title: Mono_D6_rep1

data_processing:
Processing of raw sequencing data was performed with the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). Briefly, adapters were trimmed with cutadapt.
Trimmed reads were aligned to the hg19 reference genome with Bowtie2.
Aligned reads were filtered with Picard tools.
Peaks were called on each sample with MACS2 (p<0.01).
A 500 bp fixed-width union peak set was created for each dataset by merging peak sets from each sample and removing overlapping peaks as described (Corces et al., Science 2018).
Read counts were calculated with bedtools multicov.
Genome_build: hg19
Supplementary_files_format_and_content: Raw read counts per peak in tab-delimited text format for each sample

value: Mono

tag: donor id

tag: donor sex

value: M

tag: treatment

tag: sequencing batch


title: CD11clotDC_omni_D4_rep1

status: Public on Sep 22 2020

type: SRA

city: Stanford

first: Juliana

last: Idoyaga

state: California

address: 299 Campus Dr, Fairchild Science Building

department: Microbiology & Immunology

country: USA

institute: Stanford University

library_source: genomic

data_processing:
Library strategy: Omni-ATAC
Processing of raw sequencing data was performed with the ENCODE ATAC-seq pipeline (https://github.com/ENCODE-DCC/atac-seq-pipeline). Briefly, adapters were trimmed with cutadapt.
Trimmed reads were aligned to the hg19 reference genome with Bowtie2.
Aligned reads were filtered with Picard tools.
Peaks were called on each sample with MACS2 (p<0.01).
A 500 bp fixed-width union peak set was created for each dataset by merging peak sets from each sample and removing overlapping peaks as described (Corces et al., Science 2018).
Read counts were calculated with bedtools multicov.
Genome_build: hg19
Supplementary_files_format_and_content: Raw read counts per peak in tab-delimited text format for each sample

molecule: genomic DNA

organism: Homo sapiens

source_name: peripheral blood mononuclear cells

extract_protocol:
Samples were prepared according to Buenrostro et al., Nature Methods 2015 for ATAC-seq or Corces et al., Nature Methods 2017 for Omni-ATAC-seq. Briefly, 5,000-50,000 sorted cells were centrifuged, washed, and resuspended in lysis buffer to extract nuclei. Nuclei were centrifuged and resuspended in Tn5 transposition reaction mix for 30 min at 37ºC. Reactions were scaled according to number of cells. Transposed DNA was column purified and stored at -20ºC.
Samples were PCR amplified. In accordance with published protocols (Buenrostro et al., Nature Methods 2015; Corces et al., Nature Methods 2017) qPCR was used to determine the optimal number of PCR cycles to reduce GC and size bias. Samples were barcoded using custom primers as described (Buenrostro et al., Nature Methods 2013). Libraries were quantified with an Agilent Bioanalyzer and pooled for sequencing.

treatment_protocol: For non-stimulated samples, sorted cells were processed for ATAC-seq immediately. For stimulated pDCs, sorted cells were cultured for 2 days with 100 ng/mL CD40L or 5 µg/mL Imiquimod, then re-sorted to isolate live cells and immediately processed for ATAC-seq.

tag: cell type

value: F

tag: dataset


title: Large Wound Center Hic1:tdTomato-ve 14DPI aligned to tdTomato custom reference

city: Calgary

first: Jeff

last: Biernaskie

state: Alberta

address: 3330 Hospital Drive NW

department: Comparative Biology and Experimental Medicine

country: Canada

institute: University of Calgary

library_source: transcriptomic

data_processing:
All raw FASTQs reads were aligned to either the mouse GRCm38.p5 or to our custom tdTomato genome (primary assembly) reference genome using the STAR algorithm and quantified through the 10X Genomics cellranger v2.0.1 single cell pipeline, with default and recommended parameter. Only mapped reads were used for normalization before aggregating cells. The resulting gene-barcode matrix was imported into Seurat (v2.1.0 ) R toolkit for quality control and all downstream analysis. All functions were run with default or recommended parameters, unless specified otherwise. Low quality cells (<400 genes/cell and <20 cells/gene) were excluded from the overall experiment. Gene expression was log normalized to a scale factor of 10,000. To begin unsupervised clustering of cells, a selection of highly variable genes (1195 genes) was obtained and used to calculate up to 75 principle components. Significance of principle components was determined using JackStraw analysis and by creating a PCElbowPlot. PCs 1 to 20 were used to run and plot a tSNE plot for all cells. Expression of selected marker genes across cell clusters identified by graph based clustering (run in Seurat at: res = 0.2) was used to select only fibroblasts for all subsequent analysis. Differential and marker gene analysis of cells defined by FACS sorting sample or graph-clustering was also run in Seurat using the negative binomial test for genes expressed by at least 25% of cells in the defined cell group being compared.
Genome_build: Modified mm10 (GRCm38.p5) reference genome with several transgenes added (custom reference genome is attached with submission)
Supplementary_files_format_and_content: Filtered gene - barcode matrix output from CellRanger

molecule: polyA RNA

organism: Mus musculus

source_name: 14 days post injury skin wound

extract_protocol:
Large and small wounds from adult mice (n = 2 per sample) were dissected and enzymatically dissociated with dispase (StemCell Technologies) for 20 mins at 37 oC to remove the epidermis. Remaining dermis was dissociated using 0.2% collagenase for 2 hours at 37 oC. Cell suspensions were diluted with cold Hank’s Buffered Salt Solution (HBSS; Life Technologies), strained through 40 µm cell filters (Falcon) and centrifuged at 280 X g. Liberated single cells were re-suspended in 0.5% bovine serum album in HBSS before FACS purification. For FACS purification, a stringent initial forward and side scatter gates were used to exclude debris, and cell doublets. Wildtype cells were used as negative control to determine gates for detection of tdTomato-fluorescence, then cells from Hic1CreERT2:tdTomato mice were purified.
Libraries were prepared according to 10X Genomics ChromiumTM Single Cell 3’ Reagent Guidelines v2 Chemistry as per the manufacturer’s protocol. In brief, single cells were sorted into 0.1% BSA–PBS and partitioned into Gel Bead-In-EMulsions (GEMs) using 10xTM GemCodeTM Technology. This process lysed cells and enabled barcoded reverse transcription of RNA, generating full-length cDNA from poly-adenylated mRNA. DynaBeads® MyOneTM Silane magnetic beads were used to remove leftover biochemical reagents, then cDNA was amplified by PCR over 10 cycles. Quality control size gating was used to select cDNA amplicon size prior to library construction. Read 1 primer sequences were added to cDNA during GEM incubation. P5 primers, P7 primers, i7 sample index, and Read 2 primer sequences were added during library construction. Quality control and cDNA quantification was performed using Agilent High Sensitivity DNA Kit. Sequencing was performed first using Illumina MiSeq SR50 to approximate the number of recovered cells in each sample. We recovered 4061, 3776, 2604, and 3293 cells for Samples 1-4, respectively, with an estimated doublet rate of ≈3%. Based on this, we determined lane distributions for sequencing using Illumina HiSeq 4000 PE (75 bp paired-end reads) with a targeted sequencing depth of ~115,000 reads/cell.

treatment_protocol: Cre-recombination was initiated with two intraperitoneal injections of 4-hydroxy-tamoxifen (4-OHT; 1mg/20g in sterile sunflower oil, Sigma-Aldrich) at postnatal day (P) 3 and 4.

tag: transgenic strain

tag: background

tag: facs strategy

value: tdTomato-neg


title: CEMBA181016_5H_1_CEMBA181016_5H_2_C1_ad010

city: La Jolla

first: Joseph

middle: R

last: Ecker

state: CA

address: 10010 North Torrey Pines Road

department: Genomic Analysis Laboratory

institute: HHMI-Salk-Institute

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

source_name: C57BL/6J Male P56 Mouse Brain

growth_protocol: All mice are C57BL/6J Male, brain dissected in P56

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.

tag: brain region

value: PAL

tag: Sex

value: male

tag: age

tag: strain


title: BC2283: primary breast cancer patient 11

type: RNA

city: Mainz

first: Marcus

last: Schmidt

address: Langenbeckstr. 1

department: Universitäres Centrum für Tumorerkrankungen

country: Germany

institute: Universitätsmedizin Mainz

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG-U133a Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing:
CEL file not available for this patient
Raw expression data (CEL files) were normalized using frozen robust multiarray analysis (fRMA)

label: biotin

molecule: total RNA

source_name: primary breast cancer tissue

label_protocol: Starting from 5 µg total RNA, labeled cRNA was prepared using the Roche Microarray cDNA Synthesis, Microarray RNA Target Synthesis (T7) and Microarray Target Purification Kit, according to the manufacturerâ€™s instructions

extract_protocol: Approximately 50 mg of frozen breast tumor tissue was crushed in liquid nitrogen. RLT-Buffer was added and the homogenate was centrifuged through a QIAshredder column (QIAGEN, Hilden, Germany). RNeasy extraction (QIAGEN) of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: For all tumors, samples were snap frozen and stored at -80°C. Tumor cell content exceeded 40% in all samples.

tag: tissue

value: primary breast cancer

tag: node

tag: grade

tag: t-size (mm)

tag: adjuvant treatment

value: adj chemo

tag: intrinsic subtype


title: BC2282: primary breast cancer patient 10


title: BC2280: primary breast cancer patient 9


title: Mono_D5_rep1

tag: donor id

tag: donor sex

tag: treatment


title: BC2277: primary breast cancer patient 8


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B9_ad007


title: Small Wound Hic1:tdTomato+ve 8DPI aligned to tdTomato custom reference

source_name: 8 days post injury skin wound

value: tdTomato+positive


title: HAEC_Untreated_Rep3 (mRNA)

city: Shanghai

first: Zhen

last: Sheng

address: F13, Building 2, 4560 Jinke Road

country: China

institute: Amgen Biopharmaceutical Research & Development (Shanghai) Co., Ltd

description: gene expression of HAEC cells without treatment of oxLDL (mRNA)

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

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat#G2565CA, Agilent technologies, Santa Clara, CA, US) with default settings, Dye channel: Green, Scan resolution=3μm, PMT 100%, 20bit. Data were extracted with Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US).

data_processing: Raw data were normalized by Quantile algorithm, limma packages in R.

source_name: human aorta endothelial cells, untreated, replicate 3

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

growth_protocol: Human aortic endothelial cells (HAECs) were purchased from the American Type Culture Collection (ATCC, PCS-100-011) and cultured in Vascular Cell Basal Medium (ATCC, PCS-100-030) supplemented with Endothelial Cell growth kit (ATCC, PCS-100-041) and 0.1% penicillin/streptomycin (ATCC, PCS-999-002) at 37°C in an incubator with 5% CO2.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit (Cat#AM1561, Ambion, Austin, TX, US) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

treatment_protocol: HAECs were treated with oxLDL 100 μg/ml for 48 h.

tag: cell

value: human aorta endothelial cells

value: Vehicle


title: Mono_D4_rep1

tag: cell type

tag: sequencing batch

tag: dataset


title: HAEC_Untreated_Rep2 (mRNA)

source_name: human aorta endothelial cells, untreated, replicate 2


title: Mono_D7_rep1


title: HAEC_Untreated_Rep1 (mRNA)

source_name: human aorta endothelial cells, untreated, replicate 1


title: Large Wound Pheripheral Hic1:tdTomato+ve 18DPI aligned to tdTomato custom reference

source_name: 18 days post injury skin wound

tag: transgenic strain

tag: background

tag: facs strategy


title: BC2275_2: primary breast cancer patient 7

tag: age


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B9_ad008

tag: brain region

tag: Sex

tag: strain


title: Large Wound Center Hic1:tdTomato+ve 18DPI aligned to tdTomato custom reference


title: Mono_D3_rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B9_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B9_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B9_ad002


title: Mono_D3_rep1


title: Uninjuired Skin Hic1:tdTomato+ve aligned to tdTomato custom reference

source_name: P. 24 Uninjured Skin


title: BC2261: primary breast cancer patient 4

tag: tissue

tag: node

tag: grade

tag: t-size (mm)


title: BC2271: primary breast cancer patient 6

tag: adjuvant treatment

tag: intrinsic subtype


title: Small Wound Hic1:tdTomato+ve 14DPI aligned to tdTomato custom reference


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B9_ad012


title: Mono_D2_rep1

tag: donor id

tag: donor sex

tag: treatment


title: BC2254: primary breast cancer patient 2


title: Large Wound Pheripheral Hic1:tdTomato+ve 14DPI aligned to tdTomato custom reference


title: BC2256: primary breast cancer patient 3


title: BC2268: primary breast cancer patient 5


title: Large Wound Center Hic1:tdTomato+ve 14DPI aligned to tdTomato custom reference


