title: Zscan4 OE ESC IP of H3K4me1

city: Tainjin

first: Weiyu

last: Zhang

address: No.38 Tongyan Road, Jinnan District

institute: Nankai University

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt with parameters " -q 5 -m 30 -n 4 -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", then sequence reads were mapped to mm10 genome using Bowtie2 with parameters "-5 1 --very-sensitive -p 20 -I 0 -X 1000 --no-mixed --no-discordant --un-conc-gz".
Enrichment bigwig file was generated by bamCompare from Deeptools with parameter "--scaleFactorsMethod readCount -e --minMappingQuality 1 --samFlagExclude 256 --pseudocount -1 --operation ratio"
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file of histone enrichment

growth_protocol: Mouse J1 embryonic stem cells (ESCs) were cultured under 5% CO2 at 37℃ on well plate coated with 0.2% gelatin (Sigma), in medium (Hyclone) that supplement with15% FBS (Hyclone), 10ng/ml mLIF (GeneScript), 1% Penicillin-Streptomycin (Solarbiol), 1% GlutaMAX(Solarbio), 1% nonessential amino acids(Gibco), 0.1 mM β-mercaptoethanol (Sigma).

extract_protocol:
Cells were lysed and chromatin was extracted. Anti-H3K27ac, anti-H3K4me1 and anti-H3K27ac antibodies were used to immunoprecipiate FLAG-Zscan4 in mESCs. Proteins on chromatin associated with Zscan4 was digested and chromatin was decrosslinked at 65 degree overnight. DNA was extracted in phenol-chloroform.
For ChIP-seq, 5ng of Zscan4-assocated chromatin DNA was used in ChIP-seq library preparation.  Libraries were prepared according to Illumina protocols and library fragments of ~250 bp were used for sequencing.

treatment_protocol: The CDS region of Zscan4c was cloned into pCMV-FLAG vector.WT mESCs were transfected with 1000ng pCMV-tag2 vector. After transfection for 24h, the cells were treated with 500ug/ml G418 for 10 days and the medium were changed every 24h, then we picked monoclonal cells.

tag: strain background

tag: genotype/variation

value: Zscan4 overexpression

value: embryonic stem cells (ESCs)


title: HSC3_Rep1

status: Public on Jul 08 2019

type: SRA

city: Buffalo

first: Satrajit

last: Sinha

state: NY

address: 701 Ellicott Street

department: Department of Biochemistry

country: USA

institute: State University of New York at Buffalo

description: featureCounts_HNSCC_Cell_Lines_RNA_Seq.Counts

library_source: transcriptomic

data_processing:
Reads were mapped to the Homo sapiens genome (GRCH37 build) with TopHat2 (v2.1.1),using Bowtie2 (v2.2.6) as the underlying aligner.
Reads aligning to the Ensembl GRCH37 build were quantified with featureCounts (v1.5.0).
Gene-level counts were normalized and used to calculate TPM values.
Genome_build: GRCH37
Supplementary_files_format_and_content: featureCounts output containing gene-level read count summaries for each RNA-Seq sample

molecule: total RNA

organism: Homo sapiens

extract_protocol:
RNA was extracted from HNSCC Cell Lines using the Direct-zol RNA Mini-Prep kit.
Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.

tag: cell line


title: HR10_SCC

city: Houston

first: Kenneth

last: Tsai

state: TX

address: 2130 West Holcombe Blvd , LSP9.4218

department: Dermatology & Translational Molecular Pathology

institute: University of Texas MD Anderson Cancer Center

data_processing:
The mRNA-seq paired-end reads were aligned to the mouse genome build UCSC mm10 (NCBI 38), using the MOSAIK alignment software. The overlaps between aligned reads and annotated genomic features, such as genes/exons were counted using HTSeq software.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file includes HTSeq counts

organism: Mus musculus

source_name: skin

extract_protocol:
RNA was extracted from tissues by homogenizing in TRIZOL reagent and purified using Purelink Kits (Invitrogen).
Libraries were prepared in accordance with standard protocols for the Illumina HiSeq platform.

tag: cell type

value: cuSCC

tag: tissue

value: skin


title: HR10_PAP

value: papilloma


title: SCC47_Rep1


title: Zscan4 OE ESC input of H3K4me1

country: China

library_source: genomic

molecule: genomic DNA


title: Wildtype ESC IP of H3K4me1

value: Wildytpe

tag: chip antibody


title: latTII1b_rep1_tech2

city: Princeton

first: Chen

last: Cao

state: New Jersey

address: Icahn lab

department: Lewis-Sigler Institute for Integrative Genomics

institute: Princeton University

data_processing:
Basecalls performed using RTA version 1.18.64.0
Concatenated fastq files from both lanes of flowcell
Demultiplexed reads using barcode_splitter 0.18.2 (https://bitbucket.org/princeton_genomics/barcode_splitter)
Single cell analysis (alignment, cell identification, gene counts, etc.) performed by CellRanger count version 2.0.1
Single cell analysis by Seurat (v2.3.4) and URD (v1.0.0)
Genome_build: Genome used was (Ciona intestinalis (KH2012, Ghost Database) plus mchsv40 and cfpsv40 inserts
Supplementary_files_format_and_content: 10x Cell Ranger HDF5 formatted matrix files

molecule: polyA RNA

organism: Ciona intestinalis

source_name: late tail bud II_whole embryo

extract_protocol:
For each sample, 100 to 500 morphologically normal embryos were transferred into tubes pre-coated with 5% BSA in Ca2+-free artificial sea water (Ca2+-free ASW, 10mM KCl, 40mM MgCl2, 15mM MgSO4, 435 mM NaCl, 2.5mM NaHCO3, 7mM Tris base, 13mM Tris-HCl). Embryos were immediately dissociated with 0.5 to 1% trypsin in Ca2+-free ASW with 5 mM EGTA (ASW-EGTA) for 2min (gastrula and neurula stages) to 10min (tailbud stages). Embryos were pipetted 5min on ice to complete dissociation of individual cells.  Then, the digestion was inhibited with 0.2% BSA in Ca2+-free ASW or quenched by 20% FBS. Cells were collected by centrifugation at 4°C at 500g for 2 to 5min and then resuspended in ice-cold Ca2+-free ASW containing 0.5% BSA. For the swimming larva stage, the embryos were either homogenized (H100, Waverly) and dissociated using 1% trypsin or dissociated with 1% trypsin, 1mg/ml collagenase, 0.5% pronase and 0.5mg/ml cellulase in ASW EGTA. Once dissociated, the enzymes were inhibited by 20% FBS and 2mg/ml Glycine.
For all the samples, cells were lysed, cDNAs were barcoded and amplified with Chromium Single Cell 3’ Library and Gel Bead Kit v2 (10x Genomics, CA) following the instructions of the manufacturer. Illumina sequencing libraries were prepared from the cDNA samples using the Nextera DNA library prep kit (Illumina, CA). All the libraries were sequenced on Illumina HiSeq 2500 Rapid flowcells (Illumina Inc., CA) with paired-end 26nt + 125nt reads following standard Illumina protocols.

tag: developmental stage

value: late tail bud II

value: whole embryo

tag: replicates

value: biological replicate 1_technical replicate 2


title: HR10_CHR

value: nonlesional,chronically UV-exposed skin (NS)


title: CAL27_Rep3


title: Wildtype ESC input of H3K4me1


title: latTII1a_rep1_tech1

value: biological replicate 1_technical replicate 1


title: CAL27_Rep2


title: latTI2_rep2

source_name: late tail bud I_whole embryo

value: late tail bud I

value: biological replicate 2


title: CAL27_Rep1


title: Zscan4 OE ESC IP of H3K27ac


title: WT-Ang_16-1

city: Singapore

first: Aida

last: Moreno-Moral

address: 8 College Road

country: Singapore

institute: Duke-NUS Medical School

data_processing:
RNA-seq reads were assessed for quality, aligned to m38 (Ensembl Gene annotation build 89 using STAR 2.5.2b)
RNA-seq reads were quantified with RSEM 1.2.31
Genome_build: Ensembl Gene annotation build 89 (m38)
Supplementary_files_format_and_content: TPM values for all genes (TPM_genes.txt)
Supplementary_files_format_and_content: Gene counts for all genes from RSEM (raw_gene_counts.txt)

source_name: Mouse heart left ventricle

growth_protocol: WWP2 mut/wt mice were generated based on C57BL/6J in the laboratory of Dr. Weiping Yu at Agency for Science, Technology and Research (A*STAR), Singapore by CRISPR/Cas9 technology as previously reported [38, 39]. Briefly, mutant animals were generated by co-injection of Cas9 mRNA and individual gRNAs into one-cell mouse embryos. Founder animals carrying the indel mutations were identified first by PCR and T7 endonuclease I assay, and then by deep sequencing of the PCR products. Founders carrying the desired reading frame shift mutations were used to generate mutation-segregated heterozygous F1 animals by crossing with the wild type animals.  Homozygous mutant animals were generated by heterozygote crossing and used for experiments in comparison with the wild type littermates.

