title: OA_PaPE

city: Urbana

first: Karen

last: Chen

state: IL

address: 1201 W Gregory St

department: Division of Nutritional Sciences

institute: University of Illinois at Urbana-Champaign

data_processing:
Sequences generated were mapped uniquely onto the human genome (hg18) by Bowtie2. The MACS (Model-based Analysis of ChIP-Seq) algorithm was used to identify enriched peak regions (default settings) with a p-value cutoff of 6.0e-7 and FDR of 0.01, as we have described. To verify the identified binding sites from ChIP-Seq findings, ChIP-qPCR using the isolated DNA was performed using the primers designed to target the binding sites at PgR (chr11:100,904,522-100,905,458), CISH (chr3:50,642,336-50,643,191), and SREBP1c (chr17:17,743,329-17,743,912).
Genome_build: hg18
Supplementary_files_format_and_content: bedgraph

growth_protocol: MCF-7 cells were obtained from and grown as recommended by the American Type Culture Collection. Receptor expression was verified by Q-PCR and western blotting and gene expression and proliferative response to estradiol was monitored regularly. For experiments with E2 and PaPE treatment, cells were maintained in the corresponding phenol red-free medium for 7 days prior to use. At the 7th day, cells were treated with Veh (0.1% EtOH), 10 nM E2 or 1 uM PaPE for 4h or 24h.  For inhibitor experiments, cells were pretreated with 1 uM PP242 or 1 uM AZD6244 for 30 min.  Then, cells were treated witn Veh, E2 or PaPE in the presence or absence of intibitors for 4h.

extract_protocol: ChIPseq libraries were prepared with the Hyper Library Construction Kit from Kapa Biosystems with two modifications: adaptors were diluted 1:20 and adaptored DNA were amplified for 6 cycles

treatment_protocol: ERα-DNA or IgG-DNA complexes were immunoprecipitated using ERα specific HC-20 antibody (Santa Cruz Biotechnology). The ChIP DNA from is 3 pooled biological replicates. Libraries were prepared according to Illumina Solexa ChIP-Seq sample processing, and single read sequencing was performed using the Illumina HiSeq 2000.

tag: biomaterial provider

value: ATCC

tag: Sex

value: Breast

tag: antibody

value: HC-20 and F10 (Santa Cruz Biotechnology)

tag: treatment

value: Oleic Acid and PaPE-1


title: Input_V

status: Public on Jan 11 2020

type: SRA

country: USA

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

tag: cell line

value: Female

tag: tissue

value: Vehicle


title: Caco-2 after S. flexneri infection (2h), replicate 3

type: RNA

city: São Paulo

first: Hadassa Cristhina

middle: Azevedo Soares

last: Santos

state: São Paulo

address: Avenida Professor Lineu Prestes, 580

department: Department of Clinical Chemistry and Toxicology

country: Brazil

institute: University of São Paulo

description: Gene expression from Caco-2 cells after infection of S. flexneri M90T strain 5a

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering any NA per group and the expression values in Log (base 2).

molecule: total RNA

source_name: Caco-2 cells, S. flexneri infection

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: Total RNA from Caco-2 cells infected with Shigella flexneri strain 5a (S. flexneri M90T) was extracted using the RNeasy Mini Kit (Qiagen, cat no. 74104, MD, USA) according to the manufacturer’s instructions. RNA quality was assessed on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: Caco-2 cells were cultivated in DMEM complemented with 10% fetal bovine serum (FBS), 1mM L-glutamine, penicillin (100U mL-1) and streptomycin (100mgmL-1) and 1% non-essential amino acids in a humidified 5% with CO2 atmosphere. The cells were grown until confluent monolayers in a six-well tissue culture plate at a density of 1x106 cells. To infection the cells were washed with phosphate-buffered saline (PBS). After washing, 900 μL of fresh DMEM with 10% FBS (D10) was added to each well with 100 μL of D10 plus bacterial (EIEC) culture (1x107 bacteria). The assay mixture was incubated for 1,5h at 37°C in 5% CO2. DMEM containing 10% FBS and 50 mg mL-1 gentamicin was added and cells were cultured for 30 min. The cells were then washed with a fresh medium containing 10% FBS, and re-incubated for up to 3h at 37°C in 5% CO2.

tag: cell type

tag: infection time


title: Caco-2 after S. flexneri infection (2h), replicate 1


title: Caco-2 after S. flexneri infection (0h), replicate 4


title: Caco-2 cell without interaction - control (2h), replicate 2

description: Gene expression from Caco-2 cells without interaction - control

source_name: Caco-2 cell, control

extract_protocol: Total RNA from Caco-2 cells (without any interaction) was extracted using the RNeasy Mini Kit (Qiagen, cat no. 74104, MD, USA) according to the manufacturer’s instructions. RNA quality was assessed on the Agilent BioAnalyzer 2100 (Agilent, Santa Clara, CA).

treatment_protocol: Caco-2 cells (human intestinal epithelial cells) were cultivated in DMEM complemented with 10% fetal bovine serum (FBS) (Invitrogen, Carlsbad, CA), 1mM L-glutamine (Sigma-Aldrich), penicillin (100U mL-1) (Sigma-Aldrich) and streptomycin (100mgmL-1) (Sigma-Aldrich) and 1% non-essential amino acids. All cell were cultivated in a humidified 5% CO2 atmosphere. The cells were grown until confluent monolayers in a six-well tissue culture plate at a density of 1x106 cells. This cells haven’t infection, but was incubated for 1,5h at 37°C in 5% CO2 as well as infected cells. DMEM containing 10% FBS and 50 mg mL-1 gentamicin was added and cells were cultured for 30 min. The cells were then washed with a fresh medium containing 10% FBS, and re-incubated for up to 3h at 37°C in 5% CO2.

tag: sample type

value: Cellular culture


title: Input_Ctrl_V


title: Caco-2 after S. flexneri infection (1h), replicate 2


title: Caco-2 cell without interaction - control (1h), replicate 2


title: Ctrl_V


title: Input_Ctrl_PaPE


title: OA_V

value: Oleic Acid


title: Caco-2 after S. flexneri infection (1h), replicate 1


title: Input_OA_PaPE


title: LUAD brain met2 scRNA-seq

city: Shanghai

first: Wei-Lin

last: JIN

address: 800 Dongchuan Road

country: China

institute: Shanghai Jiao Tong University

library_source: transcriptomic

data_processing:
The Cell Ranger Single-Cell Software Suite was used to perform sample demultiplexing, barcode processing and single-cell 3′ gene counting.First, sample demultiplexing was performed based on the 8 bp sample index read to generate FASTQs for the Read1 and Read2 paired-end reads, as well as the 14 bp GemCode barcode.Ten base pair UMI tags were extracted from Read2. Then, Read1, which contains the cDNA insert, was aligned to an appropriate reference genome using STAR. The genome reference is "refdata-cellranger-GRCh38-3.0.0."  which was downloaded from 10x Genomics was used for read alignment.Count datasets from cell ranger were further processed with Seurat v3 R package
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix of gene counts with genes in rows and barcodes in columns
Supplementary_files_format_and_content: List of metadata for each cell

source_name: brain

extract_protocol:
The freshly dissected brain tissue was cut up and then enzymatically dissociated to obtain a suspension of cells using a Tumor Dissociation Kit (Miltenyi Biotec) by incubating at 37degree for 15 minutes. Dissociated single cells were pelleted by centrifuged at 130g for 10 minutes after filtering through a 20 μm cell strainer.
Single-cell libraries were prepared using the Chromium 3′ v2 platform (10X Genomics) following the manufacturer’s protocol

tag: disease state

value: Lung adenocarcinoma

value: brain

tag: age

value: male


title: TNBC brain met scRNA-seq

value: Triple negative breast cancer

value: female


title: LUAD brain met3 scRNA-seq


title: LUAD brain met1 scRNA-seq


title: Caco-2 after S. flexneri infection (0h), replicate 1


title: Caco-2 after S. flexneri infection (1h), replicate 3


title: Ctrl_PaPE


title: OA+PaPE-1_1

data_processing:
Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2. FASTQ files were trimmed using FASTQ Trimmer (version 1.0.0).  TopHat2 (version 0.5) was employed to map paired end RNA-Seq reads to version hg19 of the Homo sapiens reference genome in the UCSC genome browser, in conjunction with the RefSeq genome reference annotation hg19. Gene expression values (raw read counts) from BAM files were calculated using StrandNGS (version 2.1) Quantification tool.  Partial reads were considered and option of detecting novel genes and exons were selected.  Default paramteres for finding novel exons and genes were specified.  DESeq normalization algorithm using default values was selected.  Differentially expressed genes were then determined by fold-change and p-value with Benjamini and Hochberg multiple test correction for each gene for each treatment relative to the vehicle control. We considered genes with fold-change >3 and p-value < 0.05 as statistically significant, differentially expressed.
Genome_build: hg19
Supplementary_files_format_and_content: counts were generated using TopHat2

extract_protocol: Once the sample quality and replicate reproducibility was verified 2 samples from each group were subjected to sequencing. RNA at a concentration of 100 ng/µL in nuclease-free water was used for library construction.The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNAseq Sample Prep kit.  The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq2000  using a TruSeq SBS sequencing kit version 3. Fastq files were generated with the software Casava 1.8.2 (Illumina).. Briefly, the poly-A containing mRNA was purified from total RNA, RNA was fragmented, double-stranded cDNA was generated from fragmented RNA, and adapters were ligated to the ends.

treatment_protocol: For gene expression analysis, total RNA was extracted from 3 biological replicates for each ligand treatment using Trizol reagent and further cleaned using the RNAeasy kit from QIAGEN. For time course studies, MCF-7 cells were treated with Veh (0.1% EtOH), 10 nM E2 or 1 μM PaPE for 4h and 24 hours. For inhibitor studies, MCF-7 were pretreated with Ctrl (0.1% DMSO), 1 μM PP242 (mTOR pathway inhibitor) or 1 μM AZD6244 (MAPK inhibitor) for 1 h and then treated with Veh (0.1% EtOH), 10 nM E2 or 1 μM PaPE in the presence or absence of inhibitors for 4 h.


title: CTRL_1

value: Control


title: 5T9C, CD4+ T cells, IngenolB, 24hr, rep2

city: Chapel Hill

first: Corbin

middle: D

last: Jones

state: NC

address: 250 Bell Tower

department: Biology

institute: University of North Carolina

description:
BvD_normalized_counts.csv
Donor4_IngenolB_24hr

data_processing:
FASTQC  (version 0.11.1)
STAR Salmon v0.7.3.2
DESeq2 v1.15
Genome_build: GRCh38.p7
Genome_build: gi|326417|gb|K02013.1|HIVBRUCG Human immunodeficiency virus type 1, isolate BRU
Supplementary_files_format_and_content: normalized_counts.csv

source_name: CD4+ T cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from leukocytes obtained by continuous-flow leukapheresis. Total CD4+ T cells were isolated from frozen PBMCs by negative selection using the EasySep Human CD4+ T cell Enrichment kit (StemCell, Vancouver Canada) per the manufacturer’s recommendations. Resting CD4+ T cells were isolated by negative selection with an immunomagnetic column as described previously (27) and either cryopreserved immediately or maintained for two days in IMDM medium (Gibco), 10% FBS, 2 µg/mL IL-2 (Peprotech) and antitrerovirals to prevent viral expansion.

extract_protocol:
Cells were lysed, and RNA and DNA were co-extracted using an AllPrep 96 RNA/DNA kit (Qiagen, Valencia CA) per the manufacturer’s instructions, adjusting the volume of lysis buffer to 0.6 mL, adding an on-column Dnase I treatment (Qiagen) and eluting RNA in 50 µL of water.
Total RNA samples were then processed into stranded, mRNA libraries using the KAPA library preparation kit (KAPA BioSystems, F. Hoffmann-La Roche Ltd).

treatment_protocol: For each LRA treatment, three biological replicates of 5x106 total or resting CD4+ T cells were treated for 48 hours at 37°C in one mL of RPMI medium 1640, 10% FBS, 10 µg/mL of enfurvitide (Sigma), and 200 nM rilpivirine.