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B8_ad008


title: Mono_D1_rep2

tag: cell type

tag: sequencing batch

tag: dataset


title: F.T. DEHP treated rep3

city: Urbana

first: Mary

last: Laws

address: 2001 S. Lincoln Ave.

institute: University of Illinois

data_processing:
Fastq files were generated and demultiplexed with with the bcl2fastq v2.17.1.14 Conversion Software (Illumina).
Raw reads were checked for quality using FASTQC (v 0.11.5) then trimmed and filtered using Trimmomatic (v 0.36) to remove residual adapter content, low quality bases (Phred quality score < 28), and resulting reads shorter than 30 nt.
Adaptors have been trimmed from the 3'-end of the reads. Sequence of adaptors used to make the libraries (used portion in bold font for adaptor trimming). Adaptor sequence in read1:  AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG (NNNNNNNN= 8 nt index)  Adaptor sequence in read2:  AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCAT
The quality-scores line in fastq files use an ASCII offset of 33 known as Sanger scores
Reads are 100 nt in length.
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Trimmed/filtered reads were aligned to NCBI’s Mus musculus GRCm38.p6 genome and gene model annotation release 106 using STAR (v 2.5.3a). Post-alignment gene counts were then determined for each NCBI EntrezGene ID using featureCounts from Subread (v 1.5.2-pl) with multi-mapping reads excluded. Post-alignment gene counts were then determined for each NCBI EntrezGene ID using featureCounts from Subread (v 1.5.2-pl) with multi-mapping reads excluded.
Supplementary_files_format_and_content: The raw read counts were input into R (v 3.4.3) for pre-processing and analysis together using Bioconductor packages as listed below. There were ~23 million reads aligned uniquely within the 41,595 M. musculus genes. We used TMM method in the edgeR package (v 3.20.5) to normalize the counts to log2-transformed counts per million (logCPM), using the cpm() function with prior.count = 3.  25,141 genes did not have logCPM > log2(0.5) in at least three samples and were filtered out, leaving 16,454 genes to be analyzed for differential expression. TMM-values and logCPM normalized values were re-calculated with prior.count = 3 after gene filtering.  Multiple hypothesis test correction was done using the False Discovery Rate method.
Supplementary_files_format_and_content: Column explanations in txt file: ENTREZID-Entrez gene ID of NCBI's Mus musculus GRCm38.p6 genome and gene set annotation release 106; SYMBOL-Gene symbol for the ENTREZID; GENENAME-Gene name for the ENTREZID; logCPM-Average expression level across all samples; logFC-Fold Change for this pairwise comparison; FC-Fold Change for this pairwise comparison, regular scale; negative values indicate lower expression in the Treated group (i.e, -2 instead of 0.5); PValue-Raw p-value for pairwise comparison between control vs treated; FDR-False discovery rate adjusted for testing differences between control vs treated; logCPM.C.A-Gene expression level of this individual in log2 scale; logCPM.C.C-Gene expression level of this individual in log2 scale; logCPM.C.E-Gene expression level of this individual in log2 scale; logCPM.T.B-Gene expression level of this individual in log2 scale; logCPM.T.D-Gene expression level of this individual in log2 scale; logCPM.T.F-Gene expression level of this individual in log2 scale; BP-Gene Ontology's Biological Process terms for this gene; CC-Gene Ontology's Cellular Component terms for this gene; MF-Gene Ontology's Molecular Function terms for this gene; KEGGpathway-KEGG pathways for this gene pulled directly from http://www.genome.jp/kegg using the KEGGREST package (v 1.18.0) on January 8, 2018. ENTREZID, SYMBOL, GENENAME, BP, CC, and MF from Bioconductor's org.Mm.eg.db database (v 3.5.0).

source_name: ovary

extract_protocol:
Ovaries were removed and flash frozen in liquid nitrogen. Total RNA (>100 ng) was extracted from the whole ovaries using the AllPrep DNA/RNA Mini Kit (Qiagen, Austin, TX, USA) according to the manufacturer's protocol, including DNase digestion.
The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded mRNAseq Sample Prep kit' (Illumina). Read 1 aligns to the ANTISENSE strand and Read 2 aligns to the SENSE strand. The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from one end of the fragments on a HiSeq 4000 using a HiSeq 4000 sequencing kit version 1.

treatment_protocol: F0 generation dams were treated with vehicle control or 20ug/kg/day DEHP

value: ovary

value: 20 ug/kg/day DEHP

value: post natal day 21

tag: generation


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B8_ad010

tag: age


title: cDC2_D7_rep2


title: Mono_D2_rep2


title: BC2248: primary breast cancer patient 1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B8_ad004

tag: brain region


title: cDC2_D7_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B8_ad001

tag: Sex


title: cDC2_D6_rep2


title: D.T. DEHP treated rep2

tag: strain


title: C.C. Control rep2

tag: tissue

value: vehicle control


title: cDC2_D6_rep1


title: HaSKpw_rep2

city: Darmstadt

first: Alexander

last: Rapp

address: Schnittspahnstr. 10

department: Biology

institute: Technische Universität Darmstadt

hyb_protocol: 58°C for 20 h, spike-in and mismatch controls were added. Post hybridisation arrays were washed in High Temp Wash buffer (Illumina Inc.) at 55°C C and then twice in E1BC buffer at room temperature.

scan_protocol: Standard Illumina scanning protocol.

data_processing: Data extraction was done for all beads individually, and outliers were removed when > 2.5 MAD (median absolute deviation). Quality control was performed using Genome Studio (Illumina). Further processing steps were carried out using Bioconductor with the following packages GOstats, GenomicRanges, Biostrings, beadarray, limma, GEOquery, illuminaHumanv4.db, topGO, org.Hs.eg.db and clusterProfiler.

source_name: HaSKpw cell culture

label_protocol: Illumina Total Prep RNA Amplification Kit using biotin label was used.

growth_protocol: HaCaT cells (Human adult low Calcium High Temperature) were cultured in DMEM (4.5 g/L Glucose, L-Glutamine, Sodium pyruvate, 3.7 g/L NaHCO3) (Pan Biotech) containing 10% FCS and 0.1 % Pen/Strep (Pan Biotech). HaSKpw cells (Human adult Skin Keratinocyte, p53 wild type) were cultured in FAD complete medium (50% DMEM Medium, 50 % DMEM/F12 ((1+1) with 15 mM Hepes, with L-glutamine) (Pan Biotech)) supplemented with 0.1% Pen/Strep (Pan Biotech), 5 % FBS (Biochrom), 5 mg/L Insulin (Sigma Aldrich), 24 mg/L Adenine (Sigma Aldrich), 0.4 mg/L Hydrocortisone (Sigma Aldrich), 8 μg/L Cholera toxin (Sigma Aldrich) and 1 μg/L rhEGF (Thermo Scientific).

extract_protocol: Total RNA was extracted from HaCaT and HaSKpw cell lines using RNeasy (Qiagen) following the manufacturer's instructions.

tag: gender

value: female

value: skin

value: keratinocyte

tag: cell line

value: HaSKpw


title: HaSKpw_rep3


title: HaSKpw_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B9_ad004


title: B.T. DEHP treated rep1


title: Mono_D1_rep1

value: Mono

value: F


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B8_ad006

value: PAL


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B8_ad007

value: male


title: A.C. Control rep1


title: E.C. Control rep3


title: Memory CD4 T cells, M2R2

city: New York City

first: Joshua

middle: Ian

last: Gray

state: New York

address: 630 168th Street

department: CCTI

institute: Columbia University

data_processing:
Sequence reads were trimmed to remove contaminants from adaptor sequences and low-quality or undetermined reads using Cutadapt.
Sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and mapped to the Mus Musculus reference genome GRCm38.p6 using HISAT2.
Reads were quantified and assembled to construct a comprehensive transcriptome using Kallisto.
Differential expression analysis was conducted using the R package DESeq2 with differentially expressed genes selected based on a log2 fold change >2 or <-2 with statistical significance (q value) <0.05.
DAVID functional annotation analysis was carried out on these genes to form a list of enriched gene ontogeny (GO) terms associated with molecular function, biological process or cell components. Enriched GO terms were visualised using a Bubble plot, found in the R package ‘ggplot2’. Heatmaps were generated using R v3.5.3 and the heatmap.2 function from the gplots package  and over-representation of GO terms determined using Panther
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Abundance tsv files with read counts included for each sample

source_name: Antigen-specific memory CD4 T cells

extract_protocol:
Lymphoid organs were removed, processed and EYFP+ memory CD4 T cells were sorted and collected into RLT buffer using a FACS Aria IIU cell sorter. RNA was extracted using the Qiagen RNeasy Micro Kit. Briefly, cells were manually homogenized with a pipette and eluted using an RNeasy MinElute spin column. A DNase step was included to remove contaminant DNA and extracted RNA was stored in RNase-free water.
Library construction was conducted using an Illumina Hiseq 4000 following the manufacturer’s recommended protocol.

treatment_protocol: TRACE reporter mice given doxycycline on days -2 to day 5 were immunised on day 0 with 40µg of ovalbumin (OVA) protein conjugated to 20µm polyethylene carboxylate beads with 20µg of polyinosinic:polycytidinic acid (polyIC) and 20µg of anti-CD40 subcutaneously (s.c) in the scruff in 100µl PBS. TRACE mice were euthanised 8 days post-immunisation and single cell suspensions  prepared. Lymphoid organs, including spleen, mediastinal, axillary, brachial and mesenteric lymph nodes, from individual mice were pooled and pre-enriched for CD4 T cells using EasySepTM Mouse T Cell Isolation Kit (Stemcell Technologies) according to the manufacturer’s protocol. Live, single, EYFP+ CD4 T cells that were negative for MHCII, B220 and F4/80 were sorted on a BD FACS Aria IIU. Sorted cells were washed in PBS and 100,000 cells transferred i.v. into naïve C57BL/6 mice. Recipients of TRACE EYFP+ T cells were administered with 40µg of OVA peptide or 40µg of OVA peptide with 10µg lipopolysaccharide (LPS) intravenously (i.v.) in 100µl of PBS 14 days later. Following a further 30 days, mice were immunised with 40µg of OVA tumbled with 0.1mg of aluminium hydroxide gel ((Alhydrogel©) Invivogen)) in 100µl of PBS intraperitoneally. Immunised recipients of EYFP+ CD4 T cells were euthanised and single cell suspensions were prepared. Lymphoid organs, including spleen, mediastinal, axillary, brachial and mesenteric lymph nodes, from individual mice were pooled and subsequently pre-enriched for CD4 T cells again using EasySepTM Mouse T Cell Isolation Kit (Stemcell Technologies) according to the manufacturer’s protocol. EYFP+ CD4 T cells were sorted as above. Cell were sorted into RLT buffer and stored at -20°C prior to RNA extraction.