extract_protocol:
Total RNA from tissue was isolated from left ventricles of 9 Wwp2Mut/Mut and 9 WT mice with 28 days of Angiotensin II infusion.
mRNA libraries were constructed from poly(A)-selected RNA using the NEBNext Ultra Directional RNA library prep kit (Illumina, New England BioLabs)

treatment_protocol: Alzet mini osmotic pump (Model No. 1004, Durect Corporation) was subcutaneuously implanted in eight-weeks old mice anaesthetized with 2% isoflurane. Miniosmotic pumps loaded with  Angiotensin II (Sigma Aldrich, #A9525) were implanted to deliver Ang II at 500ng/kg/min for a period of 4 weeks.

tag: stimulation

value: Angiotensin II 500ng/kg/min 28 days

tag: genotype

value: WT


title: Zscan4 OE ESC IP of H3K14ac


title: latTI1b_rep1_tech2


title: HR9_PAP


title: HSC3_Rep2


title: latTI1a_rep1_tech1


title: HR9_CHR


title: SCC25_ETS1_501A

description: Processed file generated by running IDR on SCC25_ETS1_C20_Rep1, SCC25_ETS1_C20_Rep2 and SCC25_ETS1_501A ChIPs

data_processing:
Raw sequencing reads were mapped to the Homo Sapiens genome (hg19 build) using Bowtie v1.1.1 with the following parameters: m = 1.
Pooled data files were generated using replicates with merge function in samtools v1.3
Genome_build: hg19
Supplementary_files_format_and_content: Bed File

extract_protocol:
Chromatin was extracted from Mesenchymal HNSCC Cell Line (SCC25) using a low SDS shearing kit (Diagenode: C01020010). Lysates were sonicated with a Bioruptor for 30-40 min. IPs were carried out using the Active-Motif High Sensitivity ChIP Kit using the C20 (Santa Cruz) and 501A (Bethyl Labs) antibodies for ETS1.
Libraries were prepared using ThruPLEX DNA-seq kits from Rubicon Genomics. The samples were then 50 bp single-end sequenced on an Illumina HiSeq 2500.

tag: antibody

value: 501A (Bethyl Labs) antibodies for ETS1


title: Zscan4 OE ESC input of H3K27ac and H3K14ac


title: HR8_SCC


title: latTII2_rep2


title: SCC25_ETS1_C20_Rep2

value: C20 (Santa Cruz) antibodies for ETS1


title: Wildtype ESC IP of H3K27ac


title: HR8_PAP


title: SCC25_ETS1_C20_Rep1


title: midTII2_rep2

source_name: middle tail bud II_whole embryo

value: middle tail bud II


title: Wildtype ESC IP of H3K14ac

value: embryonic stem cells (ESCs)


title: HR8_CHR


title: midTII1_rep1

value: biological replicate 1


title: HR9_SCC

value: cuSCC

value: skin


title: Hfq_RIPseq: PNIP-1

first: Nicholas

last: De Lay

state: Texas

address: 6431 Fannin St

department: Microbiology and Molecular Genetics

institute: University of Texas Health Science Center

description: processed data file : none

data_processing:
Illumina adapters and low-quality ends < 20 Phred were trimmed using Cutadapt version version 1.16 with the parameters -m 18 -q 20,20 -a AGATCGGAAGAGC -A AGATCGGAAGAGC. Reads were mapped to the Escherichia coli MG1655 genome (NC_000913.3) using bwa-mem version 0.7.13-r1126 with the parameters -t 24 -v 3 -r 1 -I 150,50,600,1.
Quantification of gene counts was performed using featureCounts version 1.6.2 using parameters -T 24 -s 2 -p -B -C. Differential gene expression analysis and normalized gene counts were calculated using the DESeq2 R package, version 1.22.1.
Identification of mRNA fragments in Hfq input samples was performed by using DESeq2 to identify significantly increased expression in the Δpnp Hfq Input versus the wild type Hfq Input over 5 nt segments tiled over the entire genome. Contiguous segments of 60 nt or greater were merged as individual fragments, and those fragments with a log2 fold change > 1.5, a z-score of fragment versus local Δpnp coverage > 1.0, and average Δpnp coverage > 300 were retained.
Genome_build: NC_000913.3
Supplementary_files_format_and_content: Supplemental Table S3.xlsx: differentially expressed genes. Supplemental Table S4.xlsx: mRNA fragments upregulated in the absence of pnp. counts_HfqIP_WTIN_PNIN_WTIP_PNIP.txt: gene counts for WTIN, PNIN, WTIP, and PNIP.  counts_KR10000_NRD999.txt: gene counts for KR10000 and NRD999.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: cells

growth_protocol: Strains were grown with aeration in LB broth at 37°C to an OD600 of 1.0

extract_protocol:
RNA was isolated using hot phenol-chloroform and alcohol precipitation
Libraries of total RNA samples were generated by removing DNA by DNase treatment (DNase Turbo; Ambion), depleting rRNA using the Ribo-Zero rRNA Removal Kit for gram-negative bacteria (Illumina), and subsequently utilizing the TruSeq Stranded Total RNA Library Kit (Illumina). Libraries of Hfq input and IP samples were generated by applying the RNA Fragmentation Kit (Ambion), removing 5' triphosphates via RNA 5' polyphosphatase (Epicenter), and subsequently utilizing the TruSeq Small RNA Library Kit (Illumina).

tag: strain

value: rph-1 delta-pnp

tag: molecule subtype

value: Hfq IP output, fragmented RNA (rRNA-depleted)


title: earTI2_rep2

source_name: early tail bud I_whole embryo

value: early tail bud I

value: whole embryo


title: Hfq_RIPseq: PNIP-2

description: processed data file : none


title: HR7_SCC


title: Hfq_RIPseq: PNIN-2

description: processed data file : none

value: Hfq IP input, fragmented RNA (rRNA-depleted)


title: HR7_PAP

value: papilloma


title: Wildtype ESC input of H3K27ac and H3K14ac

value: Wildytpe


title: HR7_CHR

value: nonlesional,chronically UV-exposed skin (NS)


title: Hfq_RIPseq: PNIN-1

description: processed data file : none


title: earTI1_rep1


title: iniTI2_rep2

source_name: initial tail bud I_whole embryo

value: initial tail bud I

value: biological replicate 2


title: iniTI1_rep1


title: Hfq_RIPseq: WTIP-2

description: processed data file : none


title: OE_Zscan4 rep1

description:
OE_Zscan4_2
OE_gene_table.txt and OE_repName_table.txt

data_processing:
Illumina RTA software used for image identification and basecalling.
Adaptor sequence and low-quality sequence were trimmed by Cutadapt with parameters " -q 5 -m 30 -n 4 -O 1 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT", then sequence reads were mapped to mm10 using Hisat2 with parameters "-5 1 -k 20 -p 25 -I 0 -X 1000 --no-mixed --no-discordant".
Genes were annotated according to Ensembl database.
Transposable element annotations were from UCSC Genome Browser (RepeatMasker).
Fragments were counted using featureCounts with parameter "-s 0 -p -P -d 0 -D 600 -B  -O  -M  --fraction" to retain multi-mapped reads.
The features with low count (mean of count < 5) were filtered and normalized by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Normalized count by DESeq2

source_name: Embryonic stem cell

growth_protocol: Mouse J1 embryonic stem cells (ESCs) were cultured under 5% CO2 at 37℃ on well plate coated with 0.2% gelatin (Sigma),in medium (Hyclone) that supplement with15% FBS (Hyclone),10ng/ml mLIF (GeneScript)，1% Penicillin-Streptomycin (Solarbio),1% GlutaMAX (Solarbio), 1% nonessential amino acids(Gibco), 0.1 mM β-mercaptoethanol (Sigma). .

extract_protocol:
Total RNA was extracted with Trizon Reagen (CWBIO) and was subjected to DNaseI(Thermo Scientific) for 30min
Next generation sequencing library preparations were constructed according to the manufacturer’s protocol (VAHTS mRNA-seq V2 Library Prep Kit for Illumina). The mRNA fragmentation and priming was performed using VAHTSFirst Strand Synthesis Reaction Buffer and VAHTS Random Primers. First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase and the second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix. The purified double-stranded cDNA（byAxyPrep Mag PCR Clean-up (Axygen)was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA, USA).

