set to SAMtag to annotate which reads passed WASP filtering. Reads that passed WASP filtering (indicated by the vW:i:1 tag) were retained while all other reads that did not pass WASP filtering (e.g., multi-mapping) were removed prior to downstream analysis. Duplicate reads were removed using the Picard (v3.1.1) MarkDuplicates function (parameter REMOVE_DUPLICATES set to true).
ASEReadCounter (GATK v 4.3.0.0) was then used to calculate allele counts per allele for downstream allele-specific expression analysis. Input VCFs used to the generate allele count data were derived from filtered donor VCFs that only contained exonic, heterozygous SNPs representing synonymous mutations. Secondary analyses included missense and nonsense variants alongside synonymous variants for allele-specific read count calculations (Extended Data Fig.5). Gene regions were then defined from exon bed files created from the GRCh38 gtf file (Homo_sapiens.GRCh38.100.gtf). Summary tables of allele-specific read counts were generated at the level of each SNP using a custom script created by the Gimelbrant Lab (counts_to_snp.R),
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files with heterozygous SNPs (synonymous and/or missense) in exons from healthy donors
Supplementary files format and content: comma-delimited files with allele-specific expression data (synonymous and/or missense SNPs) from T cell clones

source_name: T cells

growth_protocol: Single T cells sorted into one well of a 96-well plate. Each well of the 96-well plate contained 10,000 CD3-autologous PBMC irradiated feeder cells in 50uL of complete RPMI supplemented with 10 IU/mL IL-2 (BioLegend) and 1 ug/mL PHA (Sigma Aldrich).

extract_protocol:
Total RNA from T cell clones was isolated from sorted T cells using the RNeasy Mini Kit (Qiagen). Cells in RLT buffer were vortexed for 1 minute to homogenize the lysate prior to adding 100uL of 80% ethanol, mRNA was then isolated following the manufacturer’s instructions, and mRNA concentration was quantified using a NanoDrop™ 2000/2000c Spectrophotometer (ThermoFisher).
Bulk RNA-seq libraries were prepared using NEBNext Ultra II RNA Library Prep (Illumina). Libraries (i.e., clones) were sequenced to an average depth of 30,000,000 reads using an Illumina HiSeq 4000 instrument or equivalent, with > 90% of bases being >Q30.

value: T cells

value: WT


title: ILD094

last: He

address: 1081 Burrard St Room 166

institute: University Of British Columbia

extract_protocol: RNA was extracted from PAXgene samples using the PAXgene Blood miRNA Kit (PreAnalytiX, Hombrechtikon, Switzerland), and RNA quality was confirmed by the RNA 6000 Nano Kit (Agilent, Santa Clara, California, USA) via RNA integrity numbers obtained from Bioanalyzer analysis. Blood gene expression was profiled using 100 ng of purified RNA with a custom NanoString nCounter Elements assay (NanoString Technologies, Seattle, WA) that measures 166 transcripts.

value: HP

value: White


title: D96F-8-RNAseq


title: FEC4_S19_RRBS


title: MEC1_S11_RRBS


title: ILD081

value: F


title: Treatment 1

value: Bone

value: cancer cell

value: Ugonin V


title: ILD078


title: D96F-19-RNAseq


title: FEC3_S18_RRBS

value: Sprague-Dawley


title: D96F-18-RNAseq


title: MC3_S3_RRBS

value: brain

value: control


title: MC4_S4_RRBS

value: neonatal

value: male


title: D96F-16-RNAseq


title: ILD065


title: FEC1_S16_RRBS

value: female

value: wild-type


title: ILD019

value: SSc-ILD


title: D68-Clone-G3-RNAseq


title: D68-Clone-F1-RNAseq


title: ILD003

value: AntiInflammatory


title: FC5_S10_RRBS


title: KPC cells, mA2 dRNA, rep2

first: Nadya

last: Dimitrova

address: 260 Whitney Ave

department: Molecular, Cellular and Developmental Biology

data_processing:
Adapter content was trimmed from ATAC-seq reads using Fastp(Chen et al., 2018) and quality was confirmed using Fastqc.
Reads were mapped to the mouse genome (mm10) with Bowtie 2 (Langmead and Salzberg, 2012).
PCR duplicates were removed using Picard (https://broadinstitute.github.io/picard/).
Reads mapping to mitochondria and ENCODE blacklist regions (Amemiya et al., 2019) were removed.
Peaks were called for each sample separately using MACS2 with parameters -f BAMPE, --nomodel and --call-summits (Zhang et al., 2008).
The R package Diffbind (http://bioconductor.org/packages/release/bioc/html/DiffBind.html) was used to quantify differential chromatin accessibility within consensus regions.
Consensus regions were assigned to overlapping and nearby genes using the annotatePeak function in the R package Chipseeker (Wang et al., 2022) with parameter TSSRegion = c(-1000,1000).
Assembly: mm10
Supplementary files format and content: bigwig files for individual samples, converted from processed BAM files using the bamCoverage function in deepTools with parameters -bs 5 --normalizeUsing RPKM
Supplementary files format and content: tab-delimited text file, includes all consensus regions (col A-D) with gene annotations (col E-H), log2 average read concentrations (col I-K), log2 fold change in read concentration in mA2 versus Con with statistics (col L-N), and normalized counts for each sample (col O-R).