value: IngenolB

tag: time

value: CD4+ T cells


title: 5T9C, CD4+ T cells, IngenolB, 24hr, rep1


title: ATAC-seq_normal-fibroblast-rep 2

city: Los Angeles

first: Randall

middle: B.

last: Widelitz

state: California

address: 2011 Zonal Ave HMR 305

department: Department of Pathology

institute: University of Southern California

data_processing:
The RNA-seq and ATAC-seq analysis was conducted using Chuong lab local-installed Galaxy, version 18.5. FastQC was used for prealignment QC and Qualimap 2 for post QC. Replicate correlation was calculated using DeepTools multiBigwigSummary and plotCorrelation.
For RNA-seq analysis, data was cleaned and trimmed using fastq_groomer and fasq_trimmer_by_quality (window size 3; min score >= 20).
For RNA-seq analysis, TopHat2 was used to map the transcipts to the genome.
For RNA-seq analysis, Partek genomics Suite software, version 6.6, build 6.14.0514 (Partek Inc.) was used to quantify and identify differentially expressed genes. Samples were normalized to 1X genome coverage and bigWig files generated using Deeptools bamCoverage.
For RNA-seq analysis, Ingenuity Pathway Analysis (Qiagen, Inc.) was used to assess pathway enrichment and predict upstream regulators
For ATAC-seq analysis, tools and parameters used include fastq_groomer, fast_quality_fiilter, fast_trimmer_by_quality (window size 3; min score  >= 20.
For ATAC-seq analysis, mapping was performed using bowtie2 (--very-sensitive. -maxins 2000).
For ATAC-seq analysis, peak calling was assessed using QuEST (-sam_align_ChIP. ./ATAC-seq-sample.sam. -rp./hg38 -ap ./ATAC-seq-sample -ChIP_name QuEST_analysis).
For ATAC-seq analysis, differentially ATAC annotated peaks were predicted by HOMER getDifferentiaPeaksReplicates.pl command (-t tag-ATAC-seq-keloid-rep1 tag-ATAC-seq-keloid-rep2 -I tag-ATAC-seq-control-rep1 tag-ATAC-seq-control-rep2-genome hg38 > Result_differential-annotated-peaks_replicates.txt).
For ATAC-seq analysis, Motif Prediction was determined using the HOMER findMotifsGenome command (findMotifsGenome.pl Result_differential-annotated-peaks_replicates.txt hg38 Result_Motif_KELOIDvsNormal -size 200).
Genome_build: hg38 (UCSC)
Supplementary_files_format_and_content: Bam files were generated as decribed mapping methods above; wig files of ATAC were generated using QuEST as described above in the peak-calling step; tab-deliminated text files ofr a all-gene list and a DEG list from RNA-seq were generated on Partak Genomic Suite (PGS) using ANOVA to calculate p-value and fold changes and IPA to annotate the genes. A tab-deliminated text file listing 1597 differential ATAC Regions (DARs) and their nearest gene promoters and their genomic locations was generated using HOMER as described above.

source_name: Normal fibroblast cell strain N102

growth_protocol: Fibroblasts were cultured on 100 mm cultures dishes in DMEM supplemented with 2% FBS and primocin (100 ug/ml, Invivogen). Fibroblasts were harvested at 95% confluence and then rocessed for RNA-seq and ATAC-seq analyses.

extract_protocol:
For RNA-seq, total RNAs of indicated tissues were extracted followed by the standard Trizol extraction protocol (Invitrogen, Cat.15596026). For ATAC-seq, the protocol was adapted from Dr. Howard Chang’s laboratory (Buenrostro, J.D. et al. Nat Methods. 2013). 5x10^4 cells were thawed at 37℃ and the freezing medium was removed promptly. Cells were washed in iced-cold 1X PBS once and lysed in iced-cold 50 µl of ATAC lysis buffer (10 mM Tris-HCl pH=7.4, 10 mM NaCl, 3 mM MgCl2, and freshly added 0.1% IGEPAL CA-630). Nuclei were pelleted by 500 x g at 4℃ for 10 min and chromatin was transposed by adding 2.5 µl of Tn5 transpose in total 50 µl of 1X TD buffer (Illumina, Cat. FC-121-1030) and incubating at 37℃ for 30 min. The transposed DNA was purified using a MinElute PCR Purification Kit (QIAGEN, Cat. 28004).
For RNA-seq library concstruction, libraries were prepared with TruSeq RNA Prep Kit v2 (Illumina, RS-122-2002). After amplification, the library was cleaned using 0.8X AMPure XP beads (Beckman, A63880). For ATAC-seq library construction, the transposed DNA fragments were amplified for 5 cycles using NEBNext High-Fidelity 2X PCR Mater Mix (NEB, Cat. M0541S). To obtain numbers of additional amplification cycles prior to saturation, 5 µl out of the 50 µl PCR product was used in real-time qPCR and a number of cycle that was corresponded to ¼ of maximum fluorescent intensity was used for the rest 45 µl of the PCR sample. After library amplification, 1X AMPure XP bead (Beckman, A63880) clean-up was performed for size selection and removal of adapter-dimers.

treatment_protocol: No treatment.

value: patient-derived normal fibroblast

tag: strain

tag: passages

tag: original location of the cell

value: breast

tag: ethnicity classification

value: African American

tag: gender


title: ATAC-seq_normal-fibroblast-rep 1


title: ATAC-seq_keloid-fibroblast-rep2

source_name: Keloid fibroblast cell strain K119

value: patient-derived Keloid fibroblast

value: wrist


title: 5T9C, CD4+ T cells, IngenolB, 6hr, rep2

description:
BvD_normalized_counts.csv
Donor4_IngenolB_06hr


title: 5T9C, CD4+ T cells, IngenolB, 6hr, rep1


title: RNA-seq_normal-fibroblast-rep 2


title: ATAC-seq_keloid-fibroblast-rep1


title: RNA-seq_normal-fibroblast-rep 1


title: Caco-2 after S. flexneri infection (0h), replicate 2


title: 5T9C, CD4+ T cells, IngenolB, 2hr, rep1

description:
BvD_normalized_counts.csv
Donor4_IngenolB_02hr


title: 5T9C, CD4+ T cells, DMSO, 24hr, rep2

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T9C-DMSO-24H
Donor4_DMSO_24hr

value: DMSO


title: ATAC-seq_Suspension rep3

city: New York

first: Josephine

last: Wesely

state: NY

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Fastq files were trimmed with Trimmomatic to remove adapter sequences and aligned to GRCh37.75 (hg19) using Bowtie2 alignment tool
low quality PE reads with MAP < 20 were removed using samtools and duplicate reads were removed using Picard
We then called peaks for each replicate using macs2 with the following parameters (-p 1e-1 --nomodel --shift -37 --extsize 73).
Differential accessibility analysis was performed using R-package “DESeq2”
We used FIMO to search for motif hits in the ATAC-seq atlas with default parameters using CIS-BP Single Species DNA Homo_sapien motif database (http://meme-suite.org/db/motifs), restricted to expressed TFs only, based on our RNA-seq filtering thresholds
Genome_build: GRCh37.75 (hg19)
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sample, log2FC and padj of DESeq2 of A vs S

extract_protocol:
Samples were processed as follows: nuclei were isolated by washing with ATAC buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2) and lysing with 50 ul of ATAC lysis buffer (10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40). 1ml of ATAC buffer was added to dilute lysis buffer
Illumina Nextera DNA Sample Preparation Kit

value: iPSC-derived hematopoietic cells

tag: time-point

value: day 16 of differentiation

tag: harvest

value: manual separation


title: 5T9C, CD4+ T cells, DMSO, 24hr, rep1


title: 5T9C, CD4+ T cells, DMSO, 6hr, rep2

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T9C-DMSO-06H
Donor4_DMSO_06hr


title: ATAC-seq_Suspension rep1


title: RNA-seq_keloid-fibroblast-rep1


title: OA_1

tag: biomaterial provider

value: ATCC

tag: Sex

value: Female

value: Breast

value: Oleic Acid


title: 5T9C, CD4+ T cells, DMSO, 2hr, rep2

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T9C-DMSO-02H
Donor4_DMSO_02hr

tag: treatment


title: ATAC-seq_Adherent rep3


title: 5T9C, CD4+ T cells, DMSO, 6hr, rep1


title: 5T9C, CD4+ T cells, AZDS581, 24hr, rep2

description:
AvsD_normalized_counts.csv
5T9C-AZDS581-24H


title: 5T9C, CD4+ T cells, DMSO, 2hr, rep1


title: 5T9C, CD4+ T cells, AZDS581, 24hr, rep1


title: ATAC-seq_Adherent rep2


title: RNA-seq_keloid-fibroblast-rep2

value: female


title: ATAC-seq_Adherent rep1


title: 5T9C, CD4+ T cells, AZDS581, 6hr, rep2

description:
AvsD_normalized_counts.csv
5T9C-AZDS581-06H


title: ATAC-seq_Suspension rep2


title: 5T9C, CD4+ T cells, AZDS581, 6hr, rep1


title: 5T6C, CD4+ T cells, IngenolB, 24hr, rep2

description:
BvD_normalized_counts.csv
Donor3_IngenolB_24hr


title: RNA-seq_Suspension rep2

data_processing:
Fastq files were aligned to GRCh37.75 (hg19) using STAR alignment tool
Aligned bam files were filtered for uniquely aligned reads with MAQ > 10
Differential expression analysis was performed using R-package “DESeq2”.
Genome_build: GRCh37.75 (hg19)
Supplementary_files_format_and_content: tab-delimited text files include normalized counts for each sample, log2FC and padj of DESeq2 of A vs S

extract_protocol:
Total RNA was extracted with the RNeasy mini kit (Qiagen)
NEXTflex Rapid Directional RNA-Seq Library Prep Kit


title: 5T9C, CD4+ T cells, AZDS581, 2hr, rep2

description:
AvsD_normalized_counts.csv
5T9C-AZDS581-02H


title: 5T6C, CD4+ T cells, IngenolB, 24hr, rep1


title: RNA-seq_Suspension rep1


title: RNA-seq_Adherent rep3


title: RNA-seq_Adherent rep2


title: RNA-seq_Adherent rep1


title: 5T9C, CD4+ T cells, IngenolB, 2hr, rep2


title: 5T6C, CD4+ T cells, IngenolB, 6hr, rep2

description:
BvD_normalized_counts.csv
Donor3_IngenolB_06hr


title: MED1 DHE Input

city: Houston

first: Steven

middle: Gregory

last: Call

state: TX

address: One Baylor Plaza M509

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

data_processing:
ChIP-Seq reads were initially trimmed with Trim Galore. ChIP-Seq reads were then aligned to hg19 using bowtie2 followed by peak detection using MACS2. MED1 signal tracks were generated using bedtools software.
RNA-seq and ChIP-Seq reads were initially trimmed with Trim Galore. RNA-Seq transcript abundance was quantified with Salmon 0.11.0 using the human Gencode v29 as a reference transcriptional database. Differential gene expression was then calculated with DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: Excel sheet representing differential gene expression. Bed graph files for ChIP-Seq peaks.

source_name: MOLM-14_DHE (10uM)

growth_protocol: MOLM-14 cells were maintained in RPM1 1641 supplemented with PenStrep and 10% FBS. For short-term drug treatments, cells were plated at 6x105 cells/mL.

extract_protocol:
Total RNA for RNA-Seq was extracted from treated MOLM-14 cells using a Qiagen RNeasy Kit with on-column Dnase treatment. For ChIP-Seq, genomic DNA was precipitated using lysate from treated MOLM-14 cells and purified using a Qiagen PCR Purification Kit.
For RNA-Seq,  RNA samples were normalized to 250ng each, based on picogreen quantitation, and ERCC RNA controls were incorporated into each sample. Samples then went through ribosomal RNA reduction and subsequently fragmented and primed with random hexamers to produce first strand cDNA. During second strand cDNA synthesis, RNA templates were removed and replaced with cDNA strands containing dUTP. The ds-cDNA was then purified using Beckman Coulter AMPure XP beads. Libraries were created from the cDNA by attaching an adenosine to the 3’ end and ligating unique adapters to the ends. The ligated products were then amplified. The resulting libraries were quantitated using a NanoDrop spectrophotometer and fragment size assessed with the Agilent 2100 Bioanalyzer. A qPCR assay was performed on the libraries to determine the concentration of adapter ligated fragments using the Applied Biosystems ViiA 7 Quantitative PCR instrument and a Library Quantification Kit (KAPA, KK4824). All samples were pooled equimolarly and quantitated by qPCR, and also assessed on the Bioanalyzer. ChIP-Seq library prep was done using a ThruPLEX DNA-Seq 6S Kit (Takara Bio) following the manufacturer's instructions.