treatment_protocol: The shRNA of Zscan4 was cloned into pSuper puro vector and the CDS region of Zscan4c was cloned into pCMV-tag2 vector.WT mESCs were transfected with 1000ng pSuper puro vector.After transfection for 24h, the cells were treated with 2ug/ml puromycine for 7days and the medium were changed every 24h，then we picked monoclonal cells。WT mESCs were transfected with 1000ng pCMV-tag2 vector.After transfection for 24h,the cells were treated with 500ug/ml G418 for 10days and the medium were changed every 24h，then we picked monoclonal cells。

value: Zscan4c overexpressed


title: Hfq_RIPseq: WTIP-1

description: processed data file : none


title: HR3_PAP


title: OE_control rep2

description:
OE_Zscan4_Control_4
OE_gene_table.txt and OE_repName_table.txt

value: wild type


title: HR3_SCC


title: Hfq_RIPseq: WTIN-2

description: processed data file : none


title: HR3_CHR


title: latN1_rep1

source_name: late neurula_whole embryo

value: late neurula


title: OE_control rep1

description:
OE_Zscan4_Control_2
OE_gene_table.txt and OE_repName_table.txt


title: Hfq_RIPseq: WTIN-1

description: processed data file : none


title: latN2_rep2


title: HR2_SCC


title: earN2_rep2

source_name: early neurula_whole embryo

value: early neurula


title: earN1_rep1

value: biological replicate 1


title: KD_Zscan4 rep2

description:
KD_Zscan4_2_4
KD_gene_table.txt and KD_repName_table.txt

value: Zscan4 knocked down


title: RNAseq: NRD999-B

description: processed data file : none

value: rph+ delta-pnp

value: total RNA (rRNA-depleted)


title: HR2_PAP

value: skin


title: RNAseq: NRD999-A

description: processed data file : none


title: KD_Zscan4 rep1

description:
KD_Zscan4_2_2
KD_gene_table.txt and KD_repName_table.txt


title: HR2_CHR


title: midG1_rep1

source_name: middle gastrulation_whole embryo

value: middle gastrulation


title: KD_random_control rep1

description:
KD_Zscan4_Control_2
KD_gene_table.txt and KD_repName_table.txt


title: KD_random_control rep2

description:
KD_Zscan4_Control_4
KD_gene_table.txt and KD_repName_table.txt


title: midG2_rep2

value: whole embryo


title: OE_Zscan4 rep2

description:
OE_Zscan4_4
OE_gene_table.txt and OE_repName_table.txt


title: RNAseq: KR10000-A

description: processed data file : none

value: rph+


title: iniG1_rep1

source_name: initial gastrulation_whole embryo

value: initial gastrulation


title: Pig-AEC

status: Public on Jul 07 2019

city: Shenzhen

first: junfang

last: zhang

address: NO.3002 Sungang Road

institute: Institute of Translational Medicine, Shenzhen Second People's Hospital

description:
pig aortic endothelial cells
Pig_kidvsPig_AEC.DEG.txt

data_processing:
All methods are available in the pdf: Methods.TransRef.pdf
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
In this step, clean data (clean reads) were obtained by removing reads containing adapter,reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were aligned TopHat v2.0.12.
HTSeq v0.6.1 was used to count the reads numbers mapped to each gene.
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor.
Differential expression analysis of two conditions was performed using the DEGSeq R package (1.20.0). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.005 and log2(Fold change) of 1 were set as the threshold for significantly differential expression.
Genome_build: Pig: Sscrofa11.1, GCF_000003025.6, ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/
Genome_build: Monkey: Macaca_fascicularis_5.0, GCF_000364345.1, ftp://ftp.ncbi.nlm.nih.gov/genomes/Macaca_fascicularis/
Genome_build: Human: GRCh38, GCA_000001405.15, ftp://ftp.ensembl.org/pub/release-77/fasta/homo_sapiens/dna/
Supplementary_files_format_and_content: text file with normalized read count (all samples) and differential expression statistics (pig samples only).

organism: Sus scrofa

source_name: pig aortic endothelial cells

growth_protocol: cells were cultures in ECM medium (typically 2–3 × 10^6 cells into a T75 flask)

extract_protocol:
Total RNA was extracted using TRIzol solution (Invitrogen, Waltham, MA USA), according to the manufacturer’s protocol. RNA sequencing libraries were constructed using TruSeq RNA Sample Preparation Kit V2(Illumina, San Diego, CA, USA), following the manufacturer’s protocol. In brief, RNA concentration was measured by Nanodrop and the quality was measured by agarose and Agilent 2100.
The RNA sample passed quality control before libary preparation. Following purification, the mRNA was fragmented into small pieces using divalent cations at 94℃ for 5min. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA polymerase I and RNase H. (These cDNA fragments undergo an end-repair process, the addition of a single ‘A’ base, and then ligation of the adapters.) The products were then purified and enriched by PCR (15-cycle) to create the final cDNA library. After purification, quantification, and validation, validated DNA libraries were sequenced on an Illumina Sequencing System (HiSeq2000, San Diego, CA, USA), following the manufacturer’s standard workflow. (This work was carried out by Novogene, Beijing, China).

value: blood vessel

value: GGTA1/CMAH double-knockout

tag: source

value: primary cell


title: q2

description:
pig aortic endothelial cells
gene_exp.gtko.xlsx

data_processing:
Reads were mapped against the pig reference genome (assembly 10.2) with Tophat v.2.1.1, and differential gene and transcript expression analysis of RNA-seq experiments with Cufflinks v.2.2.1.
Genome_build: Sscrofa11.1, GCF_000003025.6, ftp://ftp.ncbi.nlm.nih.gov/genomes/Sus_scrofa/
Supplementary_files_format_and_content: Cuffdiff output

growth_protocol: cells were cultures in ECM medium (typically 2–3 × 106 cells into a T75 flask)

extract_protocol:
Total RNA was extracted using TRIzol solution (Invitrogen, Waltham, MA USA), according to the manufacturer’s protocol. RNA sequencing libraries were constructed using TruSeq RNA Sample Preparation Kit V2(Illumina, San Diego, CA, USA), following the manufacturer’s protocol. In brief, RNA concentration was measured by Nanodrop and the quality was measured by agarose and Agilent 2100.
The RNA sample passed quality control before libary preparation. Following purification, the mRNA was fragmented into small pieces using divalent cationsat 94℃ for 5min. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. This was followed by second strand cDNA synthesis using DNA polymerase I and RNase H. (These cDNA fragments undergo an end-repair process, the addition of a single ‘A’ base, and then ligation of the adapters.) The products were then purified and enriched by PCR (15-cycle) to create the final cDNA library. After purification, quantification, and validation, validated DNA libraries were sequenced on an Illumina Sequencing System (HiSeq2000, San Diego, CA, USA), following the manufacturer’s standard workflow. (This work was carried out by Novegene, Beijing, China).

value: GGTA1 knockout


title: q1

description:
pig renal microvascular endothelial cells
gene_exp.gtko.xlsx

value: kidney


title: Pig-kid

description:
pig renal microvascular endothelial cells
Pig_kidvsPig_AEC.DEG.txt


title: K7

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

country: Germany

institute: Ludwig-Maximilians-Universität München

data_processing:
Basecalling from raw image files was done by RTA 1.18.64 (Illumina) and sequence data were stored in fastq format.
Demultiplexing was done using a custom Demultiplex tool allowing one mismatch in barcode sequence.
Adapter sequences were removed from the 3’ end using a custom tool. Reads were filtered to a minimal length of 20bp allowing 0 mismatches.
The output was mapped to the mouse genome (mm10) using STAR RNA-seq read mapper (v.2.4.1b).
The number of reads was analyzed using HTSeq-count (v1.0.0) and a differential gene expression analysis (CD vs. HFD) was performed using DESeq2 (v1.0.19).
Genome_build: mm10
Supplementary_files_format_and_content: tab seprated file with read counts per gene obtained from HTSeq-count for each sample.

source_name: Spermatozoa

growth_protocol: 16 three-week-old male mice received either a modified D12492 high-fat, high-calorie diet (HFD) (E15741-34; ssniff, Soest, Germany) or a control diet to D12492 (CD) (ssniff) for a period of nine weeks prior to sperm isolation.

extract_protocol:
Total RNA was extracted from purified sperm using the miRNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. The RNA samples were concentrated and purified by an RNA-bead cleanup with Agencourt® RNAClean® XP Beads (Beckman Coulter, Krefeld, Germany).
2 ng of isolated RNA were treated with DNaseI (Thermo Scientific). Afterwards, the RNA was used to generate double-stranded cDNA using the Ovation RNA Seq V2 Kit (NuGEN) according to the manufacturer’s instructions. Sequencing libraries were generated using the Ovation Rapid DR Multiplex System (NuGEN) according to the manufacturer’s instructions. 250 ng of fragmented and purified cDNA were used to prepare the libraries.