value: Memory CD4 T cells

tag: activation status

value: Tolerised

value: Lymphoid tissue

value: Male


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B8_ad002


title: cDC2_D4_rep1


title: Memory CD4 T cells, M2T1


title: cDC2_D3_rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B8_ad012


title: cDC2_D5_rep2

value: M


title: cDC2_D5_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B7_ad002


title: TGFb12h, biological rep1 [RNA-seq]

city: Sevilla

first: Jose

middle: C.

last: Reyes

address: Av. Américo Vespucio

department: Genome biology

country: Spain

institute: CABIMER

data_processing:
RNA-Seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
Data were aligned using subjunc function from Rsubread package, to map reads to the mm9 mouse reference genome using TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bamfiles with duplicates removed using the samtools (v0.1.19) rmdup command
FeatureCounts() function from Rsubread package was used to assign reads to UCSC mm9 KnownGenes (miRNAs were discarded from the analysis) using GTF.featureType=“exon”,  GTF.attrType=“gene_id” and strandSpecific = 2 parameters on duplicate removed bamfiles. Then differential gene expression analysis was performed using the voom/limma (v.3.34.9) and edgeR (v.3.20.9) Bioconductor packages
Genome_build: mm9 mouse reference genome
Supplementary_files_format_and_content: Raw counts per UCSC knownGenes at exon level for all treatments.

growth_protocol: Normal murine mammary gland NMuMG epithelial cells were cultured in Dulbecco's modified Eagle's medium containing 10% serum and 10 μg/ml insulin, until reaching 70–80% confluency

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen)
The libraries were prepared with the TruSeq Stranded TOTAL RNA kit (Illumina, San Diego, CA, USA) and the sequencing was performed with the HiSeq 1x50bp length

treatment_protocol: For TGFβ treatment, cells were washed with phosphate-buffered saline (PBS), changed to serum-free medium for 6 hours and then treated with 5 ng/ml TGFβ1 diluted in 4 mM HCl, 1 mg/ml BSA (240-B, R&D Systems) for the indicated time; or 4 mM HCl 1 mg/ml BSA as control (vehicle).

value: NMuMG

value: normal murine mammary gland (NMuMG) epithelial cells

value: 5 ng/mL TGFβ1 for 12 hours


title: TGFb2h, biological rep1 [RNA-seq]

value: 5 ng/mL TGFβ1 for 2 hours


title: TGFb2h, biological rep2 [RNA-seq]


title: cDC2_D3_rep1


title: veh, biological rep2 [RNA-seq]

value: vehicle (Tris-HCl, BSA) for 2 hours


title: TGFb12h, biological rep2 [RNA-seq]


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B7_ad006


title: cDC2_D2_rep2


title: HaCat_rep1

source_name: HaCaT cell culture

value: female

value: skin

value: HaCat


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B7_ad012


title: Memory CD4 T cells, M2T3

data_processing:
Sequence reads were trimmed to remove contaminants from adaptor sequences and low-quality or undetermined reads using Cutadapt.
Sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and mapped to the Mus Musculus reference genome GRCm38.p6 using HISAT2.
Reads were quantified and assembled to construct a comprehensive transcriptome using Kallisto.
Differential expression analysis was conducted using the R package DESeq2 with differentially expressed genes selected based on a log2 fold change >2 or <-2 with statistical significance (q value) <0.05.
DAVID functional annotation analysis was carried out on these genes to form a list of enriched gene ontogeny (GO) terms associated with molecular function, biological process or cell components. Enriched GO terms were visualized using a Bubble plot, found in the R package ‘ggplot2’. Heatmaps were generated using R v3.5.3 and the heatmap.2 function from the gplots package  and over-representation of GO terms determined using Panther
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: Abundance tsv file with read counts included for each sample

treatment_protocol: TRACE reporter mice given doxycycline on days -2 to day 5 were immunized on day 0 with 40µg of ovalbumin (OVA) protein conjugated to 20µm polyethylene carboxylate beads with 20µg of polyinosinic:polycytidinic acid (polyIC) and 20µg of anti-CD40 subcutaneously (s.c) in the scruff in 100µl PBS. TRACE mice were euthanized 8 days post-immunisation and single cell suspensions  prepared. Lymphoid organs, including spleen, mediastinal, axillary, brachial and mesenteric lymph nodes, from individual mice were pooled and pre-enriched for CD4 T cells using EasySepTM Mouse T Cell Isolation Kit (Stemcell Technologies) according to the manufacturer’s protocol. Live, single, EYFP+ CD4 T cells that were negative for MHCII, B220 and F4/80 were sorted on a BD FACS Aria IIU. Sorted cells were washed in PBS and 100,000 cells transferred i.v. into naïve C57BL/6 mice. Recipients of TRACE EYFP+ T cells were administered with 40µg of OVA peptide or 40µg of OVA peptide with 10µg lipopolysaccharide (LPS) intravenously (i.v.) in 100µl of PBS 14 days later. Following a further 30 days, mice were immunized with 40µg of OVA tumbled with 0.1mg of aluminium hydroxide gel ((Alhydrogel©) Invivogen)) in 100µl of PBS intraperitoneally. Immunized recipients of EYFP+ CD4 T cells were euthanized and single cell suspensions were prepared. Lymphoid organs, including spleen, mediastinal, axillary, brachial and mesenteric lymph nodes, from individual mice were pooled and subsequently pre-enriched for CD4 T cells again using EasySepTM Mouse T Cell Isolation Kit (Stemcell Technologies) according to the manufacturer’s protocol. EYFP+ CD4 T cells were sorted as above. Cell were sorted into RLT buffer and stored at -20°C prior to RNA extraction.

value: Tolerized


title: HaCat_rep3

value: keratinocyte


title: Memory CD4 T cells, M1T3


title: veh, biological rep1 [RNA-seq]


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B7_ad001

value: PAL


title: HaCat_rep2


title: cDC2_D2_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B7_ad008

value: male


title: Memory CD4 T cells, F2R1

value: Memory CD4 T cells

value: Activated

value: Female


title: Memory CD4 T cells, M1R2

value: Lymphoid tissue

value: Male


title: Memory CD4 T cells, FT3


title: cDC1_D7_rep1

value: F


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B6_ad002


title: Memory CD4 T cells, FR1


title: TGFb2h, biological rep2 [Chromatin-enriched RNA-seq]

data_processing:
RNA-Seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
Data were aligned using subjunc function from Rsubread package, to map reads to the mm9 mouse reference genome using TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bamfiles with duplicates removed using the samtools (v0.1.19) rmdup command
BamCoverage from Deeptools suite was used to create bigWig files using RPKM normalization
Genome_build: mm9 mouse reference genome
Supplementary_files_format_and_content: bigWig read densitity files

extract_protocol:
Cells were resuspended in 400 μl cold cytoplasmic lysis buffer (0.15% NP-40, 10 mM Tris pH 7.5, 150 mM NaCl) and incubated on ice for 5 min. The lysates were layered onto 1 ml cold sucrose buffer (10 mM Tris pH7.5, 150 mM NaCl, 24% sucrose w/v), and centrifuged in microfuge tubes at 3500 g for 10 minutes. The nuclear pellets were gently resuspended into 250 μl cold glycerol buffer (20 mM Tris pH 7.9, 75 mM NaCl, 0.5 mM EDTA, 50% glycerol). An additional 250 μl of cold nuclei lysis buffer (20 mM HEPES pH 7.6, 7.5 mM MgCl2, 0.2 mM EDTA, 0.3 M NaCl, 1 M urea, 1% NP-40, 1 mM DTT) was added to the samples, followed by a pulsed vortexing and incubation on ice for 2 minutes. Samples were then spun in microfuge tubes for 2 min at 13000 g. 50 μl of cold PBS was added to the remaining chromatin pellet, and gently pipetted up and down over the pellet, followed by a brief vortex. Then RNA was extracted using TRIZOL and treated with TURBO DNA-free kit (AM1907, Invitrogen) for DNA removal according to manufacturer's instructions
The libraries were prepared with the TruSeq Stranded TOTAL RNA kit (Illumina, San Diego, CA, USA) and the sequencing was performed with the HiSeq2000 1x50bp length

value: NMuMG

value: normal murine mammary gland (NMuMG) epithelial cells


title: TGFb12h, biological rep1 [Chromatin-enriched RNA-seq]

value: 5 ng/mL TGFβ1 for 12 hours


title: Memory CD4 T cells, F2R2


title: TGFb2h, biological rep1 [Chromatin-enriched RNA-seq]

value: 5 ng/mL TGFβ1 for 2 hours


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B6_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B6_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B6_ad001


title: cDC1_D6_rep1

value: M


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B6_ad006


title: cDC1_D5_rep1


title: cDC1_D3_rep1


title: cDC1_D4_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B6_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B5_ad012


title: cDC2_D1_rep2


title: cDC2_D1_rep1


title: TGFb12h, biological rep2 [Chromatin-enriched RNA-seq]


title: cDC1_D2_rep2


title: veh, biological rep1 [Chromatin-enriched RNA-seq]

value: vehicle (Tris-HCl, BSA) for 2 hours


title: veh, biological rep2 [Chromatin-enriched RNA-seq]


title: H3k4me3_TGFb12h, biological rep2

data_processing:
ChIP-Seq data were primarily filtered using the FASTQ Toolkit v1.0.0 program
Two biological replicates of the ChIP-seq data for each condition and for each histone modification (H3K27ac, H3K4me1 and H3K4me3) were primarily filtered using the FASTQ Toolkit program. Data were aligned using align function from Rsubread package, to map reads to the mm9 mouse reference genome using type = 1, TH1=2 and unique=TRUE parameters. The downstream analysis was performed on bamfiles with duplicates removed using the samtools rmdup command
BamCoverage from Deeptools suite was used to create bigWig files using RPKM normalization
Genome_build: mm9 mouse reference genome
Supplementary_files_format_and_content: bigWig

extract_protocol: Cells were crosslinked in 1% formaldehyde for 10 min at room temperature followed by addition of glycine (125 mM final concentration) for 5 min. Nuclei were isolated using lysis buffer 1 (5 mM Pipes pH 8, 85 mM KCl, 0.5% NP40, and complete protease inhibitor cocktail (Roche)) and were lysed using lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.1, and complete protease inhibitor cocktail (Roche)). Chromatin was sheared into an average size of 500 bp by 8 s pulses (30 s pause between pulses) at 4 °C in the water bath sonicator Bioruptor (Diagenode, Liège, Belgium). Thirty micrograms of chromatin were incubated overnight at 4 °C in rotation, diluted 1:10 in IP buffer (0.01% SDS, 1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl pH 8.1, and 167 mM NaCl, 1% sodium deoxycholate) and with the respective antibodies: 3 µg of anti-H3K27ac (Ab4729, Abcam.), 3 µg of anti-H3K4me1 (Ab8895, Abcam) and 3 µg of anti-K3m4me3 (Ab8580, Abcam). Immunoprecipitations were incubated for 2 h at 4 °C in rotation with protein A Dynabeads (Invitrogen) and then washed with wash buffer 1 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, and 150 mM NaCl, 1% sodium deoxycholate), wash buffer 2 (0.1% SDS, 1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.1, and 500 mM NaCl, 1% sodium deoxycholate), wash buffer 3 (0.25 M LiCl, 1% NP40, 1% sodium deoxycholate, 1 mM EDTA, and 10 mM Tris-HCl pH 8.1), and twice with TE buffer (10 mM Tris-HCl pH 8.0 and 1 mM EDTA). The complexes were eluted from the beads with elution buffer (1% SDS in TE buffer) by incubating twice 10 min at 65 °C. The eluates and the inputs were incubated overnight at 65 °C for de-crosslinking and chipped DNA was purified with phenol:chloroform extraction followed by ethanol precipitation and resuspended in miliQ water

tag: chip antibody


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B5_ad004


title: H3k4me3_TGFb12h, biological rep1


title: cDC1_D2_rep1


title: H3k4me3_TGFb2h, biological rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B5_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B5_ad002


title: H3k4me3_TGFb2h, biological rep1


title: H3k4me3_veh, biological rep2


title: H3k4me3_veh, biological rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B5_ad006


title: pDC_D7_rep1

value: pDC


title: pDC_D6_rep2


title: pDC_D6_rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B5_ad008


title: H3K4me1_TGFb12h, biological rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B4_ad010


title: RNA-Seq of Helianthus annuus SF342: stress R3

city: Castanet-Tolosan

first: Ludovic

last: Legrand

address: 24 Chemin de Borde Rouge

country: France

institute: INRA/CNRS

data_processing: The transcriptomic study was performed with the EdgeR package version 3.16.5 on R version 3.3.3 (Another Canoe).CPM were computed with the cpm function from the edgeR package. 30,831 genes were found with at least 3 CPM in 3 libraries. Count normalization was performed as described in the edgeR user guide with the calcNormFactors function using the TMM method (Trimmed Mean normalization).