treatment_protocol: For RNA-Seq in response to NR4A1 expression, MOLM-14 cells were electroporated with equimolar concentrations (100nM) of either GFP or NR4A1 in vitro-transcribed RNA and incubated for 6 hours. For RNA-Seq in response to DHE treatment, MOLM-14 cells were treated with vehicle (DMSO) or 10uM DHE and incubated for 6 hours. For MED1 ChIP-Seq, MOLM-14 cells were treated with vehicle (DMSO) or 10uM DHE for 4 hours.

tag: cell line

value: Human AML Cells

value: DHE (10uM)

tag: chip antibody

value: MED1 (CRSP1/TRAP220)  (Bethyl, cat# A300-793A)


title: RNA-seq_Suspension rep3

tag: cell type


title: NR4A DHE

value: NR4A (Cat# sc-990)


title: MED1 DHE2


title: 5T6C, CD4+ T cells, IngenolB, 6hr, rep1

value: IngenolB

value: CD4+ T cells


title: 5T6C, CD4+ T cells, DMSO, 24hr, rep2

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T6C-DMSO-24H
Donor3_DMSO_24hr


title: MED1 DHE1


title: 5T6C, CD4+ T cells, DMSO, 6hr, rep1

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T6C-DMSO-06H
Donor3_DMSO_06hr


title: 5T6C, CD4+ T cells, DMSO, 6hr, rep2


title: 5T6C, CD4+ T cells, DMSO, 24hr, rep1


title: 5T6C, CD4+ T cells, DMSO, 2hr, rep1

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T6C-DMSO-02H
Donor3_DMSO_02hr


title: 5T6C, CD4+ T cells, DMSO, 2hr, rep2


title: DHE2


title: MED1 Veh1

source_name: MOLM-14_Veh (DMSO)

value: Veh (DMSO)


title: MED1 Veh2


title: 5T6C, CD4+ T cells, AZDS581, 24hr, rep2

description:
AvsD_normalized_counts.csv
5T6C-AZDS581-24H


title: MED1 Veh Input


title: NR4A1-1

source_name: MOLM-14_NR4A1 IVT RNA

value: NR4A1 IVT RNA


title: Veh2


title: NR4A1-2


title: 5T6C, CD4+ T cells, IngenolB, 2hr, rep1

description:
BvD_normalized_counts.csv
Donor3_IngenolB_02hr


title: 5T6C, CD4+ T cells, IngenolB, 2hr, rep2


title: Veh1


title: 5T6C, CD4+ T cells, AZDS581, 6hr, rep2

description:
AvsD_normalized_counts.csv
5T6C-AZDS581-06H


title: 5T6C, CD4+ T cells, AZDS581, 6hr, rep1


title: 5T6C, CD4+ T cells, AZDS581, 2hr, rep2

description:
AvsD_normalized_counts.csv
5T6C-AZDS581-02H


title: GFP2

source_name: MOLM-14_GFP IVT RNA

value: GFP IVT RNA


title: 5T6C, CD4+ T cells, AZDS581, 2hr, rep1


title: GFP1


title: DHE1


title: 5T21, CD4+ T cells, IngenolB, 24hr, rep1

description:
BvD_normalized_counts.csv
Donor2_IngenolB_24hr


title: 5T9C, CD4+ T cells, AZDS581, 2hr, rep1


title: 5T21, CD4+ T cells, IngenolB, 6hr, rep2

description:
BvD_normalized_counts.csv
Donor2_IngenolB_06hr


title: 5T21, CD4+ T cells, IngenolB, 24hr, rep2


title: 5T6C, CD4+ T cells, AZDS581, 24hr, rep1


title: 5T21, CD4+ T cells, IngenolB, 6hr, rep1


title: D7_C

city: Ithaca

first: Andrea

middle: J

last: De Micheli

address: 161 Weill Hall

department: Biomedical Engineering

institute: Cornell University

data_processing:
Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to mm10 using Cell Ranger v2 pipeline (10X Genomics)
Gene expression data was processed with Seurat v2.3.4 (Satija lab) using R  v3.6.2 (2019-12-12)
Initial data filtering (minimum cells to express an included gene = 3, minium genes to be expressed in an included cell = 200)
Filtering by percent mitochondiral genes in included cells (maximum 0.2), number of UMIs in included cells (minimum 1000, maximum 60000), and number of mapped genes in included cells (maximum 8000)
Log-normalization of expression data
Cell annotations in metadata derived from unsupervised clustering in CCA space (CCA coefficients obtained by MultiCCA from Seurat (Satija Lab).
Genome_build: mm10
Supplementary_files_format_and_content: .txt tabulated files of metadata information, normalized gene expression matrix, and raw gene expression matrix

molecule: polyA RNA

organism: Mus musculus

source_name: Tibialis anterior muscle

extract_protocol:
The tibialis anterior muscle was digested into a single-cell suspension in Collagenase D and Dispase II for about 1h, then filtered to remove debris. Red blood cells were lyzed.
Single-cell RNA-sequencing libraries were prepared using a Chromium Single Cell 3' Reagent Kit (10X Genomics, v2 kit for all sample except D0_Cv3 with version 3) following the directions of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: genotype

value: 4 months

value: F

tag: injury

value: Notexin, day 7 post-injury


title: D7_D

tag: age

value: M


title: 5T21, CD4+ T cells, IngenolB, 2hr, rep1

description:
BvD_normalized_counts.csv
Donor2_IngenolB_02hr

tag: time


title: 5T21, CD4+ T cells, DMSO, 24hr, rep1

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T21-DMSO-24H
Donor2_DMSO_24hr

value: DMSO


title: D0_Cv3

value: 5 months

value: No injury (Day 0)


title: D2_C

value: Notexin, day 2 post-injury


title: D5_A

value: Notexin, day 5 post-injury


title: 5T21, CD4+ T cells, IngenolB, 2hr, rep2


title: 5T21, CD4+ T cells, DMSO, 24hr, rep2


title: 5T21, CD4+ T cells, DMSO, 6hr, rep2

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T21-DMSO-06H
Donor2_DMSO_06hr


title: D0_A

value: 7 months


title: D7_FACS

description:
DeMicheli_D7_FACSatlas_rawdata.txt
DeMicheli_D7_FACSatlas_normalizeddata.txt
DeMicheli_D7_FACSatlas_metadata.txt

data_processing:
Libraries were sequenced on Illumina NextSeq 500 using paired-end 26 + 8 + 58 (according to 10X Chromium Single Cell 3' protocol)
Sequences were aligned to mm10 using Cell Ranger v2 pipeline (10X Genomics)
Gene expression data was processed with Seurat v2.3.4 (Satija lab) using R  v3.6.2 (2019-12-12)
Initial data filtering (minimum cells to express an included gene = 3, minium genes to be expressed in an included cell = 200)
Filtering by percent mitochondiral genes in included cells (maximum 0.2), number of UMIs in included cells (minimum 1000, maximum 60000), and number of mapped genes in included cells (maximum 8000)
Log-normalization of expression data
Cell annotations in metadata derived from unsupervised clustering in PCA space.
Genome_build: mm10
Supplementary_files_format_and_content: .txt tabulated files of metadata information, normalized gene expression matrix, and raw gene expression matrix

extract_protocol:
The tibialis anterior muscle was digested into a single-cell suspension in Collagenase D and Dispase II for about 1h, then filtered to remove debris. Red blood cells were lyzed.
The single-cell suspension enriched for live cells by FACS using live/dead staining with PI/Calcein-AM.
Single-cell RNA-sequencing libraries were prepared using a Chromium Single Cell 3' v2 Reagent Kit (10X Genomics) following the directions of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: 4 month


title: D0_B


title: D5_FACS

description:
DeMicheli_D5_FACSatlas_rawdata.txt
DeMicheli_D5_FACSatlas_normalizeddata.txt
DeMicheli_D5_FACSatlas_metadata.txt


title: 5T21, CD4+ T cells, DMSO, 2hr, rep1

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T21-DMSO-02H
Donor2_DMSO_02hr


title: 5T21, CD4+ T cells, DMSO, 2hr, rep2


title: 5T21, CD4+ T cells, DMSO, 6hr, rep1


title: D0_FACS_02

description:
These two sequencing runs were processed together
DeMicheli_D0_FACSatlas_rawdata.txt
DeMicheli_D0_FACSatlas_normalizeddata.txt
DeMicheli_D0_FACSatlas_metadata.txt


title: 5T21, CD4+ T cells, AZDS581, 24hr, rep2

description:
AvsD_normalized_counts.csv
5T21-AZDS581-24H


title: D0_FACS_01


title: 5T21, CD4+ T cells, AZDS581, 24hr, rep1


title: D2_FACS

description:
DeMicheli_D2_FACSatlas_rawdata.txt
DeMicheli_D2_FACSatlas_normalizeddata.txt
DeMicheli_D2_FACSatlas_metadata.txt

value: 7 month


title: 5T11, CD4+ T cells, IngenolB, 24hr, rep2

description:
BvD_normalized_counts.csv
Donor1_IngenolB_24hr

value: IngenolB


title: 5T21, CD4+ T cells, AZDS581, 2hr, rep2

description:
AvsD_normalized_counts.csv
5T21-AZDS581-02H

value: CD4+ T cells


title: 5T21, CD4+ T cells, AZDS581, 6hr, rep2

description:
AvsD_normalized_counts.csv
5T21-AZDS581-06H


title: 5T21, CD4+ T cells, AZDS581, 2hr, rep1


title: 5T21, CD4+ T cells, AZDS581, 6hr, rep1


title: 5T11, CD4+ T cells, IngenolB, 24hr, rep1


title: 5T11, CD4+ T cells, IngenolB, 6hr, rep2

description:
BvD_normalized_counts.csv
Donor1_IngenolB_06hr


title: 5T11, CD4+ T cells, IngenolB, 6hr, rep1


title: 5T11, CD4+ T cells, IngenolB, 2hr, rep2

description:
BvD_normalized_counts.csv
Donor1_IngenolB_02hr


title: 1980Med_K

city: La Jolla

first: Gary

middle: S

last: Firestein

state: CA

address: 9500 Gilman Dr MC0656

institute: UC San Diego

data_processing:
Data were demultiplexed using Illumina's CASAVA software
Raw read quality was evaluated using Fastqc
Adapter and low quality bases below a quality score of 15 were trimmed from raw RNA-seq reads using Cutadapt.  After trimming, reads with less than 30bp were further discarded.
The reads were aligned to human reference genome hg38 using HISAT2 and assembled and quantified by HTSeq
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include normalized log-cpm values for each sample

source_name: RA knee

growth_protocol: Fibroblast like synoviocytes extracted from RA synovial tissue were cultured in 10% FCS/DMEM medium.  Cells at passages 3-4 were used in the experiment

extract_protocol:
After removing medium, the cells were incubated with RNA-STAT60 for 5 min and total RNA was extracted according to manufacturer's protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols for Illumina HiSeq (2x150bp)

treatment_protocol: Fibroblast like synoviocytes were serum starved in 0.1% FCS/DMEM medium for 18h.  The cells were treated with IL-6 (7.5ng/ml) for 2h.