treatment_protocol: Motile sperm was isolated and added to QIAZOL buffer (QIAGEN, Hilden, Germany), sonicated with a low amplitude (Bioruptor Plus, Diagenode SA, Seraing, Belgium) for five cycles (30 sec pusle/90 sec rest). The samples were shock frozen in liquid nitrogen and stored at ‑80 °C. Total RNA was extracted from purified sperm using the miRNeasy Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

tag: diet

value: Control diet (CD)

value: Spermatozoa


title: male

city: Bangkok

first: Arin

last: Ngamniyom

address: 114 Sukumvit 23

department: Major in Environment, Faculty of Environmental Culture and Eco-tourism

country: Thailand

institute: Srinakharinwirot University

data_processing:
Base Quality and Phred score relationship with the Illumina CASAVA v1.8 software
Trinity (Grabherr et al., 2011) is the software chosen to complete the transcriptome reconstruction process.
Corset (Davidson et al.,2014) works by clustering contigs based on shared reads, and separates contigs when different expression patterns between samples are observed.
PFAM, the prediction of protein structure domain: HMMER 3.0 package,hmmscan, the evalue threshold is 0.01
GO: based on the protein annotation results of NR and Pfam: Blast2GO v2.5 (Götz et al., 2008)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

organism: Oryzias minutillus

source_name: body

extract_protocol:
RNeasy Mini Kit (Qiagen, Germany)
RNA libraries sequencing using standard Illumina protocols

treatment_protocol: treated with DNase I

value: whole body

tag: Sex

value: male

tag: tag

value: Thailand


title: K6


title: female

value: female


title: K8


title: iniG2_rep2

value: biological replicate 2


title: RNAseq: KR10000-B

description: processed data file : none

value: total RNA (rRNA-depleted)


title: K4


title: K5


title: K3


title: Arid1a KO_DDC_RNA-seq Rep3

city: Shanghai

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

data_processing:
Trimmed reads were aligned to the mouse genome (Mm10, Genome Reference Consortium GRCm38) using TopHat v2.0.6
FPKM (fragments per kilobase of exon per million fragments mapped) values were calculated by Cufflinks using default parameters for gene expression levels
The expression profiles were normalized by Trimmed Mean of M-values (TMM) method and log2 transformed
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include log2 tranformed fpkm values for each Sample

source_name: Arid1a KO_DDC_liver

extract_protocol:
liver were removed, flash frozen on dry ice, total RNA was extracted using Trizol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain background

value: Arid1a hepatocyte-specific KO

value: liver

tag: age

value: postnatal 10 weeks


title: Arid1a KO_DDC_RNA-seq Rep2

tag: genotype/variation


title: Arid1a KO_DDC_RNA-seq Rep1


title: F7

value: High fat diet (HFD)


title: F8


title: F6


title: WT_DDC_RNA-seq Rep3

value: wild type


title: WT_DDC_RNA-seq Rep2


title: WT_DDC_RNA-seq Rep1


title: prostate cancer dominant nodule_ Replicate 2 [C65Y2]

type: RNA

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

description:
raw data file:
C65Y1_C65Y2_US83300186_252665235932_S01_GE2_1105_Oct12_1_2.txt
Gene expression in the surgically removed prostate tumor

hyb_protocol: 825 ng from each of the Cy3 or Cy5 labeled samples were mixed with Gene Expression Hybridization Kit (Agilent Cat # 5188-5242) and the final volume adjusted to 100 µL. The solution was slowly dispensed onto the gasket (Agilent Cat# G2534-60011) placed in the (Agilent) hybridization chamber, the (Agilent) human (4x44k 60 mer features, 4 microarrays per slide) chip with the active face downward was arranged over the gasket and the “sandwich” firmly closed. The samples were hybridized to the array at 65ºC for 17 h in an (Agilent) oven while vertically rotating (10 rot/min) to wet the gasket and asses the mobility of the bubbles.

scan_protocol: The hybridized chip was washed at room temperature using the Gene Expression Wash Pack (Agilent, Cat# 5188-5327) and Stabilization and drying solution (Agilent, Cat# 5185-5979) then immediately scanned with an Agilent G2565CA microarray scanner system with SureScan high resolution technology at 5µm pixel size and 20-bit scan mode.

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Although hybridized with two-color microarrays, data were processed with our standard algorithm as resulted from a one-color microarray. Normalized to the median background subtracted signal of all valid features  in the corresponding channel. A NULL indicates that the feature was not considered because it is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

source_name: prostate cancer dominant nodule

label_protocol: Low Input Quick Amp labeling Kit two-color (Agilent, Cat # 5190-2306) that contains T7 RNA polymerase was used to simultaneously amplify total RNA and the positive controls (RNA Spike in Kit for Two Color, Agilent Cat # 5188-5279), and incorporate cyanine 3 (Cy3) or cyanine 5 (Cy5)-labeled CTP.

growth_protocol: prostatic adenocarcinoma of a 65y old black male with the dominant nodule of Gleason score 4+5=9 in the left posterior quadrant from the apex to the base

extract_protocol: Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE) Total RNA extraction was performed using RNAEasy Minikit (Qiagen, Germantown, MD, USA), following manufacturer's instructions. RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)

treatment_protocol: Radical prostatectomy

value: 65 years old

tag: status

value: prostate cancer dominant nodule Gleason score 4+5=9

value: prostate


title: prostate cancer dominant nodule_ Replicate 3 [C65Y3]

description:
raw data file:
C65Y3_C65YC4_US83300186_252665235932_S01_GE2_1105_Oct12_1_1.txt
Gene expression in the surgically removed prostate tumor

tag: tissue


title: prostate cancer dominant nodule_ Replicate 1 [C65Y1]


title: prostate cancer dominant nodule_ Replicate 4 [C65Y4]


title: cancer free prostate resection margins_Replicate 1 [N65Y1]

description:
raw data file:
N65Y1_N65Y2_US83300186_252665235932_S01_GE2_1105_Oct12_1_4.txt
Gene expression in the surgically removed prostate tumor

source_name: cancer free prostate resection margins

value: prostate cancer free resection margins


title: F5


title: cancer free prostate resection margins_Replicate 4 [N65Y4]

description:
raw data file:
N65Y3_N65Y4_US83300186_252665235932_S01_GE2_1105_Oct12_1_3.txt
Gene expression in the surgically removed prostate tumor


title: cancer free prostate resection margins_Replicate 2 [N65Y2]


title: cancer free prostate resection margins_Replicate 3 [N65Y3]


title: Day_11_14-376

city: Coventry

first: Jan

middle: J

last: Brosens

address: University Hospital Coventry and Warwickshire

department: Warwick Medical School

country: United Kingdom

institute: University of Warwick

data_processing:
Transcriptomic maps of paired-end reads were generated using bowtie-2.2.6, samtools-1.2, and tophat-2.1.0 against the University of California Santa Cruz (UCSC) hg19 reference transcriptome (2014) using the fr-unstranded setting.
Transcript counts were assessed by HTSeq-0.6.1 using stranded-no setting and intersection-non-empty mode and counts were assigned to gene IDs. Transcripts per million (TPM) were calculated according to Wagner et al. (2012) http://www.ncbi.nlm.nih.gov/pubmed/22872506.
Genome_build: hg19
Supplementary_files_format_and_content: [.txt] A tab-delimited text file including TPM values for each sample

source_name: Day 11, Human microdissected endometrial gland

extract_protocol:
Luteinizing hormone (LH)-timed endometrial biopsies were subjected to laser microdissection of the endometrial glands followed by RNA-sequencing. The biopsies were obtained 5, 8 and 11 days after the LH surge, identified by urine test, immediately frozen in liquid nitrogen and then embedded in cryomatrix OCT. Ten micron slices cut in a cryotome were mounted on a membrane slide and stained with 70% (v/v) cresyl violet and 30% (v/v) eosin Y. Endometrial glands were captured using a laser microdissection system. RNA was extracted, quantity was assessed by spectrophotometry and integrity was checked by Agilent 2100 Bioanalyzer system. For all samples, the RNA integrity number (RIN) was above 5 and the rRNA ratio [28s/18s] above 0.9.
Amplified cDNA was obtained from total RNA using NuGen Ovation RNA-Seq System V2. NuGen Ovation Ultralow System V2 1-16 was applied for library preparation and sample barcoding. A 100bp paired end run with Illumina NGS was performed by Wellcome Trust Centre for Human Genomics - High Throughput Genomics, Oxford, UK.

tag: cycle day

tag: live births

tag: pregnancy losses

tag: bmi

value: microdissected endometrial gland


title: F4

value: Spermatozoa


title: Day_11_14-345


title: F3


title: K2

value: Control diet (CD)


title: K1


title: F1


title: F2


title: Day_8_15-011

source_name: Day 8, Human microdissected endometrial gland


title: ctrl_rep6

data_processing:
Basecalling from raw image files was done by RTA 1.18.66.3 (Illumina) and sequence data were stored in fastq format.
Demultiplexing was done using a custom Demultiplex tool allowing one mismatch in barcode sequence.
Adapter sequences were removed from the 3’ end using Galaxy Clip Adaptor Sequence v1.0.0 (seed 10, mismatch 0, minimum length after clipping 20).
The output was mapped to the mouse genome (mm10) using STAR RNA-seq read mapper (Galaxy Version 2.4.1b).
The number of reads was analyzed using Galaxy HTSeq-count v1.0.0 and a differential gene expression analysis (CD vs. HFD) was performed based on the negative binominal distribution using DESeq2 (v1.0.19) setting the FDR < 0.05.
Genome_build: mm10
Supplementary_files_format_and_content: HTseqCount_all: tab seprated file. Data in this file was processed by using HTSeq-count and grouped by genes.

source_name: Oocyte

growth_protocol: Female mice received either a modified D12492 high-fat, high-calorie diet (HFD) (E15741-34; ssniff, Soest, Germany) or D12492 (CD, ssniff) (n=6 in both cohorts), respectively, for a period of nine weeks prior to being mated with vasectomized male mice. During mating, all animals were fed a CD and screened for vaginal plugs every morning and evening.