organism: Helianthus annuus

source_name: leaves

growth_protocol: For the Heliaphen phenotyping platform experiment conducted from May 31st to July 16th. Bleach-sterilized seeds were germinated on Petri dishes with Apron XL and Celeste solutions (Syngenta, Basel, Switzerland) for 3 days at 28C. Germinated plantlets were transplanted in individual pots, and each pot contained two or three plants. Pots were filled with 15 L of P.A.M.2 potting soil (Proveen distributed by Soprimex, Chateaurenard, Bouches-du-Rhone, France) and covered with a 3-mm-thick polystyrene sheet to prevent evaporation. On June 17th, plants were thinned to keep one plant per pot representative of the genotype. Plants were fertilized with 500ml of Peter's Professionnal 17-07-27 (0,6g/l) and Hortilon (0,46g/l) solution. On June 21st, Polyaxe at 5mg/l was applied on foliage against thrips. The XRQ plants were part of a larger experimental design that will not be completely studied in this article. In total, 144 plants, corresponding to 24 genotypes, two drought stress conditions and three replicates were arranged in a split-split-plot design with three blocks. The stress intensity (i.e., FTSW) was the main factor within the block, the genotype was the second factor. Each pot was fertilized and irrigated as in Rengel et al., (2012) before the beginning of the water stress application. For this study, we retained only the six XRQ plants (three irrigated and three non-irrigated plants). Pots were saturated with water on July 5th 2013, 35 days after germination. The following morning, excessive water was drained for two hours and pots were weighed to obtain the saturation mass. On July 8th, irrigation was stopped for stressed plants. Both control and stressed plants were weighed three or four times per day by the Heliaphen robot to estimate evapotranspiration. The water lost was added back automatically by the robot to control plants. Pairs of stressed and control plants were harvested when the FTSW of the stressed plant reached 0.1 which happened between July 12th to 16th. Leaves were harvested between 11:00 and 13:00. To select the leaf to harvest, the total leaf number was estimated, and leaves at the rank position corresponding to two thirds of the total leaf number from the bottom were tagged and termed the nth leaf. For transcriptomic studies, we selected the n+1 leaves.

extract_protocol: Leaves were cut without their petiole and immediately frozen in liquid nitrogen (greenhouse) or in dry ice (field). Grinding was performed using a ZM200 grinder (Retsch, Haan, Germany) with a 0.5-mm sieve. Total RNA was extracted using QIAzol Lysis Reagent following the manufacturers instructions (Qiagen, Dusseldorf, Germany). The RNA quality was checked by electrophoresis on an agarose gel and quality and quantity were assessed using the Agilent RNA 6000 nano kit (Agilent, Santa Clara, CA, USA). Sequencing was performed on the Illumina HiSeq 2000 by DNAVision (Charleroi, Belgium) as paired-end libraries (2*100 bp, oriented) using the TruSeq sample preparation kit (Illumina San Diego, CA, USA) according to manufacturers instructions.

treatment_protocol: Stressed plants have water status FTSW = 0.1.

tag: cultivar

value: leaves

value: Stressed plants - water status FTSW = 0.1.


title: H3K4me1_TGFb2h, biological rep2


title: H3K4me1_TGFb12h, biological rep1


title: RNA-Seq of Helianthus annuus SF342: stress R2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B4_ad007

value: PAL


title: H3K4me1_TGFb2h, biological rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B4_ad012

value: male


title: RNA-Seq of Helianthus annuus SF342: stress R1


title: pDC_D7_rep2

tag: donor id


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B4_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B4_ad006


title: H3K4me1_veh, biological rep2


title: RNA-Seq of Helianthus annuus SF342: control R3

treatment_protocol: Control plants have water status FTSW = 1.

value: Control plants - water status FTSW = 1.


title: H3K4me1_veh, biological rep1


title: RNA-Seq of Helianthus annuus SF326: stress R3


title: pDC_D4_rep1

tag: donor sex


title: pDC_D3_rep1

tag: treatment


title: pDC_D4_rep2

tag: cell type


title: RNA-Seq of Helianthus annuus SF326: stress R2


title: pDC_D3_rep2

tag: sequencing batch


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B4_ad001


title: H3K27ac_TGFb12h, biological rep1


title: H3K27ac_TGFb2h, biological rep2


title: pDC_D5_rep2

tag: dataset


title: pDC_D2_rep2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B3_ad008


title: pDC_D5_rep1


title: pDC_D2_rep1


title: H3K27ac_TGFb2h, biological rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B3_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B3_ad012


title: pDC_D1_rep2


title: RNA-Seq of Helianthus annuus SF326: control R1


title: RNA-Seq of Helianthus annuus SF326: control R2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B3_ad006


title: H3K27ac_TGFb12h, biological rep2


title: H3K27ac_veh, biological rep2


title: pDC_D1_rep1


title: RNA-Seq of Helianthus annuus SF317: stress R3


title: NSD2_ChIP-seq

city: Chuo-ku, Kumamoto

first: Mitsuyoshi

last: Nakao

state: Kumamoto

address: 2-2-1 Honjo

department: Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics

country: Japan

institute: Kumamoto university

data_processing:
Basecalls and conversion to FASTQ files were performed using BaseSpace Onsite (Illumina).
Low quality reads were trimmed out using Trimmmomatic (Galaxy v.0.36.3).
Reads were alignmened onto the human reference genome hg19 using BWA algorithm (Galaxy v.0.7.15.1).
Duplicate reads were trimmed out using Picard MarkDuplicates (Galaxy v.1.136.0).
Genome_build: hg19
Supplementary_files_format_and_content: The bigwig files were generated using deepTools bamCompare (Galaxy v.2.5.0.0).

source_name: Growing IMR-90 cells

growth_protocol: IMR-90 cells were cultured in Dulbecco-modified eagle’s medium (DMEM)/F12 supplemented with 10% (v/v) heat-inactivated fetal bovine serum.

extract_protocol:
Crosslinked nuclear extracts were subjected to DNA fragmentation by Bioruptor, and chromatin-DNA complexes were pulled down using specific antibodies.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) according to the manufacturer's instructions. Briefly, ChIP DNA was end-repaired using an end prep enzyme. After adapter ligation, DNA was PCR amplified with NEB Index primers. The purified DNA was checked for quality on Agilent TapeStation instrument with an Agilent High Sensitivity D1000 kit. The library DNA was approximately 200–400 bp in length. Libraries ware quantified using quantitative real-time PCR with the GenNext NGS Library Quantification Kit (Toyobo). Diluted library DNA was subjected NextSeq sequencers (Illumina) according to the manufacturer's protocols.

value: Human fibroblasts

value: NSD2 (Abcam, ab75359)


title: RNA-Seq of Helianthus annuus SF317: stress R2


title: H3K27ac_veh, biological rep1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B3_ad002


title: Input_DNA


title: input_TGFb12h, biological rep2


title: RNA-Seq of Helianthus annuus SF317: stress R1


title: RNA-Seq of Helianthus annuus SF326: stress R1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B3_ad010


title: input_TGFb12h, biological rep1


title: RNA-Seq of Helianthus annuus SF326: control R3


title: L. interrogans mutant M776 with 10 µM H2O2 repl. #4

city: Paris

first: Rachel

last: Legendre

address: 28, rue du docteur Roux

department: Research and Resource Center for Scientific Informatics

institute: Institut Pasteur

description:
M776 in EMJH with 10 µM H2O2
wt-wtO2-mut-mutO2.complete.txt
mutO4

data_processing:
Reads were cleaned of adapter sequences and low-quality sequences using cutadapt version 1.11
Bowtie version 1.2 with default parameters, was used for alignment on the reference genome (L. interrogans serovar Manilae strain UP-MMC-NIID LP, from MicroScope Platform).
Genes were counted using featureCounts version 1.4.6-p3 from Subreads package (parameters: -t CDS -g locus_tag -s 1)
Count data were analyzed using R version 3.5.1 and the Bioconductor packageDE Seq2 version 1.20.0f. The normalization and dispersion estimation were performed with DESeq2 using the default parameters and statistical tests for differential expression were performed applying the independent filtering algorithm. A generalized linear model was set in order to test for the differential expression between all conditions. For each pairwise comparison, raw p-values were adjusted for multiple testing according to the Benjamini and Hochberg (BH) procedure and genes with an adjusted p-value lower than 0.05 were considered differentially expressed.
Genome_build: interrogans serovar Manilae strain UP-MMC-NIID LP, from MicroScope Platform
Supplementary_files_format_and_content: Matrix from DESeq2

organism: Leptospira interrogans serovar Manilae

source_name: Isolated from liver of infected hamsters

growth_protocol: Leptospira cells were grown aerobically at 30°C in Ellinghausen-McCullough-Johnson-Harris medium (EMJH) with shaking at 100 rpm.

extract_protocol:
Harvested cells were resuspended in 1 ml TRIzol (ThermoFisher Scientific) and stored at -80°C. Nucleic Acids were extracted with chloroform and precipitated with isopropanol as described earlier (Kebouchi et al., 2018). Contaminating genomic DNA was removed by DNAse treatment using the RNAse-free Turbo DNA-freeTM turbo kit (ThermoFisher Scientific) as described by the manufacturer. The integrity of RNAs (RIN > 7.6) was verified by the Agilent Bioanalyzer RNA NanoChips (Agilent technologies, Wilmington, DE).
From 0.5 μg of total RNA, we depleted ribosomal RNAs using the Ribo-Zero rRNA Removal Kit (Bacteria) from Illumina. On these rRNA-depleted RNAs, the sequencing libraries were constructed using the TruSeq Stranded mRNA Sample preparation kit following the manufacturer’s instructions (Illumina). The directional libraries were controlled on Bioanalyzer DNA1000 Chips (Agilent Technologies) and concentrations measured with the Qubit® dsDNA HS Assay Kit (ThermoFisher).  Sequences of 65 bases were generated on the Illumina Hiseq 2500 sequencer.

treatment_protocol: Exponentially grown L. interrogans cells were incubated in the presence or absence of 10 μM H2O2 for 30 min or 1 mM H2O2 for 60 min at 30°C.