source_name: KP LUAD cell line transduced with Cas9

growth_protocol: KPC cells were maintained at 37°C in a humidified incubator with 5% CO2 in DMEM (GIBCO) supplemented with 10% FBS (F0926, Sigma-Aldrich), 50 U/ml pen/strep (GIBCO), 2 mM L-glutamine (GIBCO), and 0.1 mM non-essential amino acids (GIBCO).

extract_protocol:
The Active Motif ATAC-Seq Kit was used for cell lysis, tagmentation, DNA purification and PCR amplification
The Active Motif ATAC-Seq Kit was used for cell lysis, tagmentation, DNA purification and PCR amplification

treatment_protocol: Cas9 was introduced in KP cells from lentiviral SpCas9-T2A-Puro (BRD001, gift from the Broad Institute, MIT) and selected with puromycin treatment (5 µg/ml, Sigma-Aldrich). In vitro CRISPRa was performed with a previously described lentiviral vector (lenti-SAM-Hygro (Olivero et al., 2020 Mol Cell))

value: KP LUAD cell line transduced with Cas9

value: mA2 dRNA


title: D68-Clone-E3a4-RNAseq

value: T cells

value: WT


title: KPC cells, Con dRNA, rep2

value: Con dRNA


title: D68-Clone-F12a4-RNAseq


title: KPC cells, mA2 dRNA, rep1


title: FC3_S8_RRBS


title: BEC5F_RNAseq

value: e-cig aerosol vapor


title: 42DsiFOXA1-2

city: sacramento

first: Xiong

last: Zhang

address: 4645 2nd Ave

institute: University of California, Davis

data_processing:
Sequencing was performed on an Illumina HiSeq 2000 Sequencer. The FASTQ-formatted sequence data were analyzed using a standard BWA-Bowtie-Cufflinks workflow.
Briefly, sequence reads were aligned to the reference human genome assembly (hg19) with BWA and Bowtie software. Subsequently, the Cufflinks package was applied for transcript assembly and quantification gene expression.
To avoid spurious fold levels due to low expression values, only subsets of genes that have expression value of FPKM (fragments per kilobase of exon model per million mapped reads) above 1 for either the vehicle treated cell, or the compound treated cells are included.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include raw counts for each Sample

extract_protocol:
Total RNA was isolated from cells using TRIzol™ Reagent
RNA-seq libraries from 1μg total RNA were prepared using Illumina Tru-Seq RNA Sample Prep Kit, according to the manufacturer’s instructions. Libraries were validated with an Agilent Bioanalyzer

value: prostate cancer

tag: time

value: 48 hours


title: FC4_S9_RRBS

value: Sprague-Dawley


title: 42DsiCtrl

value: sictrl


title: Btg4tm-2

city: Nanjing

first: Jiashuo

last: Li

address: 101Longmian Avenue, Jiangning District, Nanjing 211166, P.R. China

institute: Nanjing Medical University

data_processing:
For RNA-seq data, adaptors and low-quality bases were removed with trim_galore (v0.6.10) and sequences were mapped to mouse reference genome (GRCm38) using HISAT2 (v2.2.0) with gencode annotation (vM25). Read quantification was carried out with FeatureCounts (v2.0.6) (parameters: -t exon -g gene_id -Q 10 --primary -s 0 -p).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: oocyte

extract_protocol:
Transcriptome profiling.The zona pellucidae of oocytes were removed with 0.5% pronase E (Sigma). 15 oocytes per sample (3 samples for each group) were lysed and subjected to first strand synthesis.
Transcriptome profiling. The single-strand RNA molecules were reversed with oligo (dT) primer. Amplified cDNA was fragmented into ~300 bp fragments and then constructed by TruePrep DNA Library Prep Kit (Vazyme).

value: oocyte

value: MII


title: FEC2_S17_RRBS

value: brain

value: neonatal


title: D68-Clone-CD8c-RNAseq


title: D68-Clone-CD8b-RNAseq


title: Btg4wt-2


title: BEC2F_RNAseq

value: female

value: wild-type


title: BEC4F_RNAseq


title: 42DshBRD4

value: shBRD4 lentivirus


title: Btg4tm-1


title: 42DshGFP

value: shGFP lentivirus


title: D68-Clone-CD8a-RNAseq


title: 42DJQ1

value: JQ1 500 nM


title: 42DsiFOXA1-1


title: KPC cells, Con dRNA, rep1

value: KP LUAD cell line transduced with Cas9


title: Btg4wt-1


title: BEC1F_RNAseq


title: D68-Clone-A6-RNAseq

value: T cells

value: WT


title: BEC5M_RNAseq

value: male

value: e-cig aerosol vapor


title: BY4741 mock (3)

scan_protocol: Scan Power : 100 PMT Volts : 460 Pixel Size : 10 Laser on time : 437338 Laser Power : 1.90 Scan Date : 2003-01-30 Scan Temperature : 37.41 Scan Time : 10:13:24 Scanner Make : Axon Instruments (V1.00) Scanner Model : GenePix 4000A [47263] Scanning software : AxImageIO Scanning software version : 2.0.2.3 Focus Position : 0