tag: disease state

value: Rheumatoid Arthritis

tag: tissue

value: Fibroblast-like Synoviocytes

tag: site

value: Knee


title: 1732IL6_K


title: 1732Med_K


title: 1980IL6_K


title: 1540Med_K


title: 906IL6_K


title: 5T11, CD4+ T cells, IngenolB, 2hr, rep1


title: 906Med_K


title: 1177IL6_K


title: 1177Med_K


title: 5T11, CD4+ T cells, DMSO, 2hr, rep2

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T11-DMSO-02H
Donor1_DMSO_02hr


title: 5T11, CD4+ T cells, DMSO, 24hr, rep2

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T11-DMSO-24H
Donor1_DMSO_24hr


title: 5T11, CD4+ T cells, DMSO, 6hr, rep2

description:
AvsD_normalized_counts.csv
BvD_normalized_counts.csv
5T11-DMSO-06H
Donor1_DMSO_06hr


title: 5T11, CD4+ T cells, DMSO, 24hr, rep1


title: 952IL6_H

source_name: RA hip

value: Hip


title: 952Med_H


title: 5T11, CD4+ T cells, DMSO, 2hr, rep1


title: 5T11, CD4+ T cells, AZDS581, 24hr, rep2

description:
AvsD_normalized_counts.csv
5T11-AZDS581-24H


title: 5T11, CD4+ T cells, AZDS581, 24hr, rep1


title: Caco-2 after S. flexneri infection (0h), replicate 3

description: Gene expression from Caco-2 cells after infection of S. flexneri M90T strain 5a

tag: infection time


title: 5T11, CD4+ T cells, AZDS581, 6hr, rep1

description:
AvsD_normalized_counts.csv
5T11-AZDS581-06H


title: 1540IL6_K


title: 1624Med_H


title: 1784Med_H


title: 2600Med_H


title: 1624IL6_H


title: 5T11, CD4+ T cells, AZDS581, 2hr, rep2

description:
AvsD_normalized_counts.csv
5T11-AZDS581-02H


title: 630IL6_H


title: 5T11, CD4+ T cells, AZDS581, 2hr, rep1


title: 5T11, CD4+ T cells, DMSO, 6hr, rep1


title: 1784IL6_H


title: ESC_NPC_line2_Exp2

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

description: without  APH treatment

data_processing:
Library strategy: GRO-Seq
Reads were aligned using bowtie 2.2.8 with --non-deterministic flag
RPKM values were calculated with GFOLD V1.1.2
wig files were produced using MACS2
Genome_build: mm9
Supplementary_files_format_and_content: wig files contain peak information for samples

source_name: Culture-induced neural progenitor cells from embryonic stem cell line 2

growth_protocol:
embryonic stem cells: DMEM medium (Corning, 10-013-CV) supplemented with 15% FBS
embryonic stem cells-derived neural progenitor cells : N2B27+ 1% B27 (without retinyl acetate) for differentiation and NBBG + 2% B27 (without retinyl acetate) for culture maintainance

extract_protocol:
Briefly, 10 million cells were collected and permeabilized with the buffer (10 mM Tris-HCl pH 7.4, 300 mM sucrose, 10 mM KCl, 5 mM MgCl2, 1 mM EGTA, 0.05% Tween-20, 0.1% NP40 substitute, 0.5 mM DTT, protease inhibitors and Rnase inhibitor). The permeabilized cells were resuspended in 100 ml of storage buffer (10 mM Tris-HCl pH 8.0, 25% (V/V) glycerol, 5 mM MgCl2, 0.1 mM EDTA and 5 mM DTT) for nuclear run-on with 2X run-on mix (5 mM Tris-HCl PH 8.0, 2.5 mM MgCl2, 0.5 mM DTT, 150 mM KCl, 0.5 mM ATP, 0.5 mM CTP, 0.5 mM GTP, 0.5 mM BrUTP, RNase inhibitor, 1% sarkosyl) at 37o for 5 min. RNA was extracted by Trizol and followed by hybrolyzation with NaOH at a final concentration of 0.2 N on ice for 18 min. After quenching with ice-cold Tris-HCl PH6.8 at a final concentration of 0.55 M and exchanging buffer via Bio-Rad P30 columns, the RNA was incubated with Br-dU antibody-conjugated beads (Santa Cruz biotechnology, sc-32323-ac) for 1 hr. The enriched run-on samples were incubated with RppH (NEB, M0356S) and hydroxyl repair with T4 PNK (NEB, M0201S), followed by ligating the 5’ and 3’ RNA adaptor. RT-PCR was performed from the adaptor-ligated RNA to obtain cDNA
Half of the cDNA was subjected to making Groseq libraries by two rounds of PCR with barcode primers.  200-500 bp products from the first round of PCR were subjected to the second round of PCR with the number of PCR cycles determined by test PCR amplification. The second round of PCR products were size-selected by SPRIselect beads (Beckman Coulter, B23318) or gel PAGE purification

tag: strain

value: non-homologous end-joining deficient


title: ESC_NPC_line2_Exp3

description: without  APH treatment


title: 630Med_H


title: ESC_NPC_line1_Exp1

description: without  APH treatment

source_name: Culture-induced neural progenitor cells from embryonic stem cell line 1


title: ESC_NPC_line1_Exp2

description: without  APH treatment


title: ESC_NPC_line1_Exp3

description: without  APH treatment


title: ESC-NPC line 2 Chr12_DMSO_ExpC

description:
HTGTS
ESC-NPC_line2_chr12_DMSO

data_processing:
Library strategy: LAM-HTGTS
HTGTS Miseq and Nextseq reads were de-multiplexed and adapter sequence trimmed using the fastq-multx tool from ea-utils (http://code.google.com/p/eautils/) and the SeqPrep utility (https://github.com/jstjohn/SeqPrep) respectively.
HTGTS reads were mapped to the mm9 reference genome using Bowtie2 (http://bowtiebio.sourceforge.net/bowtie2/manual.shtml) with the top fifty alignments reported that had an alignment score above 50, representing a perfect 25nt local alignment.
Best-path searching algorithm was used to select the optimal sequence of alignments that describe the read’s composition. Aligned reads were filtered on the following conditions: (1) reads must include both a bait alignment and a prey alignment and (2) the bait alignment cannot extend more than 10 nucleotides beyond the targeted site.
We compared discarded alignments to the selected prey alignment; if any of the discarded alignments surpassed both a coverage and score threshold with respect to the prey alignment, the read was filtered due to low mapping quality.
The bait alignment must extend 10 nucleotides past the primer to avoid possible mispriming events and other artifacts
Potential duplicates were removed by comparing the coordinates of the end of the bait alignment and the start of the prey alignment across all reads. A read will be marked as a duplicate if it has a bait alignment offset within 2nt and a prey alignment offset within 2nt of another read’s bait and prey alignments.
Reads with greater than 30bp gap between bait and prey sequences were filtered out.
Additional stringency was applied to post-filtered HTGTS junctions: reads with shorter than 50bp bait sequences were eliminated from downstream analysis due to potential artifacts; only one unique junctions at each location were preserved for downstream analysis.
Genome_build: mm9
Supplementary_files_format_and_content: HTGTS: tab delimited text files (translocation junctions) contain filtered unique junctions and include the following information: sequence ID (Qname); prey chromosome (Rname), prey junction coordinate (Junction), chromosome orientation of prey junction (Strand), beginning (Rstart) and end (Rend) nucleotide position of prey junction aligning to the genome build; bait chromosome (B_Rname); beginning (B_Rstart) and end (B_Rend) nucleotide position of the bait junction; chromosome orientation of the bait junction (B_Strand); position on the read where the bait sequence begins (B_Qstart) and ends (B_Qend); position on the read where the prey junction begins (Qstart) and ends (Qend); the length of the combined and stitched paried end read (Qlen); cigar for bait sequence (B_Cigar); cigar for prey sequence (Cigar); the entire stitched paired end read sequence (Seq); 10 bp sequence around the junction, 5bp from bait and 5bp from prey (J_seq); barcode used for demultiplex (Barcode); number of unaligned sequences (unaligned);  pass (0) or fail (1) the “Bait only” filter (baitonly); pass (0) or fail (1) the “Uncut” filter (uncut); number of nucleotides not aligned to the bait (misprimed); pass (0) or fail (1) the “Frequent cutter” filter (freqcut); number of nucleotides between bait and prey sequences (largegap); pass (0) or fail (1) the “Map quality” filter (mapqual); pass (0) or fail (1) the “Breaksite” filter (breaksite); pass (0) or fail (1) the “Sequential” filter (sequential); pass (0) or fail (1) the “Repeat sequence” filter (repeatseq); number of duplicates in this library (duplicate); and the experiment associated with the read (note).

source_name: Induced neural progenitor cells line 2

extract_protocol:
Genomic DNA was extracted overnight at 55 degC in a lysis buffer containing: 200mM NaCl, 0.4% SDS, 100mM Tris-HCl pH7.5, 5mM EDTA pH 8.0, 0.2 mg/mL proteinase K, prior to DNA fragmentation
HTGTS: LAM-PCR-mediated HTGTS (Frock et al., 2015 and Hu et al., 2016; see manuscript for details)

treatment_protocol: See details in Tena et al.; treatment of samples is indicated in "characteristics: treatment" column


title: ESC-NPC line 2 Chr12_DMSO_ExpD

description:
HTGTS
ESC-NPC_line2_chr12_DMSO


title: 5T11, CD4+ T cells, AZDS581, 6hr, rep2


title: ESC-NPC line 2 Chr15_DMSO_ExpC

description:
HTGTS
ESC-NPC_line2_chr15_DMSO


title: 2600IL6_H


title: ESC-NPC line 2 Chr12_DMSO_ExpA

description:
HTGTS
ESC-NPC_line2_chr12_DMSO


title: ESC-NPC line 2 Chr15_DMSO_ExpA

description:
HTGTS
ESC-NPC_line2_chr15_DMSO


title: ESC-NPC line 2 Chr15_APH_ExpC

description:
HTGTS
ESC-NPC_line2_chr15_APH

value: APH


title: ESC-NPC line 2 Chr12_APH_ExpC

description:
HTGTS
ESC-NPC_line2_chr12_APH


title: ESC-NPC line 2 Chr12_APH_ExpD

description:
HTGTS
ESC-NPC_line2_chr12_APH


title: ESC-NPC line 2 Chr12_APH_ExpB

description:
HTGTS
ESC-NPC_line2_chr12_APH


title: ESC-NPC line 2 Chr15_APH_ExpD

description:
HTGTS
ESC-NPC_line2_chr15_APH


title: ESC-NPC line 2 Chr15_APH_ExpB

description:
HTGTS
ESC-NPC_line2_chr15_APH


title: ESC_NPC_line2_Exp1

description: without  APH treatment


title: ESC-NPC line 2 Chr7_DMSO_ExpB

description:
HTGTS
ESC-NPC_line2_chr7_DMSO


title: ESC-NPC line 2 Chr7_DMSO_ExpA

description:
HTGTS
ESC-NPC_line2_chr7_DMSO


title: ESC-NPC line 2 Chr7_APH_ExpA

description:
HTGTS
ESC-NPC_line2_chr7_APH


title: adlib WT/CrebH KO

city: Tsukuba

first: Yoshimi

last: Nakagawa

state: Ibaraki

department: Internal Medicine (Endocrinology and Metabolism)

country: Japan

institute: University of Tsukuba

hyb_protocol: 0.6 μμg of Cy3 and Cy5-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 mouse GE 8x60K Microarray (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing: Agilent Feature Extraction Software was used for background subtraction and LOWESS normalization.

source_name: Pooled mouse liver

label_protocol: Cyanine3 (Cy3) and Cy5 labeled cRNA were prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was isolated from the liver using Trizol (Lifetechnologis).

treatment_protocol: Mice were fasted for 24h and fed ad lib.

tag: genotype/variation

value: wild type

value: fed ad lib

value: Liver

tag: strain background

value: CREBH KO


title: ESC-NPC line 2 Chr15_DMSO_ExpD

description:
HTGTS
ESC-NPC_line2_chr15_DMSO

value: DMSO


title: ESC-NPC line 2 Chr7_APH_ExpC

description:
HTGTS
ESC-NPC_line2_chr7_APH


title: ESC-NPC line 2 Chr7_APH_ExpD

description:
HTGTS
ESC-NPC_line2_chr7_APH


title: Liver HFHS Tg

hyb_protocol: 0.6 μμg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 mouse GE 8x60K Microarray (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.