tag: genotype

value: Transposon insertion in LMANV2_v2_280031

tag: in vitro passage

value: 2 passages

tag: growth

value: EMJH with 10 µM H2O2


title: RNA-Seq of Helianthus annuus SF317: control R3


title: input_TGFb2h, biological rep2

value: NMuMG


title: L. interrogans mutant M776 with 10 µM H2O2 repl. #3

description:
M776 in EMJH with 10 µM H2O2
wt-wtO2-mut-mutO2.complete.txt
mutO3


title: input_TGFb2h, biological rep1

value: normal murine mammary gland (NMuMG) epithelial cells


title: RNA-Seq of Helianthus annuus SF317: control R2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B2_ad010

tag: brain region

tag: Sex

tag: age


title: L. interrogans mutant M776 with 10 µM H2O2 repl. #2

description:
M776 in EMJH with 10 µM H2O2
wt-wtO2-mut-mutO2.complete.txt
mutO2

tag: strain


title: input_veh, biological rep2

tag: cell line


title: RNA-Seq of Helianthus annuus SF317: control R1

tag: tissue


title: L. interrogans mutant M776 with 10 µM H2O2 repl. #1

description:
M776 in EMJH with 10 µM H2O2
wt-wtO2-mut-mutO2.complete.txt
mutO1


title: RNA-Seq of Helianthus annuus SF279: stress R3


title: input_veh, biological rep1

tag: chip antibody


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B2_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B3_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B2_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B2_ad006


title: L. interrogans mutant M776 repl. #3

description:
M776 in EMJH
wt-wtO2-mut-mutO2.complete.txt
mut3

value: EMJH


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B2_ad012


title: L. interrogans mutant M776 repl. #4

description:
M776 in EMJH
wt-wtO2-mut-mutO2.complete.txt
mut4


title: RNA-Seq of Helianthus annuus SF279: stress R1

tag: cultivar


title: RNA-Seq of Helianthus annuus SF279: stress R2


title: L. interrogans mutant M776 repl. #1

description:
M776 in EMJH
wt-wtO2-mut-mutO2.complete.txt
mut1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B2_ad004


title: L. interrogans mutant M776 repl. #2

description:
M776 in EMJH
wt-wtO2-mut-mutO2.complete.txt
mut2


title: WT L. interrogans with 10 µM H2O2 repl. #4

description:
WT in EMJH with 10 µM H2O2
wt-wtO2-mut-mutO2.complete.txt
wtO4

value: WT


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B2_ad002


title: RNA-Seq of Helianthus annuus SF279: control R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B2_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B12_ad007


title: RNA-Seq of Helianthus annuus SF279: control R1


title: WT L. interrogans with 10 µM H2O2 repl. #3

description:
WT in EMJH with 10 µM H2O2
wt-wtO2-mut-mutO2.complete.txt
wtO3


title: RNA-Seq of Helianthus annuus SF193_SF342: stress R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B12_ad006


title: RNA-Seq of Helianthus annuus SF193_SF342: stress R2


title: WT L. interrogans with 10 µM H2O2 repl. #1

description:
WT in EMJH with 10 µM H2O2
wt-wtO2-mut-mutO2.complete.txt
wtO1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B12_ad004


title: RNA-Seq of Helianthus annuus SF193_SF342: stress R1


title: RNA-Seq of Helianthus annuus SF193_SF342: control R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B12_ad001


title: WT L. interrogans repl. #4

description:
WT in EMJH
wt-wtO2-mut-mutO2.complete.txt
wt4


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B12_ad012


title: WT L. interrogans repl. #3

description:
WT in EMJH
wt-wtO2-mut-mutO2.complete.txt
wt3


title: RNA-Seq of Helianthus annuus SF279: control R2


title: WT L. interrogans repl. #2

description:
WT in EMJH
wt-wtO2-mut-mutO2.complete.txt
wt2


title: RNA-Seq of Helianthus annuus SF193_SF342: control R2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B12_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B12_ad008


title: RNA-Seq of Helianthus annuus SF193_SF326: stress R3


title: WT L. interrogans repl. #1

description:
WT in EMJH
wt-wtO2-mut-mutO2.complete.txt
wt1


title: WT L. interrogans with 1 mM H2O2 replicate #4

description:
WT in EMJH with 1 mM H2O2
wt-wtO2-mut-mutO2.complete.txt
wt-H2O2-4

value: EMJH with 1 mM H2O2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B11_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B11_ad001


title: RNA-Seq of Helianthus annuus SF193_SF326: stress R1


title: WT L. interrogans with 1 mM H2O2 replicate #2

description:
WT in EMJH with 1 mM H2O2
H2O2vsWT.complete.txt
wt-H2O2-2


title: WT L. interrogans with 10 µM H2O2 repl. #2

description:
WT in EMJH with 10 µM H2O2
wt-wtO2-mut-mutO2.complete.txt
wtO2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B11_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B11_ad008


title: RNA-Seq of Helianthus annuus SF193_SF326: control R2


title: RNA-Seq of Helianthus annuus SF193_SF326: control R3


title: WT L. interrogans with 1 mM H2O2 replicate #1

description:
WT in EMJH with 1 mM H2O2
H2O2vsWT.complete.txt
wt-H2O2-1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B11_ad010


title: WT L. interrogans replicate #4

description:
WT in EMJH
H2O2vsWT.complete.txt
wt-4


title: RNA-Seq of Helianthus annuus SF193_SF326: control R1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B11_ad006


title: WT L. interrogans replicate #3

description:
WT in EMJH
H2O2vsWT.complete.txt
wt-3


title: RNA-Seq of Helianthus annuus SF193_SF317: stress R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B11_ad012


title: WT L. interrogans replicate #2

description:
WT in EMJH
H2O2vsWT.complete.txt
wt-2


title: RNA-Seq of Helianthus annuus SF193_SF342: control R1


title: RNA-Seq of Helianthus annuus SF193_SF317: stress R2


title: RNA-Seq of Helianthus annuus SF193_SF317: stress R1


title: WT L. interrogans replicate #1

description:
WT in EMJH
H2O2vsWT.complete.txt
wt-1


title: WT L. interrogans with 1 mM H2O2 replicate #3

description:
WT in EMJH with 1 mM H2O2
H2O2vsWT.complete.txt
wt-H2O2-3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B10_ad010


title: RNA-Seq of Helianthus annuus SF193_SF317: control R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B10_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B10_ad001


title: RNA-Seq of Helianthus annuus SF193_SF317: control R2


title: RNA-Seq of Helianthus annuus SF193_SF326: stress R2


title: RNA-Seq of Helianthus annuus SF193_SF317: control R1


title: RNA-Seq of Helianthus annuus SF193_SF279: stress R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B10_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B10_ad002


title: RNA-Seq of Helianthus annuus SF193_SF279: stress R2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B10_ad007


title: RNA-Seq of Helianthus annuus SF193_SF279: stress R1


title: ascending.194LDLR.HO

description: gene expression of ascending aorta tissue from mouse 194 with homozygous-mutated LDLR (miRNA)

hyb_protocol: Each slide was hybridized with 100ng Cy3-labeled RNA using miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) in hybridization Oven (Cat # G2545A, Agilent technologies, Santa Clara, CA, US) at 55°C，20 rpm for 20 hours according to the manufacturer’s instructions, hybridization section. After hybridization, slides were washed in staining dishes (Cat # 121, Thermo Shandon, Waltham, MA, US) with Gene Expression Wash Buffer Kit (Cat #5188-5327, Agilent technologies, Santa Clara, CA, US).

scan_protocol: Slides were scanned by Agilent Microarray Scanner (Cat # G2565CA, Agilent technologies, Santa Clara, CA, US) and Feature Extraction software 10.7 (Agilent technologies, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by Quantile algorithm, included in the R package AgiMicroRna(López-Romero, P. BMC Genomics. 2011.).

source_name: ascending aorta tissue from mouse 194 with homozygous mutated LDLR

label_protocol: miRNA molecular in total RNA was labeled by miRNA Complete Labeling and Hyb Kit (Cat # 5190-0456, Agilent technologies, Santa Clara, CA, US) followed the manufacturer’s instructions, labeling section.

extract_protocol: Total RNA was extracted and purified using mirVana™ miRNA Isolation Kit without phenol (Cat # AM1561, Ambion, Austin, TX, US), following the manufacturer’s instructions and checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

value: ascending aorta tissue

value: mutated


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B1_ad008


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B1_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B1_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B1_ad004


title: ascending.184LDLR.HO

description: gene expression of ascending aorta tissue from mouse 184 with homozygous-mutated LDLR (miRNA)

source_name: ascending aorta tissue from mouse 184 with homozygous mutated LDLR


title: ascending.158LDLR.WT

description: gene expression of ascending aorta tissue from mouse 158 with widetype LDLR (miRNA)

value: wild type


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B1_ad010

source_name: C57BL/6J Male P56 Mouse Brain


title: uterine tissue_PKRASWT_1406

city: Houston

first: Kwong-Kwok

last: Wong

state: TX

address: T4-3900, 1515 Holcombe Boulevard

department: Gynecologic Oncology and Reproductive Medicine

institute: UT M. D. Anderson Cancer Center

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were processed with RNA-seq workflow in CLC Genomics Workbench version 12. Reads were mapped to mouse reference genome GRCm38 with default setting.
Gene expression is estimated with the EM estimation algorithm and reported as TPM (Transcripts Per Million)
Genome_build: GRCm38
Supplementary_files_format_and_content: TPM

source_name: uterine tissue

extract_protocol:
Total RNA were extracted from mouse uterine tissues that have been stored in RNAlater solution using Qiagen RNeasy Mini Kit.
Sequencing libraries were prepared using KAPA Stranded mRNA seq Kit and run in a single lane using Illumina HiSeq 4000 or NextSeq500 instruments.

tag: genetic background

value: Ahmr-Cre Pten flox/flox

value: mixed C57BL/6 x 129

value: 15 weeks

value: uterine tissue


title: uterine tissue_PKRASWT_13

value: 14 weeks


title: RNA-Seq of Helianthus annuus SF193_SF279: control R2

value: leaves

value: Control plants - water status FTSW = 1.


title: RNA-Seq of Helianthus annuus SF193_SF279: control R1


title: uterine tissue_PKRASWT_1

value: 19 weeks


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B1_ad007

value: PAL

value: male


title: RNA-Seq of Helianthus annuus SF193: stress R2

extract_protocol: Leaves were cut without their petiole and immediately frozen in liquid nitrogen (greenhouse) or in dry ice (field). Grinding was performed using a ZM200 grinder (Retsch, Haan, Germany) with a 0.5-mm sieve. Total RNA was extracted using QIAzol Lysis Reagent following the manufacturer s instructions (Qiagen, Dusseldorf, Germany). The RNA quality was checked by electrophoresis on an agarose gel and quality and quantity were assessed using the Agilent RNA 6000 nano kit (Agilent, Santa Clara, CA, USA). Sequencing was performed on the Illumina HiSeq 2000 by DNAVision (Charleroi, Belgium) as paired-end libraries (2*100 bp, oriented) using the TruSeq sample preparation kit (Illumina San Diego, CA, USA) according to manufacturer s instructions.

value: Stressed plants - water status FTSW = 0.1.


title: ascending.187LDLR.WT

description: gene expression of ascending aorta tissue from mouse 187 with widetype LDLR (miRNA)


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B1_ad006


title: RNA-Seq of Helianthus annuus SF193: stress R1


title: ascending.179LDLR.HO

description: gene expression of ascending aorta tissue from mouse 179 with homozygous-mutated LDLR (miRNA)

source_name: ascending aorta tissue from mouse 179 with homozygous mutated LDLR


title: uterine tissue_PKRASG12V_1402


title: ascending.133LDLR.WT

description: gene expression of ascending aorta tissue from mouse 133 with widetype LDLR (miRNA)


title: S3: ETFA shRNA-2#

city: Beijing

first: Jiyan

last: Zhang

state: China

address: 27 Taiping Road, East Building, Rm0749

institute: Institute of Basic Medical Sciences

description: ETFA knockdown clone-2#

hyb_protocol: MOA v2.1 arrays were pre-heat at 60℃ for 10 mins, rehydrated by 100% ethanol following with deionized water. The slides were pre-hybridized with 5x SSPE, 0.1% SDS and 1% BSA at 42℃ for 2 hour. After the pre-hybridization, 5 µg Cy5-labeled aRNA was hybridize on MOA in the presentation of the Phalanx OneArray hybridization buffer in duplication.

scan_protocol: MOA v2.1 The arrays were scanned by Agilent Microarray Scanner (G2505C)  0.1 XDR protocol and quantify the fluoresence intensity.

data_processing: Data processing was performed and calculated by Rosetta Resolver® (Rosetta Biosoftware). The probes that ﬂag <0 in all samples were filtered out, then normalized by median scaling method between technical replicates. Pair-wise comparisons between samples were calculated by Rosetta error model and presented by log2 ratio and p-value.

source_name: SMMC-7721 stable clone expressing ETFA shRNA-2#

label_protocol: 1 µg of total RNA was reverse-transcribed and amplified using MessageAmpTM aRNA Amplification Kit (Ambion).  Indirect labeling the aa-UTP whereon by NHS-CyDye (Cy5, Amershan).