data_processing:
Extraction Software : GenePix Pro
Extraction Software Version : 3.0.6.73
Datafile type : GenePix Results 1.4
Image Origin : 2120, 17360

source_name: BY4741 tot. RNA extract (3)

value: yeast cell


title: 42DDMSO

value: prostate cancer

value: DMSO 0.1%

value: 48 hours


title: D68-Clone-D10-RNAseq


title: 42DAZD


title: D68-Clone-B4-RNAseq


title: D68-8-RNAseq


title: BEC3F_RNAseq

value: Sprague-Dawley


title: MII-2

value: oocyte

value: MII


title: MII-1


title: BEC4M_RNAseq

value: brain

value: neonatal


title: H660JQ1


title: GV-2

value: GV


title: D68-30-RNAseq


title: BEC3M_RNAseq

value: wild-type


title: H660AZD


title: H660DMSO


title: GV-1


title: BEC1M_RNAseq


title: lu-JQ1-3

value: JQ1 50 mg/kg

value: 7 days


title: D5U-Clone-CD4b-RNAseq

value: T cells


title: BC3F_RNAseq

value: female

value: control


title: BC5F_RNAseq


title: BC4F_RNAseq


title: Young TBI Istoype, scRNAseq

city: Chicago

first: Jennie

last: Chen

address: 240 E Huron St

institute: Northwestern University

data_processing:
Bases were called using the Illumina RTA3 method. RNA reads were aligned to the mm9 mouse reference genome and gene expression matrices were generated using Cell Ranger (version 7.2.0). TCR reads were also aligned to the mm10 mouse reference genome and clonotype/contig matrices were generated using Cell Ranger.
Assembly: mm9
Supplementary files format and content: rds, raw_feature_bc_matrix.tar.gz, filtered_contig_annotations.csv, clonotypes.csv

source_name: Brain

extract_protocol:
10x Genomics Chromium Next GEM Single Cell 5' v2 with immune profiling kit
10x Genomics Chromium Next GEM Single Cell 5' v2 with immune profiling kit

value: Brain

value: Young

value: Brain immune cells

tag: stress

value: TBI

value: Isotype


title: Young TBI aCD49d, scRNAseq

value: aCD49d Ab


title: D5U-Clone-CD8b-RNAseq

value: WT


title: lu-JQ1-1

value: prostate cancer


title: lu-JQ1-2


title: D4F-Clone-CD8b-RNAseq


title: Aged TBI Istoype, scRNAseq

value: Aged


title: lu-AZD2

value: AZD5153 10 mg/kg


title: D5U-Clone-CD4a-RNAseq


title: lu-AZD3


title: Aged TBI aCD49d, scTCRseq

data_processing:
Bases were called using the Illumina RTA3 method. RNA reads were aligned to the mm9 mouse reference genome and gene expression matrices were generated using Cell Ranger (version 7.2.0). TCR reads were also aligned to the mm10 mouse reference genome and clonotype/contig matrices were generated using Cell Ranger.
Assembly: mm9
Supplementary files format and content: rds, raw_feature_bc_matrix.tar.gz, filtered_contig_annotations.csv, clonotypes.csv
Library strategy: scTCR-seq


title: D68-27-RNAseq


title: Aged TBI aCD49d, scRNAseq


title: BEC2M_RNAseq

value: Sprague-Dawley

value: brain

value: neonatal

value: male

value: e-cig aerosol vapor


title: lu-AZD1

value: 7 days


title: BC2F_RNAseq

value: female

value: wild-type

value: control


title: D4F-Clone-CD8a-RNAseq

value: T cells


title: BC5M_RNAseq


title: Aged TBI Istoype, scTCRseq

value: Brain

value: Brain immune cells

value: TBI


title: BC1F_RNAseq


title: Young TBI aCD49d, scTCRseq

value: Young

value: aCD49d Ab


title: D41-Clone-H8-RNAseq

value: WT


title: D41-Clone-H5-RNAseq


title: Young TBI Istoype, scTCRseq

value: Isotype


title: lu-V3

value: prostate cancer

value: Vehicle


title: BC4M_RNAseq

value: Sprague-Dawley

value: brain

value: neonatal


title: lu-V2

value: 7 days


title: D41-Clone-E11-RNAseq


title: Mut, Heart, 12 wks, re2

city: Sendai

first: Taiki

last: Abe

address: Seiryo-machi 1-1, Aobaku

country: Japan

institute: Tohoku University

data_processing:
Trim-galore was used to filter out low-quality reads and adapters from the fastq files of the RNA-seq raw data. After quality checking, the data were aligned to the mouse GRCm39 genome using HISAT2. To analyze alterations in mRNA levels, rRNA data were excluded. The data were analyzed using the StringTie-edgeR pipeline. GSEA was performed with gene set sizes restricted to a minimum of 10 and a maximum of 500 genes using various R packages, including clusterProfiler, pathview, goProfiles, and enrichplot.
Assembly: GRCm39 from GENCODE
Supplementary files format and content: The tab-delimited csv file includes raw counts for each sample
Supplementary files format and content: The tab-delimited CSV file contains the following annotations to the edgeR output data: gene_id, logFC, LogCPM, Pvalue, FDR, gene name, and gene type.