extract_protocol:
Full-length cDNA of four pooled oocytes was generated using the SMART Seq v4 Ultra Low Input RNA kit for Sequencing (Takara Bio, Mountain View, CA, USA) according to the manufacturer’s instructions. The template switching activity of reverse transcriptases to enrich full-length cDNA as well as the addition of defined PCR adapters directly to the ends of the first strand cDNA define the SMART technology. Amplified cDNA was purified using Agencourt AMPure XP Beads (Beckman Coulter). The obtained full-length cDNA was validated using the Qubit™ fluorimeter (Thermo Fisher Scientific).
The RNA-Sequencing libraries were generated using the tagmentation technology of the NexteraXT Kit (Illumina) following the manufacturer’s instructions. Libraries were purified using Agencourt AMPure XP Beads (Beckman Coulter) and were quantified on the Bioanalyzer.

treatment_protocol: At day 0.5 p.c. female mice were sacrificed by cervical dislocation and oocytes were isolated in M2 medium. Oocytes were washed three times in PBS, separately snap frozen in PBS, and stored at -80 °C until used for further analysis.

value: Oocyte


title: Day_11_15-009


title: ctrl_rep4


title: Day_8_14-129


title: Day_5_14-108

source_name: Day 5, Human microdissected endometrial gland


title: ctrl_rep5


title: ctrl_rep3


title: Day_5_13-281


title: Pl_E12_5_CxRSDel_+-_1

first: Daniel

last: Andergassen

address: Biedersteiner Straße 29

institute: Technical University Munich

data_processing:
RNA sequencing data was aligned to the mm10 genome using STAR (version 2.5.0c). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1). Additional parameters for the STAR alignment were a maximum intron size of 100,000 bp and out-filtering of non-canonical splice junctions.
STAR alignment of ChIPseq data was conducted with different parameters to disable spliced reads, i.e. a maximum intron size of 1, and prevent soft clipping by enforcing end-to-end alignment (--alignEndsType EndToEnd). Reads mapping to multiple locations were excluded using specific parameters (STAR:--outFilterMultimapNmax 1).
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: Placenta

extract_protocol:
RNA was extracted from TRIzol using standard protocols.
The Illumina TruSeq kit was used to create polyA+ libraries from total RNA. We generated strand-specific libraries for tissues collected form the F1 crosses. All the libraries were run on a Bioanalyzer to assess fragment size, and concentration and sequenced on a HiSeq 2000

value: Placenta

tag: brackground strain

value: CAST/EiJxFVB/NJ

value: RSDEL

tag: genotype


title: Day_5_13-235


title: Pl_E12_5_CxRSDel_+-_2

tag: strain


title: Pl_E12_5_CxRSDel_+-_3


title: ctrl_rep2


title: control PANC-1 [C2]

city: HeFei

first: Mei

last: Huang

state: An Hui

address: 17#Lu Jiang Road

department: General surgery

institute: Anhui Provincial Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
Genome_build: hg19
Supplementary_files_format_and_content: Number of raw junction read

source_name: control PANC-1

growth_protocol: PANC-1 cells were obtained from Shanghai Cell Bank. Cells were cultured in RPMI1640 supplemented in 10% fetal bovine serum (FBS) with 100 U/ml penicillin-100 g/ml streptomycin within a humidified incubator containing 5% CO2 at 37 ℃.

extract_protocol:
Total RNA was isolated from tumor tissues and plasma samples using TRIzol reagent (Invitrogen, Carlsbad, CA, USA), according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cell line which was resistant to Gemcitabine was generated by selection under increasing gradient of Gemcitabine in our lab. The initial concentration of Gemcitabine in the cell culture medium was 0.1 µg/ml. The concentration increased when the survival cells entered the logarithmic growth phase. After 40 weeks of continuous Gemcitabine induced culture, the final concentration of Gemcitabine in the resistant cell culture medium reach up to 200 µg/ml. The Gemcitabine resistant cell line was named PANC-1-GR. The PANC-1-GR cell line was cultured in periodically added 10 µg/ml Gemcitabine to maintain cell resistance.

tag: cell line

tag: cell type

value: pancreatic cancer cell line

tag: phenotype

value: control


title: control PANC-1 [C1]


title: Gemcitabine resistant PANC-1-GR [H2]

source_name: Gemcitabine resistant PANC-1-GR

value: Gemcitabine resistant


title: Gemcitabine resistant PANC-1-GR [H1]


title: ctrl_rep1

tag: diet


title: HFD_rep5


title: control PANC-1 [C3]


title: Day_8_14-405


title: HFD_rep4


title: Day_11_15-181


title: Pl_E12_5_RSDelxC_-+_1

value: FVB/NJxCAST/EiJ


title: MLAD 7_96h

city: San Donato Milanese

first: Marco

last: Piccoli

address: piazza Malan 1

country: Italy

institute: IRCCS Policlinico San Donato

description:
IRI + Myriocin treatment
SAMPLE 38

data_processing:
Relative mRNA expression of target genes was normalized to the endogenous RPL13a housekeeping gene.
Target gene expression of LAD and MLAD groups were represented as fold change versus the average expression of all the controls, calculated by the comparative CT method (ΔΔCT Method).
Fold Change data file reports test/control (i.e., LAD vs Sham) ratios.

label: SYBR green

source_name: left ventricle sample - at risk area

label_protocol: PCR assays were performed using the GoTaq®qPCR Master Mix (Promega) following the Manufacturer’s instructions. Reverse transcription was performed from 1000 ng of total mRNA using the iScript™ cDNA synthesis kit (BIORAD). Quantitative real-time PCR were performed (StepOnePlus™ Real-Time PCR System, Applied Biosystems) with 40 cycles at 94°C for 15 seconds and 60°C for 60 seconds.

extract_protocol: Total mRNA was extracted with ReliaPrep™ RNA Tissue Miniprep System (Promega) followed by DNase I treatment (Promega).

treatment_protocol: Ischemia was induced in mice for 30 minutes, by left anterior descending coronary temporary ligature. Solid Lipid Nanocarriers (SLN/Myr 1mM) were diluted in sterile saline (ratio of dilution 1:4). 20µL of the diluted myriocin were injected intramuscle in the left ventricle at reperfusion start.

value: left ventricle

tag: treatment

value: IRI + Myriocin treatment

tag: time

value: 96 hours


title: HFD_rep6

value: High fat diet (HFD)


title: Pl_E12_5_RSDelxC_-+_2

tag: age


title: HFD_rep3


title: Pl_E12_5_CxRSDel_++_3


title: MLAD 6_96h

description:
IRI + Myriocin treatment
SAMPLE 37


title: MLAD 4_96h

description:
IRI + Myriocin treatment
SAMPLE 35


title: MLAD 5_96h

description:
IRI + Myriocin treatment
SAMPLE 36


title: Gemcitabine resistant PANC-1-GR [H3]


title: Pl_E12_5_RSDelxC_-+_3


title: Pl_E12_5_CxRSDel_++_1


title: MLAD 2_96h

description:
IRI + Myriocin treatment
SAMPLE 33


title: Pl_E12_5_CxRSDel_++_2


title: HFD_rep2


title: MLAD 3_96h

description:
IRI + Myriocin treatment
SAMPLE 34


title: HFD_rep1


title: Pl_E12_5_RSDelxC_++_1


title: LAD 7_96h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 31

value: Ischemia and reperfusion injury (IRI)


title: Mon-kid

description:
monkey renal microvascular endothelial cells
Mon_kid.txt

organism: Macaca fascicularis

value: kidney

value: wild type

tag: source

value: primary cell


title: MLAD 1_96h

description:
IRI + Myriocin treatment
SAMPLE 32


title: Pl_E12_5_RSDexlC_++_2


title: ATAC_BECs

data_processing:
aligned signals in raw (bam) files were filtered to remove reads that aligned to multiple locations
Peaks were identified using MACS v1.4 with the p-value cut-off 10-5
Raw signals from individual samples or merged, highly correlated replicates from a given cell type were sorted and indexed using Samtools v1.31 and converted to signal files (bigWig) using DeepTools v2.1.0
ATAC-seq signals were quantile-normalized using Haystack, with 50-bp windows
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Normal hepatocytes and DDC-injured hepatocytes were isolated by a two-step liver collagenase perfusion and followed by gravity purification. The Sox9+ reprogrammed hepatocytes (LPLCs) were isolated by sorting the RFP+ DDC-injured hepatocytes in the BD influx cell sorter based on size/granularity and RFP expression. For the isolation of biliary epithelia cells (BECs), the CK19CreERT2:RFP reporter mice were treated with three individual oral gavage of tamoxifen (150mg/kg) under resting condition. The BECs were then isolated by sorting RFP+ NPCs in the BD influx cell sorter based on size/granularity and RFP expression. Nuclei isolated from 20,000 counted cells were used for transposition reaction with transposase (Vazyme Biotech).
Libraries were prepared with NEBNext High-Fidelity 2x PCR Master Mix (New England Labs Cat #M0541)with 12 cycles

treatment_protocol: Normal hepatocytes and DDC-injured hepatocytes were isolated from adult Arid1a wild type and Arid1a liver specific KO mice livers under resting condition and 2 weeks DDC injury. For the isolation of reprogrammed hepatocytes (LPLCs), a low dosage tamoxifen (50mg/kg), was intraperitoneal injected into the 2 weeks DDC-injured Sox9CreERT2:RFP reporter mice. For the isolation of biliary epithelia cells (BECs), the CK19CreERT2:RFP reporter mice were treated with three individual oral gavage of tamoxifen (150mg/kg) under resting condition.