source_name: Pooled liver samples fron HFHS-fed CREBH-Tg mice

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

treatment_protocol: Mice were fed with HFHS diet for 12 weeks

value: CREBH-Tg

value: HFHS-diet feeding for 12wk


title: ESC line 2 Chr15_DMSO_ExpD

description:
HTGTS
ESC_line2_chr15_DMSO

source_name: Embryonic stem cells line 2


title: ESC-NPC line 2 Chr7_APH_ExpB

description:
HTGTS
ESC-NPC_line2_chr7_APH


title: ESC-NPC line 2 Chr12_DMSO_ExpB

description:
HTGTS
ESC-NPC_line2_chr12_DMSO


title: ESC line 2 Chr15_DMSO_ExpC

description:
HTGTS
ESC_line2_chr15_DMSO


title: ESC line 2 Chr15_DMSO_ExpB

description:
HTGTS
ESC_line2_chr15_DMSO


title: ESC-NPC line1 Chr12_DMSO_ExpD

description:
HTGTS
ESC-NPC_line1_chr12_DMSO

source_name: Induced neural progenitor cells line 1


title: ESC-NPC line 2 Chr12_APH_ExpA

description:
HTGTS
ESC-NPC_line2_chr12_APH


title: fast WT/CrebH KO

value: fasted for 24 h


title: Liver HFHS WT

source_name: Pooled liver samples fron HFHS-fed WT mice


title: ESC line 2 Chr15_DMSO_ExpA

description:
HTGTS
ESC_line2_chr15_DMSO


title: ESC line 2 Chr15_APH_ExpD

description:
HTGTS
ESC_line2_chr15_APH


title: ESC-NPC line1 Chr12_DMSO_ExpB

description:
HTGTS
ESC-NPC_line1_chr12_DMSO


title: ESC line 2 Chr15_APH_ExpC

description:
HTGTS
ESC_line2_chr15_APH


title: ESC-NPC line1 Chr12_APH_ExpD

description:
HTGTS
ESC-NPC_line1_chr12_APH


title: ESC-NPC line 2 Chr7_DMSO_ExpC

description:
HTGTS
ESC-NPC_line2_chr7_DMSO


title: ESC line 2 Chr15_APH_ExpB

description:
HTGTS
ESC_line2_chr15_APH


title: ESC-NPC line1 Chr12_DMSO_ExpA

description:
HTGTS
ESC-NPC_line1_chr12_DMSO


title: ESC-NPC line1 Chr12_APH_ExpC

description:
HTGTS
ESC-NPC_line1_chr12_APH


title: ESC line 2 Chr15_APH_ExpA

description:
HTGTS
ESC_line2_chr15_APH


title: ESC-NPC line1 Chr12_APH_ExpB

description:
HTGTS
ESC-NPC_line1_chr12_APH


title: ESC line 2 Chr12_DMSO_ExpD

description:
HTGTS
ESC_line2_chr12_DMSO


title: ESC-NPC line1 Chr12_APH_ExpA

description:
HTGTS
ESC-NPC_line1_chr12_APH


title: ESC_line2_Exp1

description: without  APH treatment

source_name: Blastocyst derived embryonic stem cells line 2


title: ESC_line2_Exp3

description: without  APH treatment


title: ESC-NPC line1 Chr7_DMSO_ExpD

description:
HTGTS
ESC-NPC_line1_chr7_DMSO


title: ESC line 2 Chr12_DMSO_ExpC

description:
HTGTS
ESC_line2_chr12_DMSO


title: ESC_line2_Exp2

description: without  APH treatment


title: ESC line 2 Chr12_DMSO_ExpB

description:
HTGTS
ESC_line2_chr12_DMSO


title: ESC_line1_Exp3

description: without  APH treatment

source_name: Blastocyst derived embryonic stem cells line 1


title: ESC-NPC line1 Chr12_DMSO_ExpC

description:
HTGTS
ESC-NPC_line1_chr12_DMSO


title: ESC line 2 Chr12_DMSO_ExpA

description:
HTGTS
ESC_line2_chr12_DMSO


title: ESC-NPC line1 Chr7_DMSO_ExpC

description:
HTGTS
ESC-NPC_line1_chr7_DMSO


title: ESC-NPC line1 Chr7_DMSO_ExpB

description:
HTGTS
ESC-NPC_line1_chr7_DMSO


title: ESC-NPC line1 Chr7_DMSO_ExpA

description:
HTGTS
ESC-NPC_line1_chr7_DMSO


title: ESC_line1_Exp2

description: without  APH treatment


title: ESC_line1_Exp1

description: without  APH treatment


title: ESC line 2 Chr12_APH_ExpD

description:
HTGTS
ESC_line2_chr12_APH


title: hippocampus_CD_20.1

city: St Louis

first: Joseph

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

data_processing:
raw fastq files were trimmed of adapaters and low quatlity bases using Trimmomatic, then aligned to the mm10 mouse genome using STARv2.6.1b default parameters
Htseq-count v0.9.1 was used to count the number of reads that aligned to features in the Ensembl GRCm38 version 93 gtf file.
Lowly expressed genes were defined as genes that had a cpm less than 2 across all samples. Lowly expressed genes were then filtered out of the dataset.
Genome_build: mm10
Supplementary_files_format_and_content: comma separated file. Each sample is a column and each row is a gene. The entries are read counts that mapped to that gene.

source_name: hippocampus

extract_protocol:
hippocampi were dissected and homogenized in 500ul of RIPA buffer with RNAse inhibitors. 250ul of homogenate was added to 750ul of Trizol LS and stored at -80C until RNA extraction. RNA was extracted using the Zymo clean and concentrator-5 kit with on column DNAse digestion and eluted in 30ul of RNAse free water.
1ug of RNA was used as input for the rRNA depletion kit (human/mouse/rat) (NEB#E6310) and then libraries were prepped using the NEBNext Ultra II RNA Library prep kit for Illumina (E7770L)

value: FVB/ANTJ x C57BL6/J F1 cross

value: CD

value: male

value: hippocampus


title: ESC-NPC line1 Chr7_APH_ExpD

description:
HTGTS
ESC-NPC_line1_chr7_APH


title: ESC line 2 Chr12_APH_ExpB

description:
HTGTS
ESC_line2_chr12_APH


title: hippocampus_Gtf2i*_17.3

value: female


title: hippocampus_Gtf2i*_15.1


title: hippocampus_wildtype_18.1

value: wildtype


title: hippocampus_wildtype_14.2


title: ESC-NPC line1 Chr7_APH_ExpC

description:
HTGTS
ESC-NPC_line1_chr7_APH


title: hippocampus_CD_16.2


title: hippocampus_wildtype_19.2


title: ESC line 2 Chr7_DMSO_ExpD

description:
HTGTS
ESC_line2_chr7_DMSO


title: ESC-NPC line1 Chr7_APH_ExpA

description:
HTGTS
ESC-NPC_line1_chr7_APH


title: ESC-NPC line1 Chr7_APH_ExpB

description:
HTGTS
ESC-NPC_line1_chr7_APH


title: hippocampus_CD_15.3


title: hippocampus_Gtf2i*_13.2


title: hippocampus_wildtype_17.2


title: ESC line 2 Chr7_DMSO_ExpC

description:
HTGTS
ESC_line2_chr7_DMSO


title: hippocampus_Gtf2i*_12.2


title: ESC line 2 Chr12_APH_ExpC

description:
HTGTS
ESC_line2_chr12_APH


title: ESC line1 Chr12_DMSO_ExpD

description:
HTGTS
ESC_line1_chr12_DMSO

source_name: Embryonic stem cells line 1


title: hippocampus_Gtf2i*_10.2


title: ESC line 2 Chr7_DMSO_ExpB

description:
HTGTS
ESC_line2_chr7_DMSO


title: hippocampus_CD_8.2


title: hippocampus_Gtf2i*_19.1


title: ESC line1 Chr12_DMSO_ExpB

description:
HTGTS
ESC_line1_chr12_DMSO


title: ESC line 2 Chr7_DMSO_ExpA

description:
HTGTS
ESC_line2_chr7_DMSO


title: hippocampus_CD_10.3


title: ESC line1 Chr12_DMSO_ExpC

description:
HTGTS
ESC_line1_chr12_DMSO


title: hippocampus_wildtype_7.3


title: ESC line1 Chr12_DMSO_ExpA

description:
HTGTS
ESC_line1_chr12_DMSO


title: ESC line 2 Chr7_APH_ExpC

description:
HTGTS
ESC_line2_chr7_APH


title: ESC line 2 Chr12_APH_ExpA

description:
HTGTS
ESC_line2_chr12_APH


title: Smallrnaseq day 5 in vitro treated with GDNF Replicate5

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

country: Germany

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

data_processing:
We trimmed the 3' adapters and filtered out the reads with the minimum length of 15 nucleotides using cutadapt 1.8.1 with Python 2.7.6
Read alignment done using rna-STAR version STAR_2.4.1d
parameters: readFilesCommand: zcat; outReadsUnmapped: Fastx; outSAMunmapped: Within; outFilterScoreMinOverLread: 0; outFilterMatchNmin: 16; outFilterMatchNminOverLread: 0; outFilterMismatchNoverLmax: 1; alignIntronMax: 1; alignEndsType: Local
Counts were generated by counting the mapped reads with mapq >= 30
Genome_build: mm10
Supplementary_files_format_and_content: htseq_counts

source_name: Smallrnaseq day 5 in vitro treated with GDNF_midbrain neurons

growth_protocol: Primary midbrain neurons were prepared under serum free conditions from embryonic day 12.5 C57Bl6/J mice. The ventral mesencephalon was isolated and the meninges removed. After enzymatic digestion with 0.25% trypsin and DNAse (5 mg/ml) tissue was dissociated by trituation, cell supsension was centrifuged and resuspended in culture medium (Neurobasal-A supplemented with 2 % B27-supplement, 1 % glutamine and 200 µM L-ascorbic acid). Neurons were counted and seeded into poly-L-ornithine and laminin coated cell culture plates. Cells were cultured at 37°C with 5% CO2 and 95% humidity.

extract_protocol:
RNA was isolated using Tri-reagent according to manufacturers protocol.
Library preparation and cluster generation for small RNA sequencing was performed according to Illumina standard protocols (TruSeq, Illumina).
Libraries were quality-controlled and quantified using a Nanodrop 2000 (Thermo Fisher Scientific), Agilent 2100 Bioanalyzer (Agilent Technologies) and Qubit (Thermo Fisher Scientific).

treatment_protocol: For treatment cells were cultured in the the medium supplemented with 10 ng/ml GDNF.