source_name: Heart

extract_protocol:
Mouse hearts were lysed using TRIzol reagent (Thermo Fisher Scientific, 15596026), and total RNA was extracted. Total RNA from perfused hearts was cleaned up with the RNeasy Mini kit (QIAGEN, Germantown, MD, USA, 74106).
RNA libraries for RNA-seq was prepared  using a NEBNext Ultra II RNA Library Prep Kit for Illumina.

value: Heart

value: Mutant

value: 12 weeks of age


title: BC3M_RNAseq

value: male

value: wild-type

value: control


title: 42D_BRD4_Input_siCtrl

data_processing:
Fastq files from ChIP-seq were processed by the pipeline of AQUAS Transcription Factor and Histone. Briefly, sequencing tags were mapped against the Homo sapiens (human) reference genome (hg19) using BWA 0.7.15. Uniquely mapped tags after filtering and deduping were used for peak calling by model-based analysis for ChIP-seq (MACS 2.1.0) to identify regions of enrichment over background.
Normalized genome-wide signal-coverage tracks from raw-read alignment files were built by MACS2, UCSC tools and bedTool.
Visualization of ChIP-seq signal at enriched genomic regions (avg profile and heatmap) was achieved by using deepTools.
Peak associated genes were identified using the annotatePeaks function of HOMER.
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak, broadPeak (except for Input sample)

growth_protocol: Mice bearing LuCaP145.2 tumors were treated with Vehicle, 10 mg/kg AZD5153 (i.p.) or 50 mg/kg JQ1(i.p.) for 7 days ;42D cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS), 10 μM enzalutamide and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
samples were subject to crosslinking in 1% formaldehyde for 5 min followed by quenching with glycine for 5 min on ice. Cells were pelleted by centrifugation and resuspended in lysis buffer (50 mM HEPES pH 8.0, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X100). The pellets were then resuspended in washing buffer (10 mM Tris pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl), washed and resuspended in shearing buffer (0.1% SDS, 1mM EDTA, pH 8, 10mM Tris HCl, pH 8) before sonication using Covaris E220 following manufacturer’s instruction. Chromatin fragments were precipitated using specific antibodies and Protein G beads, washed and treated with Proteinase K and RNAse A.
The ChIP complexes were washed and eluted in 50 mM NaHCO3 and 1% SDS, followed by overnight reverse crosslinking. The recovered DNAs from ChIP and ChIP-reChIP were used for library generation. Libraries were quantified with the Bioanalyzer 2100.

tag: chip antibody

value: siCtrl for 24 h


title: D41-Clone-CD8a-RNAseq

value: T cells


title: lu-V1


title: Mut, Heart, 12 wks, re3


title: BC2M_RNAseq


title: D41-30-2-RNAseq


title: D41-33-RNAseq


title: BC1M_RNAseq


title: DON113_WES

data_processing:
Heterozygous SNPs
Whole Exome Seq FASTQ files were aligned to the GRCh38 reference genome, and variants were called using GATK-DRAGEN software provided by Illumina (v4.2.4). Variants were then filtered for location, confidence, zygosity, and predicted deleterious effect (QCI Interpret, Qiagen). For our initial aRMAE analysis, we considered only heterozygous variants located within 20bp of an exon that did not confer an amino acid change (‘synonymous’) (Fig.2). Missense and nonsense variants were subsequently included in the set of variants considered for secondary analysis of aRMAE (Extended Data Fig.5).
Allele-Specific Expression
Bulk RNA-sequencing reads were mapped to the hg38 (GRCh38 release 100) human reference genome using STAR v2.7.5b. STAR was run with the parameter --waspOutputMode set to SAMtag to annotate which reads passed WASP filtering. Reads that passed WASP filtering (indicated by the vW:i:1 tag) were retained while all other reads that did not pass WASP filtering (e.g., multi-mapping) were removed prior to downstream analysis. Duplicate reads were removed using the Picard (v3.1.1) MarkDuplicates function (parameter REMOVE_DUPLICATES set to true).
ASEReadCounter (GATK v 4.3.0.0) was then used to calculate allele counts per allele for downstream allele-specific expression analysis. Input VCFs used to the generate allele count data were derived from filtered donor VCFs that only contained exonic, heterozygous SNPs representing synonymous mutations. Secondary analyses included missense and nonsense variants alongside synonymous variants for allele-specific read count calculations (Extended Data Fig.5). Gene regions were then defined from exon bed files created from the GRCh38 gtf file (Homo_sapiens.GRCh38.100.gtf). Summary tables of allele-specific read counts were generated at the level of each SNP using a custom script created by the Gimelbrant Lab (counts_to_snp.R),
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files with heterozygous SNPs (synonymous and/or missense) in exons from healthy donors
Supplementary files format and content: comma-delimited files with allele-specific expression data (synonymous and/or missense SNPs) from T cell clones
Library strategy: Whole Exome Seq (WES)

source_name: PBMCs

growth_protocol: Healthy donor PBMCs were thawed quickly in a 37°C water bath and rested overnight in RPMI medium supplemented with 10% Fetal Bovine Serum, 1% GlutaMax, and 1% Penicillin–Streptomycin (complete RPMI).