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, 100 U/ml penicillin, and 100 g/ml streptomycin and were maintained at 37 ºC with 5% CO2.

extract_protocol: RNA extraction by Trizol Reagent (Invitrogen). RNA purity was checked by optical density of NanoDrop ND-1000 and agarose electrophoresis with the result of A260/A280≧1.8, A260/A230≧1.5, no gDNA contamination. RNA integrity was measured by Agilent RNA 6000 Nano Assay (RIN≧6).

value: SMMC-7721 human hepatoma cells


title: S1: Control shRNA

description: Control clone

source_name: SMMC-7721 stable clone expressing non-targeting control shRNA


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B1_ad001


title: S2: ETFA shRNA-1#

description: ETFA knockdown clone-1#

source_name: SMMC-7721 stable clone expressing ETFA shRNA-1#


title: uterine tissue_PKRASG12V_980

value: 20 weeks


title: uterine tissue_PKRASG12V_928

value: 22 weeks


title: RNA-Seq of Helianthus annuus SF193: control R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A9_ad012


title: RNA-Seq of Helianthus annuus SF193: stress R3


title: RNA-Seq of Helianthus annuus SF193: control R2


title: uterine tissue_PKRASG12D_38


title: RNA-Seq of Helianthus annuus SF109_SF342: stress R3


title: RNA-Seq of Helianthus annuus SF193: control R1


title: uterine tissue_PKRASG12D_10


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A9_ad010


title: RNA-Seq of Helianthus annuus SF109_SF342: stress R2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A9_ad006


title: uterine tissue_PKRASG12D_1416


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A9_ad008


title: RNA-Seq of Helianthus annuus SF109_SF342: stress R1


title: RNA-Seq of Helianthus annuus SF109_SF342: control R2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A9_ad001


title: RNA-Seq of Helianthus annuus SF109_SF342: control R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A9_ad004


title: uterine tissue_PKRASG12D_217

value: 21 weeks


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A9_ad007


title: RNA-Seq of Helianthus annuus SF109_SF342: control R1


title: RNA-Seq of Helianthus annuus SF109_SF326: stress R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A8_ad002


title: TR_Rx_m.musSol_wt_32d_3

city: Lowell

first: Matthew

middle: J

last: Gage

state: MA

address: One University Avenue

institute: University of Massachusetts Lowell

description: Soleus wt rep3

data_processing:
Adaptor trimming was performs while obtaining the fastq files from initial BCL files from the sequencing facility
Base quality and the adaptor contmination in the reads were checked using FastQC software and no adapter contamination was detected. Fastq files with a per base quality score below 20 were preprocessed using the sliding window quality filtering (window size 4) in Trimmomatic v0.32
The insert sizes between paired-end reads were calculated using the Galaxy web platform. A subset of 250,000 reads from each sample was aligned to the built-in reference mouse genome (mm10) using the default settings in the BWA-aln. The CollectInsertSizeMetrics Picard tool was used to generate the alignment statistics.
The calculated average insert sizes and standard deviations of each sample were used as input paramentes along with the forwardand reverse read files to map reads to  Ensembl Mus musculus GRCm38.p4 genome using Tophat v2.1.1.
Gene-wise read counts were generated using R libraries GenomicFeatures v1.34.3 and GenomicAlignments v1.18.1. If a particular gene contain less than 10 reads aligned to at least one replicate of a muscle, such genes were considered as marginally expressed genes and removed from the dataset before downstream data analysis.
Genome_build: GRCm38.p4
Supplementary_files_format_and_content: .txt

source_name: Soleus

extract_protocol:
Muscle samples stored in RNAlater™ stabilization solution were thawed and total RNA was extracted frusing Qiagen fibrous tissue total RNA extraction mini kit
200ng of total RNA were subjected cDNA library synthesis using an Illumina TruSeq Stranded Total RNA Library Prep kit.

treatment_protocol: Extracted muscle tissues were stored in RNAlater™ stabilization solution (ThermoFisher Scientific) at -80°C before RNA extraction

value: B6C3Fe a/a-Ttnmdm/J

value: Soleus

value: Wild type


title: RNA-Seq of Helianthus annuus SF109_SF326: stress R2


title: TR_Rx_m.musSol_wt_44d_2

description: Soleus wt rep2

value: F


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A8_ad001

data_processing:
Library strategy: snmC-seq2
Reads trimed with Cutadapt for adapters and low quality bases (Phred score >= 20)
The resulting files are mapped to in-silico bisulfite converted mm10 reference genome using Bismark.
The raw BAM file will be filtered using samtools to filter reads by MAPQ > 10 and use Picard to remove PCR duplicates
Tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls will be generated with in-house developing package using the filtered BAM files
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files (ALLC files) describing the quantity of unmethylated and methylated cytosine base calls. Columns are: 1. Chromosome, 2. Position, 3. Strand, 4. Cytosin Context, 5. methylated base call, 6. total mapped base call, 7. not used, place holder column

extract_protocol:
the brain of P56 male C57BL/6J mouse will be removed and cut into 600 microns thick coronal sections using a tissue matrix. Then each region will be microdissected from the coronal tissue sections based on identified landmarks and brain atlas coordinates, as defined in Allen brain atlas CCF3 (Avaliable at: http://atlas.brain-map.org). For each dissection region, the tissue from several littermate mice will be combined together into to separate replicate groups. The number of animals in a replicate depends on the size of the tissue. Nuclei preparation will be stained with the fluorescently labeled anti-NeuN body and nucleic acid stain Hoechst 33342.
Library prepared following protocol discribed in Luo, Chongyuan, Angeline Rivkin, Jingtian Zhou, Justin P. Sandoval, Laurie Kurihara, Jacinta Lucero, Rosa Castanon, et al. 2018. “Robust Single-Cell DNA Methylome Profiling with snmC-seq2.” Nature Communications 9 (1): 3824.


title: TR_Rx_m.musSol_wt_42d_1

description: Soleus wt rep1

value: M


title: TR_Rx_m.musPso_wt_44d_3

description: Psoas wt rep3

source_name: Psoas

value: Psoas


title: RNA-Seq of Helianthus annuus SF109_SF326: stress R1


title: TR_Rx_m.musPso_wt_54d_2

description: Psoas wt rep2


title: RNA-Seq of Helianthus annuus SF109_SF326: control R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A8_ad008


title: RNA-Seq of Helianthus annuus SF109_SF326: control R2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A8_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A8_ad010


title: TR_Rx_m.musSol_wt_44d_4

description: Soleus wt rep4


title: TR_Rx_m.musEDL_wt_44d_3

description: EDL wt rep3

source_name: Extensor digitorum longus

value: Extensor digitorum longus


title: RNA-Seq of Helianthus annuus SF109_SF317: stress R3

value: leaves


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A8_ad006


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A7_ad002


title: TR_Rx_m.musEDL_wt_42d_1

description: EDL wt rep1


title: TR_Rx_m.musEDL_wt_54d_2

description: EDL wt rep2


title: RNA-Seq of Helianthus annuus SF109_SF326: control R1

value: Control plants - water status FTSW = 1.


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A8_ad007


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A7_ad001


title: RNA-Seq of Helianthus annuus SF109_SF317: stress R2


title: RNA-Seq of Helianthus annuus SF109_SF317: stress R1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A7_ad010


title: CTRL-4

city: Lyon

first: Arnaud

last: Vigneron

address: 28 rue Laënnec

department: INSERM UMR1052, CNRS UMR5286

institute: Centre de recherche en cancérologie de Lyon

data_processing:
Demultiplexing step of raw sequencing data (NextSeq™ 500 -Illumina,v2.15.0 ) :  bcl2fastq v2.19.1.403
Quality control of raw data after demultiplexing step : FastQC v0.11.5  (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
Alignment file generation: STAR v2.5.2b (2-pass mode)
Read counting and RPKM: GFOLD V1.1.4 (option: count; https://bitbucket.org/feeldead/gfold/)
Genome_build: GRCm38, version M16 (Ensembl 91)
Supplementary_files_format_and_content: Excel table file with raw count for each sample
Supplementary_files_format_and_content: Excel table files with RPKM value for each sample

source_name: Liver extract

extract_protocol:
Livers were harvested after cervical dislocation, rinsed with NaCL 0,9% and water and flash frozen in liquid nitrogen. Total RNA were extracted with RNeasy Mini Kit (Qiagen,74106) and quantified with NanoView Spectrophotometer.
mRNA were isolated with NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) from 1 µg of total RNA and RNAseq libraries were prepared from isolated mRNA with NEBNext® UltraII Directional RNA Library Prep Kit for Illumina (NEB,E7760)

value: FVB/NCrl

tag: dphp concentration


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A7_ad012

value: PAL


title: RNA-Seq of Helianthus annuus SF109_SF317: control R3

tag: treatment


title: CTRL-2


title: CerebralWhiteMatter_10

city: Ribeirão Preto

first: Carlos

middle: Alberto

last: Scrideli

state: São Paulo

address: Avenida Bandeirantes 3900

department: Pediatrics

country: Brazil

institute: Ribeirao Preto Medicine School - University of Sao Paulo

hyb_protocol: The labeled RNA was purified (MicroBioSpin 6, Bio-Rad, 732-6221), hybridized (overnight for 20 hours at 55°C and 20 rpm) and washed (Agilent, 5188-5327) before scanning.

scan_protocol: Microarray slides were scanned at 535 nm with 5 μm/pixel resolution using a DNA Microarray Scanner with SureScan High-Resolution Technology (Agilent Technologies) and the fluorescent intensities were determined by the Feature Extraction Software Version 11.5 (Agilent Technologies), to obtain Processed Signals (resulting from all intra-array pre-processing, including background corrections)  corresponding to the transcript levels.

data_processing:
The microRNA library was constructed using 100ng of total RNA and investigated with Agilent Human microRNA Microarray Kit (v3) (G4470C, Agilent Technologies, Santa Clara, CA, USA) to determine the expression prolife of microRNAs according manufacturer's instructions. This array contains 866 human and 89 human viral microRNAs sequences. Each miRNA species is printed 20 times with replicate probes on the array. Spot images were processed by Feature Extraction Software v10.7.3.1 (Agilent Technologies, Santa Clara, CA, USA) using AgiMicroRna AFE package (Agilent Feature Extraction) from the Bioconductor library in R. As recommended by AgiMicroRna AFE package, to make direct comparisons of data coming from different chips it is important to remove sources of variation of non-biological nature that may exists between arrays. Normalization is the attempt to compensate for systematic technical differences between chips, to see more clearly the biological differences between samples. Thus, the gTotalGeneSignal was normalized between arrays using the quantile method. The AFE attach to each feature a flag that identifies different quantification errors of the signal that can be used to filter out the microRNAs that do not reach a minimum of quality. Thus, the data were then filtered using a filterMicroRna to remove control features (to remove gene that are not detected (gIsGeneDetected = 0), and to filter out microRNAs which expression do not reach a certain level based on the expression of the negative controls.
The spot images were processed with Feature Extraction Software v10.7.3.1 (Agilent Technologies). Each miRNA microarray was analyzed with respect to signal intensity, background signal, as well as internal control blade and spike in controls. Box-plot was generated in order to determine the distribution of signals from each spot on each microarray as well as sample integrity and quality.