value: biliary epithelial cells

value: post natal 12 weeks


title: LAD 5_96h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 29


title: LAD 6_96h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 30


title: ATAC_reprogrammed hepatocytes-Rep2

description: ATAC_reprogrammed hepatocytes.bw

source_name: ATAC_reprogrammed hepatocytes

value: hepatocytes

value: post natal 10 weeks


title: LAD 3_96h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 27


title: Pl_E12_5_RSDelxC_++_3

value: Placenta

value: RSDEL


title: LAD 2_96h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 26


title: LAD 1_96h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 25


title: Sham 5_96h

description:
Control
SAMPLE 24

source_name: left ventricle sample

value: Control


title: VE_E12_5_CxRSDel_+-_1

source_name: Visceral yolk sac endoderm

value: Visceral yolk sac endoderm

value: CAST/EiJxFVB/NJ


title: ATAC_reprogrammed hepatocytes-Rep1

description: ATAC_reprogrammed hepatocytes.bw


title: VE_E12_5_CxRSDel_+-_2


title: DDC-KO-H3K27ac

description: S577_05B_CHG024810-Lib11-H3K27ac-arid1a-KO-Lib11-H3K27ac-arid1a-KO-GGCTAC_L005

data_processing:
aligned signals in raw (bam) files were filtered to remove reads that aligned to multiple locations,Duplicate reads were removed using DeepTools v2.1.0
Peaks were identified using MACS v1.4 with the p-value cut-off 10-5 and peaks were filtered to remove peaks that overlap with ENCODE blacklisted regions, as well as peaks mapped to chrX, chrY, chrM.
Raw signals from individual samples were converted to signal files (bigWig) using DeepTools v2.1.0
ChIP-seq signals were quantile-normalized using Haystack, with 50-bp windows
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

source_name: hepatocytes

extract_protocol:
Liver were perfused and hepatocytes were isolated and lysed. Lysates were clarified from sonicated nuclei and Histone-DNA complexes were isolated with antibody.
Purified ChIP DNA was used to prepare sequencing libraries via NEBNext Ultra DNA Library Prep Kit for the Illumina (E7370).

treatment_protocol: The 8 weeks adult WT mice and Arid1a liver specific KO mice were treated under normal diet or DDC diet for 2 weeks.

tag: genotype/variation

value: Arid1a liver-specific KO

value: DDC

tag: chip antibody

value: H3K27ac(ab4729, abcam)


title: Sham 4_96h

description:
Control
SAMPLE 23

tag: tissue

value: left ventricle

value: 96 hours


title: DDC-WT-H3K27ac

description: S577_05B_CHG024809-Lib10-H3K27ac-arid1a-WT-Lib10-H3K27ac-arid1a-WT-TAGCTT_L005

value: Arid1a WT


title: VE_E12_5_CxRSDel_+-_3


title: NoDDC-KO-H3K27ac

description: S0645_12A_CHG027780-CHG027780L-Lib04-39-Alb-plus-Arid1a-H3K27ac-TGACCA_L008

value: NoDDC


title: VE_E12_5_CxRSDel_++_2


title: Sham 1_96h

description:
Control
SAMPLE 20


title: Sham 3_96h

description:
Control
SAMPLE 22


title: VE_E12_5_CxRSDel_++_1


title: Sham 2_96h

description:
Control
SAMPLE 21


title: MLAD 7_24h

description:
IRI + Myriocin treatment
SAMPLE 19

value: IRI + Myriocin treatment

value: 24 hours


title: LAD 4_96h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 28

value: Ischemia and reperfusion injury (IRI)


title: NoDDC-WT-H3K27ac

description: S0645_12A_CHG027778-CHG027778L-Lib02-38-Alb-Arid1a-H3K27ac-CGATGT_L008

value: hepatocytes


title: MLAD 5_24h

description:
IRI + Myriocin treatment
SAMPLE 17


title: MLAD 6_24h

description:
IRI + Myriocin treatment
SAMPLE 18


title: VE_E12_5_CxRSDel_++_3


title: VE_E12_5_RSDelxC_-+_2

value: FVB/NJxCAST/EiJ


title: DDC-WT-H3K4me1

description: S0645_12A_CHG027781-CHG027781L-Lib5-230-Alb-Ari1a-H3k4me1-ACAGTG_L008

value: post natal 10 weeks

value: H3K4me1(ab8895, abcam)


title: MLAD 3_24h

description:
IRI + Myriocin treatment
SAMPLE 15


title: LAD 7_24h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 12


title: VE_E12_5_RSDelxC_-+_3

value: RSDEL


title: LAD 4_24h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 9


title: LAD 5_24h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 10


title: NoDDC-KO-H3K4me1

description: S0645_12A_CHG027779-CHG027779L-Lib3-39-Alb-plus-Ari1a-H3k4me1-TTAGGC_L008


title: VE_E12_5_RSDelxC_++_2

value: Visceral yolk sac endoderm


title: MLAD 4_24h

description:
IRI + Myriocin treatment
SAMPLE 16


title: LAD 3_24h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 8


title: VE_E12_5_RSDelxC_++_3


title: MLAD 2_24h

description:
IRI + Myriocin treatment
SAMPLE 14


title: WT-DDC-Yap-ChIP-seq

description: S577_05B_CHG024807-Lib06-Yap-arid1a-WT-Lib06-Yap-arid1a-WT-GCCAAT_L006

data_processing:
aligned signals in raw (bam) files were filtered to remove reads that aligned to multiple locations,Duplicate reads were removed using DeepTools v2.1.0
Peaks were identified using MACS v1.4 with the p-value cut-off 10-5 and peaks were filtered to remove peaks that overlap with ENCODE blacklisted regions, as well as peaks mapped to chrX, chrY, chrM.
Raw signals from individual samples were converted to signal files (bigWig) using DeepTools v2.1.0
signals were quantile-normalized using Haystack, with 50-bp windows
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

extract_protocol:
Liver were perfused and hepatocytes were isolated and lysed. Lysates were clarified from sonicated nuclei and Yap-DNA complexes were isolated with antibody.
Purified ChIP DNA was used to prepare sequencing libraries via NEBNext Ultra DNA Library Prep Kit for the Illumina (E7370).

treatment_protocol: The 8 weeks adult WT mice and Arid1a liver specific KO mice were treated with DDC diet for 2 weeks.

tag: strain background

value: wild type

value: postnatal 10 weeks

value: Yap (14074 cell signal)


title: VE_E12_5_K27me3_CF_++_1

value: CAST/EiJxFVB/NJ

tag: Sex

value: pooled male and female

value: H3K27me3 Jenuwein antibody 6523, 5th bleed


title: LAD 2_24h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 7

value: left ventricle


title: Arid1a KO-DDC-Yap-ChIP-seq

description: S577_05B_CHG024808-Lib07-Yap-arid1a-KO-Lib07-Yap-arid1a-KO-CAGATC_L006

source_name: Arid1a KO_hepatocytes

value: Arid1a liver-specific  KO


title: ATAC_DDC_KO-Rep2

description:
S603_10A_CHG025520-CHG025520L-N708-CAGAGAGG_L008
ATAC_DDC_KO.bw

value: DDC-diet


title: LAD 1_24h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 6

value: 24 hours


title: Sham 5_24h

description:
Control
SAMPLE 5

value: Control


title: DDC-KO-H3K4me1

description: S0645_12A_CHG027782-CHG027782L-Lib6-234-Alb-plus-Ari1a-H3k4me1-GCCAAT_L008

value: Arid1a liver-specific KO

value: DDC

value: hepatocytes


title: HRGEC

description:
human renal microvascular endothelial cells
HRGEC.txt

value: kidney

value: HRGEC cell line


title: Sham 4_24h

description:
Control
SAMPLE 4


title: MLAD 1_24h

description:
IRI + Myriocin treatment
SAMPLE 13

value: IRI + Myriocin treatment


title: Sham 3_24h

description:
Control
SAMPLE 3


title: LAD 6_24h

description:
Ischemia and reperfusion injury (IRI)
SAMPLE 11

value: Ischemia and reperfusion injury (IRI)


title: Sham 2_24h

description:
Control
SAMPLE 2


title: VE_E12_5_K27me3_CF_++_2

value: Visceral yolk sac endoderm

value: RSDEL


title: Sham 1_24h

description:
Control
SAMPLE 1


title: ATAC_DDC_KO-Rep1

description:
S603_10A_CHG024891-ATAC-Arid1aKO-154-ATAC-Arid1aKO-154-2-CTCTCTAC_L008
ATAC_DDC_KO.bw

value: post natal 10 weeks


title: NoDDC-WT-H3K4me1

description: S0645_12A_CHG027777-CHG027777L-Lib1-38-Alb-Ari1a-H3k4me1-ATCACG_L008

value: Arid1a WT

value: NoDDC

value: H3K4me1(ab8895, abcam)


title: fibroblast_ha2

city: Aurora

first: Philip

middle: D

last: Tatman

state: Colorado

department: Neurosurgery

institute: University of Colorado

data_processing:
fastq files were aligned to either bos tau 8 or rn6 using hisat2
read counts were calculated using Stringtie
Deseq2 was used to geometrically normalize the gene expression
Genome_build: bosTau8 and RN6

organism: Bos taurus

source_name: bovine cardiac fibroblasts_high altitude

extract_protocol:
RNA was isolate using Qiagen RNAeasy kit
illumina trueseq

treatment_protocol: Conditioned media from high altitude bovine fibroblasts was used to treat ARVMs for seven days.