extract_protocol:
Genomic DNA was isolated using the QIAmp DNA Blood Mini Kit per manufacturer’s instructions (Qiagen).
Exon capture was performed using the SureSelect Human All Exon V8 kit (Agilent) and paired-end sequencing was performed to average 50X depth of coverage with average 150bp read lengths (Illumina).

value: PBMCs


title: WT, Heart, 12 wks, re2

value: Wild-type


title: WT, Heart, 12 wks, re1


title: 42D_BRD4_siCtrl

value: BRD4 (Diagenode, #C15410337)


title: D41-30-RNAseq

value: WT


title: 42D_BRD4_siFOXA1

value: prostate cancer

value: siFOXA1 for 24 h


title: DON108_WES


title: D3-Clone-E7-RNAseq


title: DON96F_WES


title: D41-Clone-CD8b-RNAseq


title: LuCaP145.2_BRD4_JQ1

value: JQ1 50 mg/kg, 7 days


title: DON68_WES


title: D3-Clone-E4-RNAseq


title: 10x Genomics, Hashtags

city: Tartu

first: Pärt

last: Peterson

address: Ravila 19-A1038

department: Department of Biomedicine

country: Estonia

institute: Institute of Biomedicine and Translational Medicine

data_processing:
For Parse samples, we first generated an indexed genome using the mm10 mouse reference downloaded from Ensembl. Next, we used the split-pipe tool from Parse to process files from each sublibrary. The results from each sublibrary were then combined into a single gene expression matrix. For 10x samples, we performed a standard processing workflow using the CellRanger software.
Assembly: mm10
Supplementary files format and content: Gene expression matrix output from the Parse Biosciences split-pipe pipeline, CellRanger gene expression matrix outputs.

source_name: thymus

extract_protocol:
Each thymus lobe was mashed between frosted glass slides and collected in RPMI containing collagenase/dispase and DNase I. The thymic lobe samples were incubated at 37°C with gentle stirring for 15 min, washed with FACS buffer, filtered through 100 µ filter, and counted using LUNA-FL™ Dual Fluorescence Cell Counter (Logos Biosystems).
The samples were fixed using the Fixation Kit (Parse Biosciences), counted, and stored at -80°C as per the manufacturer's protocol. We loaded 19,230 cells per sample for 384,600 cells from 20 samples onto the Parse WT kit. The resulting library was split into nine sublibraries. The four 10X samples were multiplexed using TotalSeq™-B hashtag antibodies (BioLegend), washed, counted, and 20,680 cells were loaded in a single reaction using the 10x 3’ kit as per the manufacturer's protocol. All libraries were sequenced as paired-end 150-bp reads using the Illumina NovaSeq 6000 platform.

value: thymus

value: immune cell


title: 42D_BRD4_Input_siFOXA1


title: WT, Heart, 12 wks, re3

value: Heart


title: LuCaP145.2_BRD4_AZD5153

value: AZD5153 10 mg/kg, 7 days


title: DON5U_WES


title: Mut, Heart, 12 wks, re1

value: Mutant

value: 12 weeks of age


title: DON41_WES


title: 10x Genomics, Gene Expression


title: LuCaP145.2_BRD4_Input_JQ1


title: Parse Mini, sublibrary 2


title: D3-Clone-E1-RNAseq


title: DON4F_WES


title: D37-Clone-H8-RNAseq


title: Parse Mini, sublibrary 1


title: Parse WT, sublibrary 9

source_name: thymus, spleen

value: thymus, spleen

value: control, chronic stress


title: D37-Clone-H17-RNAseq


title: LuCaP145.2_BRD4_Input_AZD5153


title: LuCaP145.2_BRD4_Input_Vehicle

value: Vehicle 7days


title: D37-Clone-G7-RNAseq

value: T cells


title: D37-Clone-G3-RNAseq


title: Parse WT, sublibrary 8


title: DON311_WES

value: PBMCs


title: Parse WT, sublibrary 7


title: LuCaP145.2_H3K27ac_AZD5153


title: DON37_WES


title: D37-Clone-D11-RNAseq


title: LuCaP145.2_BRD4_Vehicle


title: LuCaP145.2_H3K27ac_Vehicle


title: Parse WT, sublibrary 6


title: D311-Clone-F9a4-RNAseq


title: D37-Clone-B11-RNAseq


title: DON1F_WES


title: CD4 T-cells, siControl, biol rep 2

city: Göttingen

first: Ivan

last: Bogeski

address: Humboldallee 23

department: Institute of Cardiovascular Physiology

country: Germany

institute: University Medical Center

data_processing:
Sequence images were transformed with Illumina software Base-Caller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20. Thesequencing quality was asserted using FastQC.
Sequences were aligned to the reference genome Homo sapiens (GRCh38.p13) using the RNA-seq alignment tool (version 2.7.8a) allowing for two mismatches within 50 bases. Subsequently, read counting was performed using featureCounts. Read counts were analyzed in the R/Bioconductor environment (version 4.0.5) using the DESeq2 package version 1.31.5.
Assembly: GRCh38.p13
Supplementary files format and content: Excel sheet containing raw counts