source_name: Cerebral white matter

label_protocol: The microRNA library was constructed using 100 ng of total RNA and investigated with the Agilent  Human microRNA Microarray Kit (v3)” (G4470C, Agilent Technologies, Santa Clara, CA, USA) to determine the expression profile of microRNAs according to manufacturer’s instructions. This array contains 866 human and 89 human viral microRNA sequences. Each miRNA species is printed 20 times with replicate probes on the array.

extract_protocol: Fresh surgical tissues were immediately snap-frozen in liquid nitrogen, stored at -80ºC and microdissected prior to RNA extraction. Total cellular RNA was extracted using TRIzol LS Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. The RNA was reverse transcribed to single-stranded cDNA using the high capacity kit (Applied Biosystems, Foster City, CA, USA).

tag: tissue type

value: Non-neoplastic Cerebral White Matter


title: CerebralWhiteMatter_12


title: TR_Rx_m.musPso_wt_42d_1

description: Psoas wt rep1


title: RNA-Seq of Helianthus annuus SF193_SF279: control R3


title: RNA-Seq of Helianthus annuus SF109_SF317: control R2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A7_ad006

value: male


title: CerebralWhiteMatter_9


title: CTRL-1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A7_ad004


title: CerebralWhiteMatter_8


title: RNA-Seq of Helianthus annuus SF109_SF279: stress R3

value: Stressed plants - water status FTSW = 0.1.


title: C3-3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A7_ad008


title: CTRL-3


title: RNA-Seq of Helianthus annuus SF109_SF279: stress R2


title: C3-2


title: CerebralWhiteMatter_11


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A6_ad006


title: CerebralWhiteMatter_7


title: RNA-Seq of Helianthus annuus SF109_SF279: stress R1


title: CerebralWhiteMatter_5


title: C3-1


title: CerebralWhiteMatter_4


title: RNA-Seq of Helianthus annuus SF109_SF279: control R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A6_ad004


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A6_ad008


title: RNA-Seq of Helianthus annuus SF109_SF279: control R2


title: C2-4


title: C2-3


title: RNA-Seq of Helianthus annuus SF109_SF317: control R1


title: CerebralWhiteMatter_3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A6_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A5_ad010


title: C3-4


title: C2-2


title: RNA-Seq of Helianthus annuus SF109: stress R3


title: CerebralWhiteMatter_6


title: CEMBA181016_5H_1_CEMBA181016_5H_2_B10_ad012


title: C2-1


title: RNA-Seq of Helianthus annuus SF109: stress R2


title: CerebralWhiteMatter_1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A6_ad002


title: C1-4


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A5_ad004


title: RNA-Seq of Helianthus annuus SF109: stress R1


title: C1-3


title: GBped_9_tumor

source_name: Glioblastoma, tumor, pediatric patient

tag: subject status

value: Glioblastoma pediatric patient

tag: subject id

value: patient 9

value: primary Glioblastoma (GBM) tumor

tag: gender

value: female

tag: age at diagnosis

tag: vital status

value: dead


title: C1-2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A5_ad002

tag: brain region


title: RNA-Seq of Helianthus annuus SF109_SF279: control R1

source_name: leaves


title: CerebralWhiteMatter_2


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A5_ad008

tag: Sex


title: C1-1


title: RNA-Seq of Helianthus annuus SF109: control R2


title: RNA-Seq of Helianthus annuus SF109: control R3


title: RNA-Seq of Helianthus annuus SF109: control R1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A4_ad001

tag: age


title: RNA-Seq of Helianthus annuus SF092_SF342: stress R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A4_ad002

tag: strain


title: TGFb2h

data_processing:
Library strategy: DnaseI-seq
One independent biological replicates of DNaseI-seq data were processed (trimmed, aligned, filtered, and quality controlled) for each condition independently using the ATAC-seq pipeline from the Kundaje lab with specific options for DnaseI-seq (https://github.com/ENCODE-DCC/atac-seq-pipeline).
The model-based analysis of ChIP-seq macs2 (v2.1.2) was used to identify the peak regions with options -B, -q 0.01–nomodel, -f BAM, -g mm9. The Irreproducible Discovery Rate (IDR) method was used to identify reproducible peaks between two biological replicates. Only peaks reproducible between the two biological replicates (with IDR ≤ 0.05) were retained for downstream analyses
BamCoverage from Deeptools suite was used to create bigWig files using RPKM normalization
Genome_build: mm9 mouse reference genome
Supplementary_files_format_and_content: bed

source_name: NMuMG cell line

extract_protocol:
DNase I hypersensitivity mapping was performed as previously described [1] with brief modifications. NMuMG cells were either vehicle or TGFβ1-treated for 2h. The cells were trypsinized and pelleted before washing and resuspension in buffer A (15 mM Tris-Cl (pH 8.0), 15 mM NaCl, 60 mM KCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0), 0.5 mM spermidine and 0.15 mM spermine). Nuclei were extracted by adding buffer A containing NP-40. The nuclei were washed with buffer A and resuspended in prewarmed lysis buffer at a concentration of 5 M/ml and then digested with 75 units of DNase I (Roche) for 5 min at 37 °C. The reactions were terminated by the addition of an equal volume of stop buffer and incubated at 55 °C. After 15 min, proteinase K (final concentration of 20 μg/ml) was added to each digestion reaction and incubated for 16 h at 55 °C. DNA was extracted by careful phenol-chloroform purification using phase-lock gel. DNA fragments of 50–300 bp were selected using low-melting agarose gel and was purified using GenElute Gel Extraction Kit (Sigma-Aldrich).
DNA was again purified using MinElute PCR Purification kit and libraries were prepared using Rubicon Genomics ThruPLEX-FD (R40012) and were sequenced using Illumina NextSeq 500  system (Illumina) with 50 bp paired-end reads.

treatment_protocol: NMuMG cells were washed with phosphate-buffered saline (PBS), changed to serum-free and insulin-free medium for 6 hours and then treated with 5 ng/ml TGFβ1 diluted in 4 mM HCl, 1 mg/ml BSA (240-B, R&D Systems) for 2 hours; or 4 mM HCl 1 mg/ml BSA as control (vehicle).

value: Cells treated with 5 ng/ml of TGFbeta1 for 2 hours  (after 6 hours of serum and insulin starvation)

tag: tissue origin

value: mammary gland

tag: cell line

value: NMuMG cell line


title: Veh

value: Cells treated with vehicle (Tris-HCl, BSA) for 2 hours (after 6 hours of serum and insulin starvation)


title: GBped_7_tumor

value: patient 7

value: alive


title: GBped_4_tumor

value: patient 4


title: GBped_6_tumor

value: patient 6


title: GBped_8_tumor

value: patient 8

value: loss to follow up


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A5_ad001

value: PAL

value: male


title: GBped_5_tumor

value: Glioblastoma pediatric patient

value: patient 5


title: GBped_3_tumor

value: patient 3

value: primary Glioblastoma (GBM) tumor


title: RNA-Seq of Helianthus annuus SF092_SF342: control R3

tag: tissue

value: leaves

value: Control plants - water status FTSW = 1.


title: GBped_2_tumor

value: patient 2

value: dead


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A4_ad010


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A5_ad007


title: RNA-Seq of Helianthus annuus SF092_SF342: stress R2

tag: cultivar

value: Stressed plants - water status FTSW = 0.1.


title: TGFb2h, FBS

data_processing:
One independent biological replicates of ATAC-seq data were processed (trimmed, aligned, filtered, and quality controlled) for each condition independently using the ATAC-seq pipeline from the Kundaje lab (https://github.com/ENCODE-DCC/atac-seq-pipeline).
The model-based analysis of ChIP-seq macs2 (v2.1.2) was used to identify the peak regions with options -B, -q 0.01–nomodel, -f BAM, -g mm9. The Irreproducible Discovery Rate (IDR) method was used to identify reproducible peaks between two biological replicates. Only peaks reproducible between the two biological replicates (with IDR ≤ 0.05) were retained for downstream analyses
BamCoverage from Deeptools suite was used to create bigWig files using RPKM normalization
Genome_build: mm9 mouse reference genome
Supplementary_files_format_and_content: bed

extract_protocol:
The ATAC experiments were performed as described (Buenrostro et al., 2013). NMuMG cells were either vehicle or TGFβ-treated for 2 or 12h, and then collected and treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina).
DNA was purified using MinElute PCR Purification Kit (Qiagen). All samples were then amplified by PCR using NEBNextHigh-Fidelity 2× PCR Master Mix (New Englands Labs) with primers containing a barcode to generate libraries. DNA was again purified using MinElute PCR Purification kit and samples were sequenced using Illumina NextSeq 500 system (Illumina) with 75 bp paired-end reads

treatment_protocol: For TGFβ10m experiment, cells were washed with phosphate-buffered saline (PBS), changed to serum-free and insulin-free medium for 6 hours and then treated with 5 ng/ml TGFβ1 diluted in 4 mM HCl, 1 mg/ml BSA (240-B, R&D Systems) for 10 minutes; or 4 mM HCl 1 mg/ml BSA as control (vehicle). For FBS experiment, cells were grown in complete medium and treated with 5 ng/ml TGFβ1 diluted in 4 mM HCl, 1 mg/ml BSA (240-B, R&D Systems) for 2 hours; or 4 mM HCl 1 mg/ml BSA as control (vehicle).

value: Cells treated with 5 ng/mL TGFbeta1 for 2 hours (in complete medium)

value: mammary gland

value: NMuMG cell line


title: RNA-Seq of Helianthus annuus SF092_SF342: stress R1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A4_ad008


title: TGFb10m, exp10m

value: Cells treated with TGFbeta1 (Tris-HCl, BSA) for 2 hours  (after 6 hours of serum and insulin starvation)


title: veh, FBS

value: Cells treated with vehicle (Tris-HCl, BSA)L  for 2 hours (in complete medium)


title: RNA-Seq of Helianthus annuus SF092_SF342: control R2


title: Veh, exp10m

value: Cells treated with vehicle (Tris-HCl, BSA) for 10 minutes (after 6 hours of serum and insulin starvation)


title: GBped_1_tumor

value: patient 1

value: female


title: PQ

city: New york

first: Jihye

last: Paik

state: NY

address: 1300 York Ave.

department: Pathology

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.17 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the UCSC mm9 mouse reference genome using tophat v2.0.11.
Transcript abundances was estimated in Reads Per Kilobase of exon per Million mapped reads (RPKM) by using Cufflinks v2.1.1 package.
Genome_build: mm9
Supplementary_files_format_and_content: excel file including gene name, RefSeq id, locus, FPKM value of each gene in each sample

source_name: NPCs

growth_protocol: NPCs were cultured with N2 media including 20 ng/ml of EGF and bFGF.

extract_protocol:
Total RNA was extracted with NuceloSpin RNA extraction kit (MN#740955.250) followed by manufacturer's instructions. Briefly, the brains were lysed with 350 uL of lysis buffer (RA) and cleaned with Nucleospin filter. Added the 70% EtOH to bound RNA to RNA column. After digest genomic DNA with DNase, the columns were washed with provided wash solutions and eluted RNA with 30 uL of RNase free water. The RNA concentrations were determined with NanoDrop.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: NPCs were treated with or without 5uM Paraquat for 48 hours

tag: cell type

value: NPCs

tag: genotype/variation

value: Ink/Ark knockout

value: paraquat


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A4_ad007

value: PAL

value: male


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A4_ad004


title: RNA-Seq of Helianthus annuus SF092_SF342: control R1

value: leaves

tag: treatment

value: Control plants - water status FTSW = 1.


title: GBadu_20_tumor

source_name: Glioblastoma, tumor, adult patient

value: Glioblastoma adult patient

value: patient 20

tag: tissue type

value: primary Glioblastoma (GBM) tumor

value: dead


title: GBadu_19_tumor

tag: subject status

value: patient 19


title: RNA-Seq of Helianthus annuus SF092_SF326: stress R2

value: Stressed plants - water status FTSW = 0.1.


title: Con

value: control


title: RNA-Seq of Helianthus annuus SF092_SF326: stress R1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A3_ad002


title: RNA-Seq of Helianthus annuus SF092_SF326: control R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A3_ad001


title: GBadu_16_tumor

tag: subject id

value: patient 16

value: loss to follow up


title: GBadu_15_tumor

value: patient 15

tag: gender


title: GBadu_17_tumor

value: patient 17

value: female

tag: age at diagnosis


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A3_ad010


title: RNA-Seq of Helianthus annuus SF092_SF326: control R2


title: GBadu_18_tumor

value: patient 18

tag: vital status


title: GBadu_14_tumor

value: patient 14


title: GBadu_13_tumor

value: patient 13

value: male


title: RNA-Seq of Helianthus annuus SF092_SF317: stress R3

value: leaves


title: RNA-Seq of Helianthus annuus SF092_SF326: control R1

value: Control plants - water status FTSW = 1.