value: bovine cardiac fibroblasts

value: serum from cows living at high altitude


title: arvm_ha211

organism: Rattus norvegicus

source_name: adult rat ventricular myocytes_high altitude

value: Sprague Dawley

value: adult rat ventricular myocytes


title: fibroblast_ha1


title: VE_E12_5_K27me3_FC_++_1

value: FVB/NJxCAST/EiJ

value: pooled male and female

value: H3K27me3 Jenuwein antibody 6523, 5th bleed


title: VE_E12_5_RSDelxC_++_1


title: VE_E12_5_K27me3_FC_++_2


title: fibroblast_co3

source_name: bovine cardiac fibroblasts_control

value: serum from cows living at low altitude (control)


title: arvm_ha209


title: WT-DDC-Input

data_processing:
aligned signals in raw (bam) files were filtered to remove reads that aligned to multiple locations
Peaks were identified using MACS v1.4 with the p-value cut-off 10-5
Raw signals from individual samples or merged, highly correlated replicates from a given cell type were sorted and indexed using Samtools v1.31 and converted to signal files (bigWig) using DeepTools v2.1.0
ChIP-seq signals were quantile-normalized using Haystack, with 500-bp windows
Genome_build: mm10
Supplementary_files_format_and_content: bigwig

value: wild type

value: postnatal 10 weeks

value: hepatocytes


title: arvm_ha2


title: fibroblast_co2


title: arvm_con6

source_name: adult rat ventricular myocytes_control


title: ATAC_DDC_WT-Rep2

description:
S603_10A_CHG025519-CHG025519L-N709-GCTACGCT_L008
ATAC_DDC_WT.bw

value: DDC-diet


title: ATAC_NoDDC_WT-Rep2

description:
S0669_04B_CHG028885-CHG028885L-333-Arid1a-WT-20k-TAGGCATG_L007
ATAC_NoDDC_WT.bw

value: normal diet


title: IP-Ulp2-Flag-1

city: New Haven

first: Hong-Yeoul

last: Ryu

state: CT

address: 266 Whitney Ave

department: MB&B

institute: Yale

data_processing:
ChIP-seq reads were trimmed using the Trim Galore (v0.5.0; http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adaptors
The trimmed reads were then aligned to aligned to the yeast reference genome (sacCer3) using BWA (v0.7.17) (Li 2013).
Peaks were called using MACS2 (v2.1.1) (Feng, Liu et al. 2012)
The normalized bedGraph files were generated using MACS2 ("-B --SPMR") and then converted to bigwig files using the bedGraphToBigWig program downloaded from the website of UCSC Genome Browser.
Genome_build: sacCer3
Supplementary_files_format_and_content: bigwig

organism: Saccharomyces cerevisiae

source_name: Yeast cells

extract_protocol:
ChIP experiments were performed as described previously (Ryu & Ahn, 2014; Ryu et al, 2016). Flag-tagged Ulp2 proteins were precipitated with anti-Flag agarose beads (Sigma). Formaldehyde was added to a final concentration of 1% for 20 min. Cross-linking was quenched by addition of glycine to 240 mM. Cells were collected by centrifugation, washed in 1× TBS, and lysed with glass beads in FA lysis buffer (50 mM HEPES-KOH at pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na deoxycholate, 0.1% SDS, 1 mM PMSF). Chromatin was sheared by sonication, therefore the average fragment size was between 200 and 700 bp.
Approximately 5-10 ng of DNA is cleaned up using Ampure XP SPRI beads (Beckman Coulter Genomics). The DNA is then end-repaired, A-tailed, adapter ligated and PCR enriched (8-10 cycles) using the KAPA Hyper Library Preparation kit (KAPA Biosystems, Part#KK8504). Indexed libraries that meet appropriate cut-offs are quantified by qPCR using the Library Quantification Kit (KAPA Biosystems, Part#KK4854) and inserts size distribution by using the Caliper LabChip GX system. Samples with a yield of ≥0.5 ng/l are used for sequencing.

value: MATa his3-<delta>200 leu2-3,112 lys2-801 trp1-1 ura3-52 ULP2-6xGly-3xFlag::HIS3MX6

value: anti-Flag agarose beads (Sigma)


title: INPUT-Ulp2-Flag-2


title: fibroblast_co1


title: ATAC_NoDDC_KO-Rep2

description:
S0638_09A_CHG026786-CHG026786L-N707-CTCTCTAC_L004
ATAC_NoDDC_KO.bw

value: Arid1a liver-specific  KO

value: post natal 10 weeks


title: ATAC_NoDDC_KO-Rep1

description:
S0638_09A_CHG026785-CHG026785L-N707-CTCTCTAC_L003
ATAC_NoDDC_KO.bw


title: IP-Ulp2-Flag-2


title: INPUT-Ulp2-Flag-1


title: arvm_con4


title: arvm_con5


title: 10X_GBM_IDHwt

city: Rehovot

first: Itay

last: Tirosh

address: Herzl 234

country: Israel

institute: WEIZMANN INSTITUTE OF SCIENCE

data_processing:
Paired-end, 38-base reads were mapped to the UCSC hg19 human transcriptome using Bowtie with parameters "-q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 -S -p 6". Expression values were calculated by   RSEM v1.2.3 in paired-end mode using parameters "--estimate-rspd --paired end -sam -p 6", from which TPM values for each gene  were extracted. For the subset of cells processed with 10X, we use CellRanger with the default parameters.
For cells processed with Smartseq2, we examined as quality control the number of genes detected in each cell. We observed a bimodal distribution and conservatively excluded 28% of the sequenced cells with fewer than 3,000 detected genes. Similarly, for cells processed with the 10X platform, we excluded 26% of the sequenced cells whose number of detected genes was less than half or more than twice the mean number of genes detected across cells coming from the same tumor.
Genome_build: hg19
Supplementary_files_format_and_content: Two tab-delimited files containing TPM values (transcript-per-million reads) for 23,686 genes across 7,930 glioma cells processed with Smartseq2 or for 30,401 genes across 16,201 glioma cells with the 10X platform.

source_name: Glioblastoma single cell

extract_protocol:
RNA from single cells was first purified with Agencourt RNAClean XP beads (Beckman Coulter)
Libraries from isolated single cells were generated based on the Smart-seq2 protocol (Picelli  2014) with the following modifications.oligo-dT were used to prime reverse transcription with Maxima reverse transcriptase and locked TSO oligonucleotide, which was followed by 20 cycle PCR amplification using KAPA HiFi HotStart ReadyMix (KAPA Biosystems) with subsequent Agencourt AMPure XP bead purification as described. Libraries were tagmented using the Nextera XT Library Prep kit (Illumina) with custom barcode adapters (sequences available upon request). Libraries from 384 cells with unique barcodes were combined and sequenced using a NextSeq 500 sequencer (Illumina). For a subset of samples, single cells were processed through the 10X Chromium 3' Single Cell Platform using the Chromium Single Cell 3’ Library, Gel Bead and Chip Kits (10X Genomics, Pleasanton, CA), following the manufacturer’s protocol. Briefly, 7,000 cells were added to each channel of a chip to be partitioned into Gel Beads in Emulsion (GEMs) in the Chromium instrument, followed by cell lysis and barcoded reverse transcription of RNA in the droplets. Breaking of the emulsion was followed by amplification, fragmentation and addition of adapter and sample index.
single cell RNA-seq

treatment_protocol: Fresh tumor tissue was minced with a scalpel and enzymatically dissociated using a gentle papain-based brain tumor dissociation kit (Miltenyi Biotec). Large pieces of debris were removed with a 100 micron strainer, and dissociated cells were layered carefully onto a 5mL density gradient (Lympholyte-H, Cedar Lane labs), which was centrifuged at 2,000 rpm for 10 min at room temperature to pellet dead cells and red blood cells.The interface containing live cells was saved and used for staining and flow cytometry. Tumor cells were blocked in 1% bovine serum albumin in Hanks buffered saline solution (BSA / HBSS). Tumors were first stained first with CD45-Vioblue direct antibody conjugate (clone REA747, Miltenyi Biotec) for 30 min at 4 °C. Cells were washed with cold PBS, and then resuspended in 1 ml of BSA / HBSS containing 1 μM calcein AM (Life Technologies) and 0.33 μM TO-PRO-3 iodide (Life Technologies) to co-stain for 30 min before sorting. For MGH143, CD45 MicroBeads (Miltenyi Biotec) were used to remove immune cells. CD45 negative cells were stained with calcein AM (Life Technologies) for viability and CD24-APC (human antibody, clone REA832, Miltenyi Biotec) and CD44-VioBlue (human antibody, clone REA690, Miltenyi Biotec) to sort subpopulations of viable non-immune cells. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488nm (calcein AM, 530/30 filter), 640nm (TO-PRO-3 or CD24-APC, 670/14 filter), and 405nm (CD45-VioBlue or CD44-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells.Viable single cells were identified as calcein AM positive and TO-PRO-3 negative. We sorted individual, viable, immune and non-immune single cells into 96-well plates containing TCL buffer (Qiagen) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80°C prior to whole transcriptome amplification, library preparation and sequencing. For samples processed on the 10x genomics platform, dead cells were removed from single-cell suspensions using Dead Cell Removal Kit (Miltenyi Biotec).