source_name: CD4 T-cells

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from leukoreduction system chambers obtained from anonymized donors at a local department of Transfusion Medicine (Ethical approval 2/3/18) by density gradient centrifugation in Lymphocyte Separation Medium 1077 (PromoCell, Cat# C‑44010), followed by erythrocyte lysis using a custom-made lysis buffer (Table EV1). Primary human naive CD4+ T-cells were isolated from the obtained PBMCs by negative microbead isolation (Miltenyi Biotec, Cat# 130-096-533), following manufacturer’s instructions. Isolated naive CD4+ T-cells were maintained in AIM V medium (Life Technologies, Cat# 12055–091) supplemented with 10% fetal calf serum (FCS) (Sigma-Aldrich, Cat# A9418). Naive CD4+ T-cell purity after isolation was confirmed by flow cytometry analysis, by staining the cells with α-CD3 (Miltenyi Biotech, Cat# 130-114-710), α-CD4 (Miltenyi Biotech, Cat# 5190304074) and α-CD8 (Miltenyi Biotech, Cat# 130-104-168) markers (FACS Canto II, BD Biosciences).

extract_protocol:
Total RNA from human CD4+ T-cells was isolated using the NucleoSpinTM RNA Plus kit (Macherey-Nagel, Cat# 740984.50), according to manufacturer’s instructions. RNA isolation from rat CD4+ T-cells was performed using the RNAEasy isolation kit (Qiagen, Cat# 74004) according to manufacturer’s instructions.
Library was prepared using Illumina_TruSeq total RNA library Kit following manufacturer's protocol.

treatment_protocol:
T-cells were generated by activation for 72 hrs with 50µL of DynabeadsTM Human T-cell Activator CD3/CD28 (Gibco, Cat# 11132D) (1:1 bead-to-cell ratio) or ImmunoCultTM Human CD3/CD28 T-cell Activator (StemCell Tech, Cat# 10991).
Introduction of small interfering (si) RNA (Table EV4) was achieved by transfecting 5-6x106 naive or effector CD4+ T-cells using the same P3 Primary Cell Nucleofector™ kit and 2 µM of siRNA working solution

value: CD4 T-cells

value: activated for 72h


title: D311-Clone-F3a4-RNAseq

value: WT


title: CD4 T-cells, siMCU, biol rep 2

value: siMCU

value: activated for 72h, knockdown with siMCU


title: LuCaP145.2_H3K27ac_Input_JQ1

value: prostate cancer

value: JQ1 50 mg/kg, 7 days


title: Parse WT, sublibrary 4

value: immune cell


title: Parse WT, sublibrary 3


title: CD4 T-cells, Effector, biol rep 2


title: DON3_WES


title: D311-Clone-F2a4-RNAseq


title: CD4 T-cells, Naive, biol rep 2

value: untreated


title: LuCaP145.2_H3K27ac_Input_Vehicle


title: LuCaP145.2, JQ1

data_processing:
Fastq files from ATAC-seq were processed by the pipeline on Github (https://github.com/ENCODE-DCC/atac-seq-pipeline).
Sequencing tags were mapped against the Homo sapiens (human) reference genome (hg19) using Bowtie 2.2.6. Mitochondrial and duplicated reads were filtered through SAMtools (v 1.2) and picard (v 2.1.1).
After filtering and deduping, uniquely mapped tags were used for peak calling by model-based analysis (MACS; 2.1.0) to identify regions of enrichment over background.
After normalization, genome-wide signal-coverage tracks from raw-read alignment files were built by MACS2, UCSC tools (bedGraphToBigWig/bedClip; http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/), and bedTools (https://github.com/arq5x/bedtools2).
The ATAC-seq signal visualization at enriched genomic regions (avgprofile and heatmap) was achieved by using deepTools (https://deeptools.readthedocs.io/en/develop/index.html).
Assembly: hg19
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Briefly, 50,000 cells per condition were washed in cold PBS and resuspended in 50 μl of cold lysis buffer. Samples were centrifuged for 10 min at 500g, 4 °C and the cell pellet resuspended in the transposition reaction mix and incubated at 37 °C for 30 min. Samples were purified using the Qiagen MinElute PCR Purification Kit.
Transposed DNA was eluted in 10 μl of elution buffer,and subjected to PCR amplification using barcoded primers and NEBNext High Fidelity PCR Master Mix. ATAC-seq libraries were purified using 2× volumes of AMPure XP beads to remove fragments below 100 bp. Library quality was assessed using a Bioanalyser High Sensitivity DNA Analysis Kit