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A3_ad012

tag: brain region

value: PAL


title: RNA-Seq of Helianthus annuus SF092_SF326: stress R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A3_ad004

tag: Sex


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A4_ad006

tag: age


title: GBadu_11_tumor

value: Glioblastoma adult patient

value: patient 11

value: primary Glioblastoma (GBM) tumor


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A3_ad006

tag: strain


title: GBadu_10_tumor

value: patient 10

value: dead


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A2_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A2_ad007


title: GBadu_9_tumor

value: patient 9


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A2_ad002


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A3_ad007


title: GBadu_8_tumor

value: patient 8


title: GBadu_7_tumor

value: patient 7


title: RNA-Seq of Helianthus annuus SF092_SF317: control R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A2_ad008


title: RNA-Seq of Helianthus annuus SF092_SF317: stress R2

value: Stressed plants - water status FTSW = 0.1.


title: RNA-Seq of Helianthus annuus SF092_SF279: stress R3


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A2_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A2_ad004


title: GBadu_6_tumor

value: patient 6


title: RNA-Seq of Helianthus annuus SF092_SF317: control R1


title: RNA-Seq of Helianthus annuus SF092_SF317: control R2


title: RNA-Seq of Helianthus annuus SF092_SF279: stress R2


title: RNA-Seq of Helianthus annuus SF092_SF317: stress R1


title: GBadu_5_tumor

value: patient 5


title: TGFb12h, biological rep2 [ATAC-seq]

data_processing:
Two independent biological replicates of ATAC-seq data were processed (trimmed, aligned, filtered, and quality controlled) for each condition independently using the ATAC-seq pipeline from the Kundaje lab (https://github.com/ENCODE-DCC/atac-seq-pipeline).
The model-based analysis of ChIP-seq macs2 (v2.1.2) was used to identify the peak regions with options -B, -q 0.01–nomodel, -f BAM, -g mm9. The Irreproducible Discovery Rate (IDR) method was used to identify reproducible peaks between two biological replicates. Only peaks reproducible between the two biological replicates (with IDR ≤ 0.05) were retained for downstream analyses
BamCoverage from Deeptools suite was used to create bigWig files using RPKM normalization
Genome_build: mm9 mouse reference genome
Supplementary_files_format_and_content: bed

value: NMuMG

value: normal murine mammary gland (NMuMG) epithelial cells

value: 5 ng/mL TGFβ1 for 12 hours

tag: molecule subtype

value: tagmentated DNA


title: GBadu_12_tumor

value: patient 12

value: male


title: RNA-Seq of Helianthus annuus SF092_SF279: stress R1

value: leaves


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A2_ad010

value: PAL


title: GBadu_4_tumor

value: Glioblastoma adult patient

value: patient 4

value: primary Glioblastoma (GBM) tumor

value: female


title: TGFb12h, biological rep1 [ATAC-seq]

tag: cell line


title: RNA-Seq of Helianthus annuus SF092_SF279: control R3

tag: tissue

value: Control plants - water status FTSW = 1.


title: GBadu_3_tumor

value: patient 3

value: loss to follow up


title: TGFb2h, biological rep2 [ATAC-seq]

value: 5 ng/mL TGFβ1 for 2 hours


title: RNA-Seq of Helianthus annuus SF092_SF279: control R2

tag: cultivar


title: TGFb2h, biological rep1 [ATAC-seq]

tag: cell type


title: RNA-Seq of Helianthus annuus SF092_SF279: control R1


title: GBadu_2_tumor

value: patient 2

value: dead


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A12_ad012


title: GBadu_1_tumor

value: patient 1


title: veh, biological rep2 [ATAC-seq]

value: NMuMG

value: normal murine mammary gland (NMuMG) epithelial cells

value: vehicle (Tris-HCl, BSA) for 2 hours


title: RNA-Seq of Helianthus annuus SF092: stress R1

value: Stressed plants - water status FTSW = 0.1.


title: RNA-Seq of Helianthus annuus SF092: stress R3

value: leaves


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A12_ad006

value: PAL

value: male


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A12_ad010


title: veh, biological rep1 [ATAC-seq]

value: tagmentated DNA


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A11_ad006


title: RNA-Seq of Helianthus annuus SF092: control R3


title: NSD2_siRNA-2

data_processing:
Basecalls and conversion to FASTQ files were performed using MiSeq Control Software(MCS) /Real Time Analysis (RTA) (Illumina).
Low quality reads were trimmed out using Trimmmomatic (Galaxy v.0.36.3).
Reads were alignmened onto the human reference genome hg19 using HISAT2 algorithm (Galaxy v.2.1.0) with gene annotation file obtained from iGenomes (Illumina).
Uniquely mapped reads were extracted using SAMTOOLS Filter SAM or BAM, output SAM or BAM (Galaxy v.1.8).
Gene expression levels were calculated using featureCounts (Galaxy v.1.6.2) with gene annotation file obtained from iGenomes (Illumina).
Genome_build: hg19
Supplementary_files_format_and_content: Differentially expressed genes in NSD2-KD cells were calculated using DESeq2 algorithm (Galaxy v.2.11.40.2) compared with Ctr-KD cells.

source_name: Growing IMR-90 cells

extract_protocol:
Total RNA was extracted using Trizol reagent.
Messenger RNA was purified using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs). Libraries were synthesized using the NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Cells were transfected with siRNA for 24 h.

value: Human fibroblasts

tag: sirna


title: NSD2_siRNA-3


title: RNA-Seq of Helianthus annuus SF092: control R2

tag: treatment


title: RJ-2

city: Oklahoma City

first: Jonathan

middle: D

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes and Human Disease

institute: Oklahoma Medical Research Foundation

data_processing:
Fastqs aligned to GRCh38 and processed using Strand-NGS software
Genome_build: GRCh38
Supplementary_files_format_and_content: normalized data

source_name: HCT116 cells

growth_protocol: HCT116 cells were grown in DMEM supplemented with 10% fetal calf serum in a 5% CO2 containing atmosphere.

extract_protocol: RNA was isolated with TriZol. After this first isolation, RNA was further purified with the Qiagen RNA easy mini kit and finally dissolved in water.

treatment_protocol: Cells were transduced with retrovirus expressing shRNA control or two different ETV1 shRNAs. Cells were then selected with 1 ug/ml puromycin.

value: colorectal tumor tissue

value: transduced with retrovirus

tag: expression

value: shRNA ETV1 #1


title: RJ-3

value: shRNA ETV1 #5


title: RJ-1

value: shRNA control


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A11_ad004

city: La Jolla

first: Joseph

last: Ecker

address: 10010 North Torrey Pines Road

institute: HHMI-Salk-Institute

source_name: C57BL/6J Male P56 Mouse Brain


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A12_ad007


title: S18-EBNA2Con-input-Rep2

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

data_processing:
Illumina Casava1.7 software used for basecalling.
ChIP-seq rawdata were filtered by fastp(version 0.19.6) with default parameters.
ChIP-seq reads were mapped to the hg38 genome assembly using bowtie2 (version 2.20.8) with parameters (-p 6, --sensitive);
Uniq mapped  ChIP-seq reads pairs were got after pcr duplication removing by Picard (version version 2.20.8) and samtools (version 1.3.1);
RPKM normalized BigWig files of  ChIP-seq were generated by bedtools (version 2.29.2);
Bed files of ChIP-seq were got from Bam file by using HOMER (version 4.10.4) with parameters (-style histone).
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using bamCoverage with normalized values for each Sample,and bed files were generated using pos2bed.pl after peak calling using findPeaks.

source_name: CNE2 cells (S18)

growth_protocol: CNE2 cells (S18) were cultured at 37℃ and 5% CO2 in  complete medium: RPMI 1640 medium  supplemented with 10% fetal bovine serum, 100U ml-1 penicillin/streptomycin.

extract_protocol: 1 x 10e6 S18 cells were washed by 1x PBS. Discard supernatant and try to remove residue，and then the cells were Resuspended by 500μL Cell lysis buffer.After incubation on ice for 10 mins，cells were centrifuged at 2000rpm for 5min at 4℃. Resuspend the cells by 100μL digestion buffer，and then incubate in 37℃ 5mins. Add 4μl of 0.2M EDTA/EGTA to stop digestion. After adding 500μL IP dilution buffer，chromatin were precipitated by antibody and rotated for 12 hours. Followed by washing buffer, protein G beads were added to samples. Samples were eluted by 50ul ChIP-elution buffer.

treatment_protocol: Two replicate was Doxycycline 10ug/ml treated for 24 hours.

value: Human  nasopharyngeal carcinoma cells

tag: chip antibody

value: untreated


title: S18-EBNA2Con-input-Rep1


title: NSD2_siRNA-1


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A12_ad008


title: RNA-Seq of Helianthus annuus SF092: control R1

data_processing: The transcriptomic study was performed with the EdgeR package version 3.16.5 on R version 3.3.3 (Another Canoe).CPM were computed with the cpm function from the edgeR package. 30,831 genes were found with at least 3 CPM in 3 libraries. Count normalization was performed as described in the edgeR user guide with the calcNormFactors function using the TMM method (Trimmed Mean normalization).

extract_protocol: Leaves were cut without their petiole and immediately frozen in liquid nitrogen (greenhouse) or in dry ice (field). Grinding was performed using a ZM200 grinder (Retsch, Haan, Germany) with a 0.5-mm sieve. Total RNA was extracted using QIAzol Lysis Reagent following the manufacturers instructions (Qiagen, Dusseldorf, Germany). The RNA quality was checked by electrophoresis on an agarose gel and quality and quantity were assessed using the Agilent RNA 6000 nano kit (Agilent, Santa Clara, CA, USA). Sequencing was performed on the Illumina HiSeq 2000 by DNAVision (Charleroi, Belgium) as paired-end libraries (2*100 bp, oriented) using the TruSeq sample preparation kit (Illumina San Diego, CA, USA) according to manufacturers instructions.

value: Control plants - water status FTSW = 1.


title: S18-EBNA2Dox10ug-H3K27ac-rep2

value: H3K27ac (Abcam, ChIP Grade ab4729)

value: Doxycycline 10ug/ml treated for 24 hours


title: S18-EBNA2Dox10ug-input-rep1


title: Ctr_siRNA_rep2

value: Ctr


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A12_ad001


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A11_ad012


title: CEMBA181016_5H_1_CEMBA181016_5H_2_A11_ad002