tag: developmental stage

value: Primary midbrain neuron culture

tag: treated with

value: 10 ng/ml GDNF


title: Smallrnaseq day 5 in vitro treated with GDNF Replicate4


title: ESC line 2 Chr7_APH_ExpB

description:
HTGTS
ESC_line2_chr7_APH

tag: treatment

value: APH


title: Smallrnaseq day 5 in vitro treated with GDNF Replicate3


title: ESC line 2 Chr7_APH_ExpA

description:
HTGTS
ESC_line2_chr7_APH


title: Smallrnaseq day 5 in vitro treated with GDNF Replicate2


title: ESC line1 Chr12_APH_ExpB

description:
HTGTS
ESC_line1_chr12_APH


title: Smallrnaseq day 5 in vitro Replicate5

source_name: Smallrnaseq day 5 in vitro_midbrain neurons


title: Smallrnaseq day 5 in vitro treated with GDNF Replicate1


title: hippocampus_wildtype_10.4

tag: Sex


title: hippocampus_CD_18.2


title: ESC-NPC line1 Chr15_DMSO_ExpD

description:
HTGTS
ESC-NPC_line1_chr15_DMSO


title: Smallrnaseq day 5 in vitro Replicate2


title: ESC line 2 Chr7_APH_ExpD

description:
HTGTS
ESC_line2_chr7_APH


title: Smallrnaseq day 5 in vitro Replicate1


title: ESC line1 Chr7_DMSO_ExpH

description:
HTGTS
ESC_line1_chr7_DMSO


title: ESC line1 Chr12_APH_ExpA

description:
HTGTS
ESC_line1_chr12_APH


title: Smallrnaseq day 5 in vitro Replicate4


title: ESC-NPC line1 Chr15_DMSO_ExpB

description:
HTGTS
ESC-NPC_line1_chr15_DMSO


title: ESC line1 Chr7_DMSO_ExpG

description:
HTGTS
ESC_line1_chr7_DMSO


title: Smallrnaseq day 1 in vitro treated with GDNF Replicate4

source_name: Smallrnaseq day 1 in vitro treated with GDNF_midbrain neurons


title: Smallrnaseq day 1 in vitro treated with GDNF Replicate5


title: Smallrnaseq day 5 in vitro Replicate3


title: ESC-NPC line1 Chr15_DMSO_ExpA

description:
HTGTS
ESC-NPC_line1_chr15_DMSO


title: ESC line1 Chr12_APH_ExpD

description:
HTGTS
ESC_line1_chr12_APH


title: Smallrnaseq day 1 in vitro treated with GDNF Replicate3


title: ESC line1 Chr7_DMSO_ExpF

description:
HTGTS
ESC_line1_chr7_DMSO


title: ESC-NPC line1 Chr15_APH_ExpD

description:
HTGTS
ESC-NPC_line1_chr15_APH


title: Smallrnaseq day 1 in vitro treated with GDNF Replicate2


title: ESC line1 Chr12_APH_ExpC

description:
HTGTS
ESC_line1_chr12_APH


title: ESC-NPC line 2 Chr15_DMSO_ExpB

description:
HTGTS
ESC-NPC_line2_chr15_DMSO


title: Smallrnaseq day 1 in vitro Replicate5

source_name: Smallrnaseq day 1 in vitro_midbrain neurons


title: ESC-NPC line1 Chr15_APH_ExpC

description:
HTGTS
ESC-NPC_line1_chr15_APH


title: Smallrnaseq day 1 in vitro Replicate4


title: ESC line1 Chr7_DMSO_ExpC

description:
HTGTS
ESC_line1_chr7_DMSO


title: ESC line1 Chr7_DMSO_ExpE

description:
HTGTS
ESC_line1_chr7_DMSO


title: Smallrnaseq day 1 in vitro Replicate3


title: ESC-NPC line1 Chr15_APH_ExpB

description:
HTGTS
ESC-NPC_line1_chr15_APH


title: ESC-NPC line1 Chr15_APH_ExpA

description:
HTGTS
ESC-NPC_line1_chr15_APH


title: ESC-NPC line1 Chr15_DMSO_ExpC

description:
HTGTS
ESC-NPC_line1_chr15_DMSO


title: Smallrnaseq day 1 in vitro Replicate2


title: ESC line1 Chr7_DMSO_ExpB

description:
HTGTS
ESC_line1_chr7_DMSO


title: ESC line1 Chr15_DMSO_ExpD

description:
HTGTS
ESC_line1_chr15_DMSO


title: ESC line1 Chr15_DMSO_ExpC

description:
HTGTS
ESC_line1_chr15_DMSO


title: Smallrnaseq day 1 in vitro Replicate1


title: ESC line1 Chr7_DMSO_ExpA

description:
HTGTS
ESC_line1_chr7_DMSO


title: ESC line1 Chr7_APH_ExpH

description:
HTGTS
ESC_line1_chr7_APH


title: ESC line1 Chr7_APH_ExpG

description:
HTGTS
ESC_line1_chr7_APH


title: ESC line1 Chr15_DMSO_ExpB

description:
HTGTS
ESC_line1_chr15_DMSO


title: ESC line1 Chr7_APH_ExpF

description:
HTGTS
ESC_line1_chr7_APH


title: Smallrnaseq day 1 in vitro treated with GDNF Replicate1


title: ESC line1 Chr15_DMSO_ExpA

description:
HTGTS
ESC_line1_chr15_DMSO


title: ESC line1 Chr7_APH_ExpE

description:
HTGTS
ESC_line1_chr7_APH


title: ESC line1 Chr7_APH_ExpC

description:
HTGTS
ESC_line1_chr7_APH


title: ESC line1 Chr15_APH_ExpC

description:
HTGTS
ESC_line1_chr15_APH


title: ESC line1 Chr7_APH_ExpB

description:
HTGTS
ESC_line1_chr7_APH


title: ESC line1 Chr15_APH_ExpB

description:
HTGTS
ESC_line1_chr15_APH


title: ESC line1 Chr7_APH_ExpA

description:
HTGTS
ESC_line1_chr7_APH


title: ChIP-seq of GFP-Rix1 in BboxD swi6-115 cells

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

data_processing:
Alignment of adapter-trimmed reads were done using BWA-MEM.
Default BWA parameters were used with the addition of the “-M” option for compatibility with Picard Tools and the “-a” option to return all alignments.
The BWA-aligned reads were deduplicated using the Picard Tools (http://broadinstitute.github.io/picard) to produce deduplicated BAM files.
Using these BAMS, read densities across the genome for samples and matched inputs were normalized to reads per million mapped reads after which input was subtracted from the sample using Bedtools (https://bedtools.readthedocs.io/en/latest/index.html) to produce input-normalized, variable-interval bedgraph files.
Bedgraphs averaged over a fixed number of non-overlapping 10 bp windows were produced from the normalized variable-interval bedgraphs using an in-house script (available upon request) and were used to extract ChIP signals in precise regions across multiple samples.
Genome_build: asm294v2.29
Supplementary_files_format_and_content: Bedgraph

organism: Schizosaccharomyces pombe

source_name: log. growing cells

growth_protocol: Standard conditions were used to produce logarithmically growing cultures in rich media (YEA). Cultures were grown at 30˚C.

extract_protocol:
Fixed cells were lysed with glass-beads, DNA sheared by sonication to 400-600bp fragments and immunoprecipitated with GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.
NEBNext Ultra II DNA Library Prep kit (NEB, E7645S) was used according to manufacturer's recommendation.
Libraries were analyzed using an Agilent 2100 BioAnalyzer (Agilent) and sequenced on the Illumina MiSeq platform.

treatment_protocol: Exponentially growing cells (at 30˚C) were incubated for 2 h at 18°C prior to fixation with 3% paraformaldehyde. Cells were subjected to additional crosslinking with 10 mM DMA for 45 min at room temperature.

value: swi6-115 with B-box deletion at IR-R

tag: antibody

value: anti-GFP (ab290)


title: ESC line1 Chr15_APH_ExpA

description:
HTGTS
ESC_line1_chr15_APH


title: ChIP-seq of WCE

tag: cell type

value: WCE, from Wild type


title: H3K9me3 ChIP in ago1D_2 cells

type: genomic

description: ChIP was performed using anti-H3K9me3 antibody (ab8898) followed by microarray analysis

hyb_protocol: Equal amounts of Cy5-labeled ChIP DNA and Cy3-labeled  whole-cell extract DNA were mixed and combined with human Cot1 DNA, Agilent Blocking Agent and Agilent Hybridization buffer, and hybridized to high-density  microarrays in Agilent SureHyb hybridization chamber for 24 hours at 65˚C, 10 rpm. After hybridization, slides were washed according to Agilent protocol.

scan_protocol: Scanned on an Agilent G2505B scanner.

data_processing: Data were extracted using Agilent Feature Extraction Software (CHIP-v1_95_May07 or ChIP-v1_10_Apr08 protocol). Signal was normalized by combined rank consistency filtering with LOWES intensity normalization.

label_protocol: ChIP and whole-cell extract DNA was amplified by random-primed PCR and conjugated with Cy5 (ChIP DNA) or Cy3 (whole-cell extract DNA).

extract_protocol: Fixed cells were lysed with glass-beads, DNA sheared by sonication to 400-600bp fragments and immunoprecipitated with H3K9me3 antibody (Abcam, ab8898) or GFP antibody (Abcam, ab290). Immunoprecipitated DNA was recovered by incubation with protein A/G slurry and reversed-crosslinked at 65˚C.

treatment_protocol: Exponentially growing cells were fixed in 3% paraformaldehyde at 30˚C. For GFP ChIPs, cultures were incubated for 2 h at 18°C prior to fixation and were subjected to additional crosslinking with 10 mM DMA for 45 min at room temperature.

tag: genotype

value: ago1D cells

value: H3K9me3 immunoprecipitated DNA

tag: fraction

value: Whole-cell extract DNA


title: H3K9me3 ChIP in pob3Dago1D cells

value: pob3D ago1D cells


title: H3K9me3 ChIP in rix1E414K cells

value: rix1E414K cells


title: H3K9me3 ChIP in WT_2 cells

value: Wild type cells


title: H3K9me3 ChIP in amo1Dago1D cells

value: amo1D ago1D cells


title: ESC line1 Chr15_APH_ExpD

description:
HTGTS
ESC_line1_chr15_APH


title: H3K9me3 ChIP in rix1E414Kago1D cells

value: rix1E414K ago1D cells


title: H3K9me3 ChIP in pob3D cells

value: pob3D cells


title: H3K9me3 ChIP in ago1D_1 cells


title: ESC line1 Chr7_DMSO_ExpD

description:
HTGTS
ESC_line1_chr7_DMSO

value: DMSO


title: H3K9me3 ChIP in WT_1 cells


title: Crb3-GFP ChIP in swi6-115 cells

description: ChIP was performed using anti-GFP antibody (ab290) followed by microarray analysis

value: swi6-115 cells

value: Crb3-GFP immunoprecipitated DNA


title: Crb3-GFP ChIP in clr4D cells

value: clr4D cells


title: ChIP-seq of GFP-Rix1 in swi6-115 cells


title: H3K9me3 ChIP in amo1D cells

value: amo1D cells


title: Ipi1-GFP ChIP in clr4D cells

value: Ipi1-GFP immunoprecipitated DNA


title: miR_Msc_4

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq SR Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina Hiseq 2500/2000 platform and 50bp single-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw datas were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses. The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Genome_build: reference sequence used for read alignment
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

organism: Cervus nippon

source_name: muscle

extract_protocol:
longissimus dorsi muscles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 3 μg total RNA per sample was used as input material for the small RNA library. Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina® (NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
the small RNA libraries were prepared for sequencing using standard Illumina protocols

value: Shuangyang Sika deer

tag: tissus

value: muscle


title: ESC line1 Chr7_APH_ExpD

description:
HTGTS
ESC_line1_chr7_APH

value: APH


title: miR_Msc_3


title: ChIP-seq of GFP-Rix1 in wild-type cells

value: Wild type

value: anti-GFP (ab290)


title: miR_Msc_2


title: Ipi1-GFP ChIP in swi6-115 cells

value: Whole-cell extract DNA


title: Crb3-GFP ChIP in WT cells


title: Ipi1-GFP ChIP in WT cells


title: ChIP-seq of GFP-Rix1 in BboxD cells

value: Wild type with B-box deletion at IR-R


title: Spinal cord, BCP rep2

city: Changsha

first: Xinran

last: Hou

state: Hunan

address: Xiangya Road 87

institute: Central South University

data_processing:
Sequencing raw reads were preprocessed by filtering out rRNA reads,sequencing adapters,short-fragments and other low-quality reads by Seqtk (https://github.com/lh3/seqtk)
Obtained clean reads were mapped to the rat Rnor_6.0 reference genome using Hisat2 (version:2.0.4)
Stringtie (version:1.3.0) was used to calculate Fragments Per Kilobase of exon model per Million mapped reads (FPKM) with a reference annotation.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: FPKMs, counts

organism: Rattus norvegicus

source_name: Spinal cord, Bone cancer pain (BCP)

extract_protocol:
The lumbar enlargement spinal cord was quickly isolated out, removed the meninges, and dissected longitudinally on ice; then the ipsilateral spinal cord was snap-frozen and preserved in liquid nitrogen. Total RNA was extracted using RNeasy Mini Kit (Cat#74106, Qiagen)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
Strand specific libraries were prepared using the TruSeq® Stranded Total RNA Sample Preparation kit (Illumina, USA). Briefly, ribosomal RNA was removed from total RNA by Ribo-Zero rRNA removal beads. Then fragmented RNA was copied into first strand cDNA using reverse transcriptase, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. After undergoing an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters, cDNA fragments were purified and enriched with PCR to create the final cDNA library.