value: JQ1 50 mg/kg

value: 7 days


title: Parse WT, sublibrary 1


title: D311-Clone-B3a8-RNAseq


title: mouse_3mth_FMC_ON2_TCR

first: David

last: Gutmann

address: 660 S. Euclid Ave

institute: Washington University in St. Louis School of Medicine

description:
F/M
10x Genomics

data_processing:
chemistry: Single Cell 5' PE
The demultiplexing, barcode processing, gene couning and aggregation were made using the cellranger pipline v6.1.1 https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger
genome build: mm10-2020-A for mus musculus , GRCh38-2020-A for homo sapiens
single cell data were processed using Partek® Flow® (Version 10.0) https://www.partek.com/partek-flow/. Gene expression and TCR V(D)J data were overlaid by R scRepertoire package.
Cell quality was evaluated by number of reads, detected gene count, and percentage of mitochondrial read, followed by CPM (counts per million) normalization. To account for library chemistry, and other possible unknown differences between experiments, cells were integrated using the Seurat3 integration method to produce batch-corrected data. PCA analysis followed by graph-based clustering using Louvain algorithm, and t-SNE/ UMAP generation employing Euclidean distance, were conducted on the first 20 principal components of the integrated expression data. Differential analyses were performed using gene specific analysis (GSA). Pathway analyses were performed using DAVID Bioinformatics platform.
Assembly: mm10-2020-A for mus musculus, GRCh38-2020-A for homo sapines
Supplementary files format and content: sequences corresponding to every barcode in the matrix table
Supplementary files format and content: sequences corresponding to every feature in the matrix table
Supplementary files format and content: matrix table with the number of unique molecular identifiers for every feature by row and every barcode by column

source_name: optic nerve

extract_protocol:
De-identified human PA samples (4 female sporadic PAs and 1 female NF1-PA; clinical information in Supplemental Table 3) were obtained under an approved Human Studies Protocol as dissociated frozen tumor single cells from the St. Louis Children’s Hospital Pediatric Tumor Bank. The frozen dissociated tumor single cells were thawed and resuspended in DMEM.The cells were then stained with 7-Aminoactinomycin D (7-AAD) (Fisher Scientific, A1310) for sorting using the MoFlo (Siteman Flow Cytometry Core at the Washington University in St Louis). Live cells were collected and submitted for single cell RNA sequencing (scRNA-seq).  Nf1-OPG optic nerves and meningeal duras were collected separately from ten 12-week old mice, and pooled to prepare a single-cell suspension. Optic nerves were collected and dissociated using the neural dissociation kit (Miltenyi Biotec, 130-095-942) followed by debris (Miltenyi Biotec, 130-107-677) and myelin (Miltenyi Biotec, 130-096-733) removal. Single cell supensions from meningeal duras were prepared as described above, stained with 7-AAD, and sorted using MoFlo. Live cells were collected and sent for scRNA sequencing with TCR V(D)J enrichment.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  Gene Expression libraries were prepared as recommended by the 10x Genomics Chromium Single Cell 5’ Reagent Kit (v2 Chemistry Dual Index) user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286) and Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library.

value: optic nerve

value: 12 weeks

value: mixed


title: LuCaP145.2_H3K27ac_JQ1


title: CD4 T-cells, siMCU, biol rep 1


title: LuCaP145.2, AZD5153

value: AZD5153 10 mg/kg


title: Parse WT, sublibrary 5

value: thymus, spleen

value: control, chronic stress


title: LuCaP145.2, Vehicle

value: Vehicle


title: CD4 T-cells, Effector, biol rep 1

value: CD4 T-cells

value: activated for 72h


title: D311-Clone-A11a8-RNAseq

value: T cells

value: WT


title: D1F-Clone-CD4a-RNAseq


title: HUVEC, MoNP-VP,TNFalpha_1

city: Tempe

first: Ting-Yun

last: Wang

state: Arizona

address: 550 E. Orange Street,  ISTB1 Building, Room 281

department: School for Engineering of Matter, Transport and Energy

institute: arizona state university

data_processing:
The sequence read pairs were aligned to the human genome (hg38) using STAR, and the number of reads for each gene was counted using StringTie
DESeq2 was used to identify differentially expressed genes (DEGs), and genes with sum of counts less than 100 across all samples were removed before the analysis
Assembly: hg38
Supplementary files format and content: tab-delimited text files include readcount for each Sample

source_name: Human umbilical vein endothelial cells

extract_protocol:
Total RNA was extracted using TRIzol reagent
mRNA library preparation (poly A enrichment) was conducted by Novogene Co., LTD

value: Human umbilical vein endothelial cells

value: endothelial cells

value: MoNP-VP


title: LuCaP145.2_H3K27ac_Input_AZD5153

value: prostate cancer

value: AZD5153 10 mg/kg, 7 days


title: mouse_3mth_FMC_ON_TCR

description:
F/M
10x Genomics


title: mouse_HET

description:
F/M
10x Genomics


title: CD4 T-cells, Naive, biol rep 1

value: untreated


title: HUVEC, MoNP-VP,TNFalpha_2


title: D108-7-RNAseq


title: D311-Clone-F2b4-RNAseq


title: NrES 16 2

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

data_processing:
Libraries were mapped to mm9 genome using STAR with the options –alignIntronMax and –AlignEndsType set to 1 and EndToEnd respectively.
Replicates wre merged together, bigwig files were produced by deeptools
Assembly: mm9
Supplementary files format and content: bigWig