treatment_protocol: Approximately (1-5) ×10e5 living or heat-killed Walker 256 breast cancer cells were implanted into medullary cavity of left tibia

value: Wistar

value: spinal cord

tag: time

value: 14 days after tumor inoculation of treated samples

tag: condition

value: BCP


title: Spinal cord, BCP rep3

tag: tissue

value: breast cancer cells were implanted into medullary cavity of left tibia


title: Msc_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped tode novo sequencing without reference genome 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.
Genome_build:de novo sequencing without reference genome
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
longissimus dorsi muscles were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: ESC-NPC line 2 Chr7_DMSO_ExpD

description:
HTGTS
ESC-NPC_line2_chr7_DMSO

source_name: Induced neural progenitor cells line 2

value: DMSO


title: ESC-NPC line 2 Chr15_APH_ExpA

description:
HTGTS
ESC-NPC_line2_chr15_APH


title: Spinal cord, sham rep3

source_name: Spinal cord, sham

value: control

value: sham


title: Spinal cord, sham rep2


title: Spinal cord, BCP rep1


title: Msc_4


title: Msc_2


title: miR_Msc_1


title: C1-150-2-1

city: Changchun Jilin

first: Dongshan

last: Zhu

address: 71 Xinmin Street

department: thracic department

institute: Jilin University First Hospital

data_processing:
The ptroject used SOAPnuke software (BGI) to filter datas.
Remove reads which include joint
Remove the unknown base reads N content is more than 10%
Removing low-quality reads (we define quality value less than 15 bases accounted for the proportion of the total base number reads more than 20% of reads reads for low quality)
HISAT was used to compare reference genome
Supplementary_files_format_and_content: FPKM values for each sample

source_name: KYSE150 treated with omipalisib(repeated)

extract_protocol:
The first step in the workflow involves purifying the poly-A containing mRNA molecules using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then have the addition of a single 'A' base and subsequent ligation of the adapter. The products are then purified and enriched with PCR amplification.  We then quantified the PCR yield by Qubit and pooled samples together to make a single strand DNA circle (ssDNA circle), which gave the final library.  DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and single-end read of 50 bp were read through on the BGISEQ-500 platform for the following data analysis study. For this step, the BGISEQ-500 platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.
RNA libraries were prepared for sequencing using standard illumina protocols

treatment_protocol: KYSE150 cells were seeded in 6-cm dishes at 8.5×10e5/dish. On the following day,  vehicle or 1 μmol/L Omipalisib was added to the cells and incubated for 8 hours. Then,  the cells were harvested by trypsinization and sent on dry ice to BGI-genomics for RNA-seq analysis.

tag: cell line

value: esophageal tumor

value: omipalisib


title: C1-150-3-1


title: Las1-GFP ChIP in clr4D cells

value: clr4D cells

value: Las1-GFP immunoprecipitated DNA


title: C1-150-1-1

source_name: KYSE150 treated with omipalisib


title: Con-150-3-1

source_name: KYSE150 not treated by omipalisib(repeated)


title: Msc_1

value: Shuangyang Sika deer

value: muscle


title: Con-150-2-1


title: Spinal cord, sham rep1


title: Con-150-1-1

source_name: KYSE150 not treated by omipalisib


title: 14-Input

status: Public on Jan 10 2020

city: Guangzhou

first: Yiming

last: Yan

address: Wushan Road

institute: South China Agricultural University

data_processing:
Q30 was used to perform quality control.
After adaptor-trimming and low quality reads removing by cutadapt software, high quality reads were generated
Then these high quality reads were aligned to chicken reference genome  (UCSC galGal4) using bowtie2 software with default parameters.
Peak calling was performed with MACS software.
Differentially methylated regions (DMRs) were identified by diffReps software .
Genome_build: UCSC galGal4
Supplementary_files_format_and_content: peaks.bed

organism: Gallus gallus

source_name: ALV-J-susceptible

extract_protocol:
Livers were removed, flash frozen on dry ice, and genomic DNA was isolated using phenol–chloroform, and subjected to high-throughput 150 base paired-end sequencing on Illumina Hiseq sequencer according to the manufacturer’s recommended protocol.
Libraries were prepared for sequencing using standard Illumina protocols

tag: resistance

value: ALV-J-susceptible

value: liver


title: 9-Input


title: 8-Input


title: Las1-GFP ChIP in swi6-115 cells

value: swi6-115 cells

value: Whole-cell extract DNA


title: GFP-Rix1 ChIP in clr4D cells

value: GFP-Rix1 immunoprecipitated DNA


title: Las1-GFP ChIP in WT cells

value: Wild type cells

value: Wild type


title: 26-Input

source_name: ALV-J-resistant

value: ALV-J-resistant


title: 4-Input


title: GFP-Rix1 ChIP in WT cells


title: 14-MeDIP


title: GFP-Rix1 ChIP in swi6-115 cells


title: 9-MeDIP


title: 26-MeDIP


title: 4-MeDIP


title: 8-MeDIP


title: KOC2

city: Barcelona

first: Maria Pia

last: Cosma

address: Dr. Aiguader

department: Gene regulation, stem cells and cancer

country: Spain

institute: CRG

data_processing:
Estimated transcript abundances were obtained using Kallisto software (Bray et al. Nat.Biotech. 2016 doi:10.1038/nbt.3519). Gencode release M10 (GRCm38.p4) transcript were used as a reference transcriptome for the pseudoalignment.
Genome_build: Gencode M10
Supplementary_files_format_and_content: comma separated values with ENSEMBL_ID, common gene name and raw counts for each sample.

source_name: β-catenin knock-out mESCs_CHIR99021

growth_protocol: Cells were cultured on feeder-free, gelatin coated dishes in DMEM supplemented with 10% FBS, non-essential aminoacids, penicillin/streptomycin and L-Glutamine.

extract_protocol:
Total RNA was extracted with Rneasy mini kit (Qiagen) following manufacturer instruction
Library was constructed using Truseq Stranded mRNA Sample Prep (Illumina) following manufacturer instructions

treatment_protocol: Cells were cultured in presence of CHIR99021  3 μM or vehicle (DMSO 0.3 μl/ml) for 72 hours

value: Blastocyst

value: embryonic stem cells (ESCs)

value: CHIR99021 3 μM

tag: time point

value: 72 hours


title: 3-MeDIP


title: WTC2

source_name: parental mESCs_CHIR99021

tag: genotype/variation


title: WTV2

source_name: parental mESCs_DMSO

tag: strain background

value: DMSO 0.3 μl/ml


title: KOV1

source_name: β-catenin knock-out mESCs_DMSO

tag: developmental stage


title: WTC1


title: KOV2


title: WT2

city: Copenhagen N

first: Hiren

last: Joshi

address: Blegdamsvej 3B

department: ICMM

country: Denmark

institute: Copenhagen University

data_processing:
The original image data is transferred into sequence data via base calling, which is defined as raw data or raw reads and saved as FASTQ file.
Primary sequencing data produced by Illumina HiSeqTM 2000, called as raw reads, is subjected to quality control (QC) that determine if a resequencing step is needed.
After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences with SOAPaligner/SOAP2.
The gene expression level is calculated by using RPKM method (Reads per kilobase transcriptome per million mapped reads), as described in Mortazavi, A., B. A. Williams, et al . Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 2008.5(7): 621-8.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file includes numbers of Unique reads, coverage and RPKM for each sample, as well as corresponding Entrez Gene ID, Gene Length and HGNC Symbol.

source_name: Keratinocyte cell line (HaCaT)

growth_protocol: HaCaT cells were grown in DMEM supplemented with 10 % FBS (HyClone) and 1 % L-glutamine. The cells were passaged 2 times per week, after reaching approximately 70 % confluency, and seeded at 12.000/cm2

extract_protocol:
Total RNA was extracted from cells 48 h post-confluency using the RNeasy® kit (Qiagen). RNA integrity and quality were determined using Bioanalyzer instrumentation (Agilent Technologies).
Tru-seq. After the total RNA extraction and DNase I treatment, magnetic beads with Oligo (dT) are used to isolate mRNA. Mixed with the fragmentation buffer, the mRNA is fragmented into short fragments. Then cDNA is synthesized using the mRNA fragments as templates. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.

value: Wild Type

tag: replicate

value: Biological


title: WT1


title: T3 KO3

value: GALNT3 KO

value: Biological (clonal cell line 3)

tag: clone name


title: T3 KO2

value: Biological (clonal cell line 2)


title: T2 KO3

value: GALNT2 KO


title: T3 KO1

value: Biological (clonal cell line 1)


title: T2 KO2


title: 3-Input

value: liver


title: T2 KO1


title: T1 KO3

value: GALNT1 KO


title: KOC1

tag: treatment


title: WTV1


title: T1 KO1


title: Methotrexate-Lactoferrin 3 [LM3]

city: San Francisco

first: Thomas

last: Wallach

address: 550 16th St. 5th floor

department: Pediatrics

institute: UCSF

data_processing:
CASAVA software for base-calling
STAR software for read alignment
Gene expression level analysis using DESeq2 package in R
Differential gene expression analysis revealed major transcriptional changes upon methotrexate exposure, which were mostly normalized upon lactoferrin co-treatment. Gene ontology analysis noted the activation of an EMT program38 in methotrexate treated cells that was absent in controls or lactoferrin treated cells.  Transcriptional changes included upregulation of SNAI2, TWIST1, ZEB2, ZEB1, N-cadherin, and STAT3, as well as downregulation of E-cadherin and Occludin. Changes in expression of these genes aligns with both the genes upregulated in initiating EMT as well as the alterations to tight and adherens junctions during EMT. We also observed upregulation of lactoferrin transcripts in MTX exposed cells, consistent with lactoferrin’s role as a signaling molecule involved in inflammation. While gene ontology did reflect additional activated pathways (most relevantly adipogenesis, hypoxia, and TNF-α) these likely reflect secondary inflammatory effects possibly driven by the initial process of EMT (FDR q-value 2.03E-91)
Genome_build: hg19
Supplementary_files_format_and_content: csv file for read counts, xls file containing differentially expressed genes based on DESeq2 analysis compare to control.

growth_protocol: P26 cells suspeneded in matrigel after passaging, cultured in DMEM with 20% FBS, pen/strep, NEAA x 5 days to allow for spheroid formation prior to experimental exposure.  No media change.

extract_protocol:
Quiagen RNeasy Kit
Library construction via Novogene Inc protocol

treatment_protocol: cells exposed to control (carrier fluid), methotrexate, methotrexate/lactoferrin, or lactoferrin x 4 hrs prior to

value: Methotrexate-Lactoferrin


title: Methotrexate 3 [M3]

source_name: Caco-2 spheroids_Methotrexate

value: Methotrexate


title: Lactoferrin 2 [L2]

source_name: Caco-2 spheroids_Lactoferrin

value: Lactoferrin


title: Methotrexate-Lactoferrin 1 [LM1]


title: Methotrexate 1 [M1]


title: Lactoferrin 3 [L3]


title: Control 3 [C3]

source_name: Caco-2 spheroids_control

value: control


title: Control 2 [C2]


title: Methotrexate 2 [M2]


title: Control 1 [C1]


title: Methotrexate-Lactoferrin 2 [LM2]


title: Lactoferrin 1 [L1]


title: Mdr1+ replicate 2

city: Jupiter

first: Mark

last: Sundrud

state: FL

address: 120 Scripps Way

department: Immunology and Microbiology

institute: The Scripps Research Institute

data_processing:
TopHat
HT-Seq Count
DESEQ2
Genome_build: mm9
Supplementary_files_format_and_content: HT-Seq Count raw counts

source_name: Sorted CD4+ Teff cells isolated from mesenteric lymph nodes of Rag deficient hosts 6 weeks post T cell transfer

extract_protocol:
Total RNA was isolated using RNeasy columns (QIAGEN) with on-column DNase treatment
Total RNA (500ng) was used to prepare libraries with Illumina TrueSeq stranded total RNA-Seq kit (Illumina)

value: FVB/N

value: mesenteric lymph nodes


title: Mdr1- replicate 3


title: Mdr1- replicate 2


title: Mdr1+ replicate 1


title: shMdr1 small intestine - Asbt -/-

source_name: Sorted CD4+ Teff cells transduced with Lmpd retroviral construct  at 6 weeks post T cell transfer from Rag deficient host

extract_protocol:
Clontech SMART-Seq v4 ultra low input RNA kit
Enriched cDNA was converted to Illumina-compatible libraries using NEBNext Ultra II DNA kit with 1ng input

tag: retrovirus

value: LMPd shMdr1

value: small intestine


title: shCD8 small intestine - Asbt +/+


title: shMdr1 spleen - Asbt -/-

value: spleen


title: shCD8 small intestine - Asbt -/-


title: shMdr1 spleen - Asbt +/+


title: shCD8 spleen - Asbt -/-

value: Rag1-/- Asbt -/-


title: shCD8 spleen - Asbt +/+


title: T1 KO2


title: shMdr1 small intestine - Asbt +/+

source_name: Sorted CD4+ Teff cells transduced with Lmpd retroviral construct  at 6 weeks post T cell transfer from Rag deficient host that have or lack Asbt


title: Blood_Sick_mouse_5

city: Linköping

first: Sandra

last: Lilja

address: Sandbäcksgatan 7

department: BKV

country: Sweden

institute: Linköping University

data_processing:
Cells where sorted so only those having a minimum of 10,000 reads and 400 transcripts and less than 20% mitochondrial genes where kept. Outliers with an overestimation of transcripts count where removed.
K-Nearest Neighbor smooting on all samples together using a k of ~0.1% of the total number of cells
Cell type identification using Reference Component Analysis, see article for details.
Genome_build: GRCm38.p5
Supplementary_files_format_and_content: Sorted, knn-smoothed and cell typed expression matrix for blood and joint samples. The columns are the cells (named: CellType_title_CellularBarcode) and the rows are the genes (Symbols). The samples from which the Joint expression matrix is created are available on the SRA database under accession PRJNA504425.

source_name: Blood

extract_protocol:
The scRNA-seq experiments were performed using the Seq-Well technique, following the guidelines as described by Gierahn et al., https://doi.org/10.1038/nmeth.4179. Library layout is paired end sequencing with read 1 covering the barcode region (20 bases) and read 2 covering the transcript from the polyA tail (50 bases). The sequenced data was extracted following the Drop-seq Core computational protocol described by Nemesh, James. "Drop-seq core computational protocol." McCarroll Laboratory http://mccarrolllab. com/wp-content/uploads/2016/03/Drop-seqAlignmentCookbookv1. 2Jan2016. Pdf (2016). The genome for assembly was constructed from GRCm38.p5.
The library was constructed following the guidelines described by Gierahn et al., https://doi.org/10.1038/nmeth.4179

value: PBMC

tag: strain

tag: trait

value: Sick (rheumatoid arthritis)

tag: disease stage

tag: Sex

value: female

value: Blood


title: Blood_Sick_mouse_4


title: Blood_Sick_mouse_6


title: Mdr1+ replicate 3


title: Blood_Sick_mouse_1


title: Blood_Healthy_mouse_4

value: Healthy


title: Blood_Healthy_mouse_2


title: Mdr1- replicate 1


title: Blood_Sick_mouse_3


title: ex_vivo-tdTpositive_1

city: Cincinnati

first: Chandrashekhar

last: Pasare

state: OH

address: 3333 Burnet Ave

institute: Cininnati Children's Hospital Medical Center

data_processing:
Alignment of RNA-seq reads on Mouse reference genome mm10 was performed using UT Southwestern BioHPC NGS pipeline.
The expression of the genes in all samples was calculated as Fragments Per Kilobase of transcript per Million mapped reads (FPKM).
Genome_build: mm10
Supplementary_files_format_and_content: txt, contains name of the gene, chromosome, strand, FPKM.

source_name: CD4+CD90+tdT+ sorted from mesenteric lymph nodes of Il17aCRE; R26tdT mice 10dpi of Cr infection replicate_1

extract_protocol:
RNA prep for mRNA-sequencing was performed using the miRNeasy (Qiagen) and treated with DNase I (Qiagen), according to the manufacturer's instructions. Quantities of extracted RNA were determined using NanoDrop2000 for cDNA synthesis or Agilent Bioanalyzer 2100 before RNA-Seq Library preparation.
RNA-seq libraries were prepared with the Illumina TruSeq Stranded mRNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol. Libraries were validated on an Agilent Bioanalyzer 2100.

tag: cell type

value: CD4 T cell

tag: experimental condition

value: 5x10^8 Cr i.g. infection 10dpi


title: cdTh17-tdTpositive_1

source_name: CD90+tdT+ sorted from Th17 polarization culture replicate_1


title: ex_vivo-tdTpositive_2

source_name: CD4+CD90+tdT+ sorted from mesenteric lymph nodes of Il17aCRE; R26tdT mice 10dpi of Cr infection replicate_2


title: cdTh17-tdTpositive_3

source_name: CD90+tdT+ sorted from Th17 polarization culture replicate_3


title: ppTh17-tdTpositive_3

source_name: CFSE-CD90+tdT+ sorted from Cr-primed culture replicate_3

value: Cr-primed


title: WT_2

data_processing:
Alignment of RNA-seq reads on Mouse reference genome mm10 was performed using UT Southwestern BioHPC NGS pipeline.
Genome_build: mm10
Supplementary_files_format_and_content: txt, contains name of the gene, chromosome, strand, raw read counts.

source_name: Cr-primed WT Th cells replicate_2

tag: genotype

value: WT


title: WT_1

source_name: Cr-primed WT Th cells replicate_1


title: C1d10_1

source_name: Cr-primed Casp1-deficient Th cells replicate_1


title: CFSEpositive_1

source_name: naïve CFSE+ sorted from Cr-primed culture replicate_1


title: ppTh17-tdTpositive_1

source_name: CFSE-CD90+tdT+ sorted from Cr-primed culture replicate_1


title: CFSEpositive_2

source_name: naïve CFSE+ sorted from Cr-primed culture replicate_2


title: C1d10_2

source_name: Cr-primed Casp1-deficient Th cells replicate_2


title: LmCFSEnegative_2

data_processing:
Alignment of RNA-seq reads on Mouse reference genome mm10 was performed on CLC Genomics Workbench 7 (Qiagen).
The expression of the genes in all samples was calculated as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
Genome_build: mm10
Supplementary_files_format_and_content: xlsx, contains name of the gene, chromosome, Expression value (RPKM) and reads information.

source_name: CFSE-CD90+ Lm-specific Th cells, replicate-2

extract_protocol:
RNA prep for mRNA-sequencing was performed using the miRNeasy (Qiagen) and treated with DNase I (Qiagen), according to the manufacturer's instructions. Quantities of extracted RNA were determined using NanoDrop2000 for cDNA synthesis or Agilent Bioanalyzer 2100 before RNA-Seq Library preparation.
RNA-seq libraries were prepared with the Illumina TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer’s protocol. Libraries were validated on an Agilent Bioanalyzer 2100.

value: CD4 T helper cell

tag: pathogen-stimulation

value: L.monocytogenes soluble lysate


title: CrCFSEnegative_1

source_name: CFSE-CD90+ Cr-specific Th cells, replicate-1

value: C.rodentium soluble lysate


title: CrCFSEnegative_2

source_name: CFSE-CD90+ Cr-specific Th cells, replicate-2


title: LmCFSEnegative_1

source_name: CFSE-CD90+ Lm-specific Th cells, replicate-1


title: CrCFSEpositive_1

source_name: CFSE+CD90+ unproliferated naïve T cell from Cr-stimulated culture


title: LmCFSEpositive_1

source_name: CFSE+CD90+ unproliferated naïve T cell from Lm-stimulated culture


title: Blood_Healthy_mouse_1

source_name: Blood

tag: tissue


title: Blood_Healthy_mouse_3


title: cdTh17-tdTpositive_2

source_name: CD90+tdT+ sorted from Th17 polarization culture replicate_2


title: RS 134_160NC

city: SEATTLE

first: THOMAS

middle: A

last: REH

state: WA

address: 1959 NE PACIFIC STREET

department: BIOLOGICAL STRUCTURE

institute: UNIVERSITY OF WASHINGTON

data_processing:
Base calling and sample were demultiplexing preformed by cellranger mkfastq (See Sample table for Cellranger version)
Sequences were alinged to genome and UMI counts were created using cellranger count (See Sample table for Cellranger version)
Downstream analysis was preformed in R (scripts avalible on Github at https://github.com/Reh-lab/Sridhar-Hoshino-Reh-2019)
Supplementary_files_format_and_content: Cellranger filtered output files, containing gene names, cellbarcodes, and expression matricies

source_name: Human Fetal Retina

growth_protocol: ES cells were directed to generate retinal organoids using established protocols. Fetal retina was either processed immediated for single cell RNA eq or cultured as spheres in the same media conditions as organoids

extract_protocol:
Cells were dissociated with papain and processed for 10x single cell rna seq analysis according to manufacturer's instructions
10x libraries were prepared according to manufacturer's instructions.

tag: nomenclature

value: Retinosphere

tag: tissue origin

value: In vitro

tag: genome

tag: cellranger version

tag: cellranger chemistry

value: Single cell 3` v2


title: RS D91_D109

value: Single cell 3` v3


title: RS D78+35


title: RS D122+14_unsorted


title: D125P Fetal

value: Fetal

value: In vivo

value: Single cell 3` v1


title: D125C Fetal


title: D105 Fetal


title: D82P Fetal


title: RS 134_160F


title: D80P_2 Fetal


title: D80C Fetal


title: D59_1 Fetal


title: D80P Fetal


title: ppTh17-tdTpositive_2

source_name: CFSE-CD90+tdT+ sorted from Cr-primed culture replicate_2


title: Day 205 Organoid

source_name: Human embryonic cell line H7

value: Organoid


title: Day104_2 Organoid


title: D82C Fetal


title: Day60_2 Organoid


title: Day90_1 Organoid


title: Day60_1 Organoid


title: Day 45 Organoid


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_H04]

city: Oxford

first: Zhiyuan

last: Hu

address: John Radcliffe Hospital/Headley Way

department: MRC Weatherall Institute of Molecular Medicine

country: United Kingdom

institute: University of Oxford

data_processing:
Sequencing files were trimmed by Trim Galore!, mapped to UCSC hg19 human genome assembly by STAR (Dobin et al., 2012) and counted by FeatureCount (Liao et al., 2014).
Genome_build: hg19
Supplementary_files_format_and_content: read counts in txt format

source_name: human fallopian tube

extract_protocol:
The fallopian tube samples were processed in 1 hour, after being collected from the hospital. The tissues were dissociated with Human Tumor Dissociated kit (Miltenyi Biotec) and filtered using 100µm SmarterStrainers (Miltenyi Biotec).
SMART-seq2 for single-cell RNA-seq

value: normal fallopian tube cells


title: human fallopian tube scRNA-seq (benign donors) [sc_b2_N05]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_C13]


title: human fallopian tube scRNA-seq (benign donors) [sc_b2_K21]


title: RS D76_D109


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_G07]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_G05]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_G21]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_F11]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_E07]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_D15]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_D12]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_E18]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_C12]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_M18]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_C07]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_L14]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_L01]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_L03]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_L10]


title: Day110_3 Organoid


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_K06]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_J23]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_J15]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_J17]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_J13]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_I16]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_H06]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_I05]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_G20]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_G18]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_F23]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_G22]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_F21]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_F09]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_E11]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_L12]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_C19]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_E01]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_E04]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_A18]


title: human fallopian tube scRNA-seq (benign donors) [sc_b2_K19]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_E15]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_E20]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_K01]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_D22]


title: human fallopian tube scRNA-seq (benign donors) [sc_b2_J13]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_E10]


title: human fallopian tube scRNA-seq (benign donors) [sc_b5_F01]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_B18]


title: human fallopian tube scRNA-seq (benign donors) [sc_b4_N24]


title: human fallopian tube scRNA-seq (benign donors) [sc_b4_N07]


title: human fallopian tube scRNA-seq (benign donors) [sc_b4_E23]


title: human fallopian tube scRNA-seq (benign donors) [sc_b5_C22]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_I08]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_H20]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_A03]


title: human fallopian tube scRNA-seq (benign donors) [sc_b2_A01]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_H04]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_H10]


title: human fallopian tube scRNA-seq (benign donors) [sc_b3_F18]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_H08]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_H07]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_H05]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_D07]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_G23]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_H01]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_G12]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_G20]


title: human fallopian tube scRNA-seq (benign donors) [sc_b6_G03]