growth_protocol: E14 mouse embryonic stem cells (mESCs) were cultured with mouse ESC medium (DMEM high glucose supplemented with 15% ES FBS (Gibco), 2mM L-glutamine (Gibco), 1X PenStrep (Gibco), 100μM MEM non-essential amino acids (Gibco), 100μM β-mercaptoethanol (Gibco), 1000 U/mL leukemia inhibitory factor (LIF; ESGRO, Millipore)),  3 μM CHIR99021 (Tocris) and 1 μM PD0325901 (Tocris). All the ESC cell lines used in this study were cultured on gelatin-coated tissue culture plates and all the cell lines were cultured at 37°C with 5% CO 2 . E14 mouse Nr1h2-activated embryonic stem cells (NrESC) were cultured in mouse ESC medium supplemented with 10µM T0901317 (MedChemExpress, HY-10626). E14 mouse expanded potential stem cells (ESC) were cultured on gelatin-coated plates in EPSC medium with DMEM/F-12 basal media (Thermo Fisher Scientific) supplemented with 20% knockout serum replacement (Thermo Fisher Scientific), 1X NEAA (Thermo Fisher Scientific), 1X L-glutamine (Thermo Fisher Scientific), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific), 10^3 units/ mL recombinant mouse LIF (Sigma-Aldrich), 3 µM CHIR99021(Tocris) and 1 µM PD0325901 (Tocris), 4 µM JNK Inhibitor VIII (Tocris), 10 µM SB203580 (Tocris), 0.3 µM A-419259 (Santa Cruz) and 5 µM XAV939 (Tocris).

extract_protocol:
Chormatin was using Illumina tagment DNA TDE1 Enzyme and Buffer kit as per manufacturer's instructions.
Library was prepared using Nextera DNA library preparation kit as per manufacturer's instructions.

value: NrESC passage 16


title: mouse_WT_M

city: Saint Louis

description: 10x Genomics

value: optic nerve

value: 12 weeks

value: Male

value: wild type


title: D113-26-RNAseq


title: Parse WT, sublibrary 2

value: thymus, spleen

value: immune cell

value: control, chronic stress


title: CD4 T-cells, siControl, biol rep 1

value: CD4 T-cells

value: activated for 72h


title: HUVEC, MoNP,TNFalpha_2

value: MoNP


title: mouse_WT_F

description: 10x Genomics

value: Female


title: NrES 16 1


title: D108-6-RNAseq

value: T cells

value: WT


title: HUVEC, MoNP,TNFalpha_1

value: Human umbilical vein endothelial cells

value: endothelial cells


title: NrES 1 1

value: NrESC passage 1


title: LPS 7d_3

city: Shenyang

first: Jianjun

last: Chang

state: Liaoning

address: No. 77 Puhe Road, Shenyang North New Area, China

data_processing:
The sequencing library was then subjected to sequencing on a Novaseq PE150 System (Illumina) and performed by Shanghai Personal Biotechnology Cp. Ltd (Shanghai, China).
The filtered Reads were aligned to the reference genome using the upgrade version of TopHat2, HISAT2 software, with the objective of achieving a sequence mapping rate exceeding 90%.
The reads were uniformly distributed across all expressed genes.
HTSeq was used to statistically compare the read count value of each gene, as the original expression amount of the gene.
Assembly: Mus_musculus.GRCm39.dna.toplevel.fa
Supplementary files format and content: tab-delimited text files include raw counts and FPKM values for each sample

source_name: brain

extract_protocol:
On day 1 after PBS/LPS injection or day 7 after LPS injection, mice were anesthetized and sacrificed, and fresh PVT tissues were collected. Total RNA was extracted using the Trizol Reagent. The concentration, quality, and integrity of the extracted RNA were evaluated using a NanoDrop spectrophotometer (Thermo Scientific, Wilmington, DE, USA).
Sequencing libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA) following manufacturer's protocols.

value: brain

value: LPS for 7 days


title: NrES 1 2


title: mouse_6w_ON

description:
F/M
10x Genomics

value: optic nerve

value: 6 weeks

value: mixed


title: LPS 7d_2


title: CAFs, CSRP1, 72 h, input

first: Qijun

last: Wu

address: No. 36, San Hao Street

institute: Shengjing Hospital of China Medical University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output
Discard a paired reads if either one read contains adapter contamination;Discard a paired reads if the proportion of low quality (Phred quality <15) bases is over 40% in either one read
Reference genome and gene model annotation files were downloaded from genome websitedirectly. Index of the reference genome was built using BWA (0.7.17) and clean reads werealigned to the reference genome using BWA mem (0.7.17)
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.05
Assembly: GRCh38
Supplementary files format and content: bigWig

source_name: cancer-associated fibroblasts

extract_protocol:
Cross-linking of DNA with formaldehyde was performed. After cell lysis, chromatin was sonicated using an ultrasonicator
The ChIP-Seq library preparation was proceeded as follows: (1) The DNA fragments were end-repaired and A-tailed. (2) The DNA fragments with A tail were ligated with sequencing adaptors. (3) The final DNA library was obtained after size selection and PCR amplification. Libraries were analyzed for size distribution and quantified by QPCR.

value: cancer-associated fibroblasts

value: CSRP1 overexpression


title: CAFs, CSRP1, 72 h, IP


title: LPS 7d_1


title: CAFs, Vec, 72 h, input