tag: sample type

value: single cells


title: Smartseq2_GBM_IDHwt


title: ATAC_DDC_WT-Rep1

description:
S603_10A_CHG024890-ATAC-Arid1aWT-152-ATAC-Arid1aWT-152-2-TAGGCATG_L008
ATAC_DDC_WT.bw


title: ATAC_NoDDC_WT-Rep1

description:
S0669_04B_CHG028884-CHG028884L-320-Arid1a-WT-20k-AAGAGGCA_L007
ATAC_NoDDC_WT.bw


title: Embryos, pros-Gal4-UASdap_2

status: Public on Jul 06 2019

city: St Lucia

first: Stefan

last: Thor

state: QLD

address: Otto Bldg (81) room 620

department: School of Biomedical Sciences

country: Australia

institute: University of Queensland

data_processing:
RNA expression profiling and fold change comparison was performed using DNAStar 12.2.0.80, SeqMan NextGen software, using standard settings
Genome_build: CDS, BDGP6, ensemble.org
Supplementary_files_format_and_content: RPKMs

organism: Drosophila melanogaster

source_name: Embryos, pros-Gal4-UASdap

growth_protocol: Drosophila melanogaster embryos, at St15-16, grown at +25C.

extract_protocol:
RNeasy Mini Kit (50) (Qiagen, Hilden, Germany). Two independent samples were analyzed for each genotype. Yields ranged from 10.7 mg to 17.8 mg of total RNA.
Transcriptome sequencing, of polyA purified RNA, was performed by (GeneWhiz, New Jersey, NJ, USA), on one lane of the HiSeq2500 with a 1x50bp single-read sequencing configuration in High Output mode (V4 chemistry).
This yielded from 20.7 to 43.4 million reads per sample.

treatment_protocol: RNA was extracted from control (pros-Gal4/+) and experimental (pros-Gal4/UAS-) embryos.

tag: developmental stage

value: Embryos, Stage 15-16

value: overexpression of wild type dacapo


title: Embryos, pros-Gal4-UASdapCRL4_2

source_name: Embryos, pros-Gal4-UASdapCRL4

tag: genotype

value: overexpression of dacapo[CRL4] (encoding a stabilized Dacapo protein)


title: Embryos, pros-Gal4-UASdapPCNA_1

source_name: Embryos, pros-Gal4-UASdapPCNA

value: overexpression of dacapo[PCNA] (encoding a stabilized Dacapo protein)


title: Embryos, pros-Gal4-UASdapCDI_2

source_name: Embryos, pros-Gal4-UASdapCDI

value: overexpression of dacapo[CDI] (encoding a stabilized Dacapo protein)


title: Embryos, pros-Gal4-UASdapPCNA_2


title: Embryos, pros-Gal4-UASdap_1


title: Embryos, pros-Gal4-UASdapCRL4_1


title: Embryos, Control_pros-Gal4_2

source_name: Embryos, Control_pros-Gal4

value: control


title: Embryos, pros-Gal4-UASdapCDI_1


title: MAN

city: Bielefeld

first: Volker

middle: F.

last: Wendisch

address: Universitaetstr. 25

institute: Universitaet Bielefeld

description: Protocol for whole transcriptome library preparation

data_processing:
The library was prepared and sequenced in paired-end mode following a protocol that allowed for the analysis of the whole transcriptome (Mentz et al., 2013). The base calling was realized with the Illumina instrument software. The sequences were trimmed using the tool Trimmomatic version 0.33 to a minimal length of 35 base pairs
The trimmed reads were mapped to the B. methanolicus MGA3 reference sequences using the software for short read alignment Bowtie (Langmead et al., 2009). The forward and reverse read were combined to one read, containing the reference sequence as an insert, if both reads were present and in inverse orientation in a maximal distance of 1 kb to each other. Sequence reads not fulfilling this criterion were retained as single mapping reads. Paired mappings with a distance larger than 1 kb were discarded from subsequent analyses.
For the visualization of the mapped reads the ReadXplorer software  (Hilker et al. 2014) was used
The differential gene expression analysis was performed with the statistical method DESeq (Anders and Huber, 2010) using the  the ReadXplorer software. In order to designate a gene as differentially expressed, the cut-off values were set to a change in expression level higher than 30, for which the P-value was adjusted to be equal to or less than 0.01.
Genome_build: GenBank accession numbers of chromosome and the two naturally occurying plasmids pBM19 and pBM69: CP007739, CP007741 and CP007740, respectively
Supplementary_files_format_and_content: The Excel file includes raw and processed differential gene expression data

organism: Bacillus methanolicus

source_name: cell culture

growth_protocol: Cells were cultivated in 2 different conditions: either 15 mM mannitol (control) or 15 mM arabitol (test) as sole carbon source.

extract_protocol:
B. methanolicus cells were harvested in the middle of the exponential growth phase followed by total RNA isolation individually for each cultivation condition using the NucleoSpin RNA isolation Kit (Machery-Nagel, Düren, Germany) and the RNase-free DNase set (Qiagen, Hilden, Germany).
Isolated RNA samples (triplicate samples per condition) were pooled in equal parts and the total RNA was subsequently used for the cDNA library preparation. The library was prepared and sequenced on a single flow cell of a MiSeq Desktop Sequencer system (Illumina, San Diego, CA, USA) in paired-end mode following a protocol that allowed for the analysis of the whole transcriptome  (Mentz et al., 2013).

tag: strain

tag: agent

value: 15 mM mannitol


title: Embryos, Control_pros-Gal4_1


title: VCaP_shDtx3L_dox_24hr_R1881, rep 2

city: Charlotesville

first: David

last: Wotton

department: Biochemistry and Molecular Genetics

institute: University of Virginia

data_processing:
Raw FASTQ files were analyzed on the Galaxy server (usegalaxy.org).
Transcripts were quantified using Salmon* (Galaxy version 0.9.1). * Patro et al, Nat Methods 14, 417-419 (2107). Doi: 10.1038/nmeth.4197.
Differential expression was analyzed using the DESeq2 ** package (Galaxy version 2.11.40.2). ** Love et al, Genome Biol. 15, 550 (2014). Doi: 10.1186/s13059-014-0550-8.
Genome_build: hg38
Supplementary_files_format_and_content: comma separated file, including read counts for each sample

source_name: prostate

extract_protocol:
RNA was extracted using the Qiagen RNeasy kit according to the manufacturer’s instructions.
Indexed libraries were made by Hudson Alpha using the standard polyA method.

treatment_protocol: Cells were plated in phenol-free medium supplemented with charcoal-stripped FBS serum for 48-72 hours prior to treatment. Cells were treated for 24hr with 2 nM R1881.

value: VCaP cells


title: VCaP_24hr_R1881  rep 2


title: VCaP_unt  rep 3


title: VCaP_shDtx3L_dox_24hr_R1881, rep 3


title: VCaP_24hr_R1881  rep 3


title: VCaP_unt  rep 2


title: VCaP_shDtx3L_dox_24hr_R1881, rep 1


title: VCaP_shDtx3L_dox_unt, rep 2


title: ARA

value: 15 mM arabitol


title: VCaP_24hr_R1881  rep 1


title: VCaP_shDtx3L_dox_unt, rep 3


title: VCaP_shDtx3L_dox_unt, rep 1


title: fibroblast_ha3

tag: cell type

value: bovine cardiac fibroblasts

value: serum from cows living at high altitude


title: VCaP_unt  rep 1


title: prostate cancer nucleus_ Replicate 4 [C47Y4]

description: Gene expression in the surgically removed prostate tumor

source_name: prostate cancer nucleus

growth_protocol: 47 years old white male with prostatic adenocarcinoma Gleason score 4+5=9 involving 75% of the bilateral lobes

treatment_protocol: Radical prostate resection

value: male

value: 47 years old

tag: status

value: prostate cancer nucleus Gleason score 4+5=9

value: prostate


title: cancer free prostate resection margins_Replicate 4 [N47Y4]

source_name: cancer free prostate resection margins

value: prostate cancer free resection margins


title: prostate cancer nucleus_ Replicate 1 [C47Y1]


title: prostate cancer nucleus_ Replicate 3 [C47Y3]


title: OVA S5

city: Helsinki

first: Harri

last: Alenius

address: Haartmaninkatu 3

department: Human Microbiome Research Program

country: Finland

institute: University of Helsinki

description: OVA-challenged control, replicate 5

hyb_protocol: Labeled cRNAs were hybridized to Agilent 2-color 60-mer oligo arrays according to the manufacturer's recommendations.

scan_protocol: Slides were washed and scanned with Agilent Microarray scanner G2505C, according to the manufacturer's recommendations.

data_processing: Raw intensity values were obtained from Agilent Feature Extraction software and quality checked according to Agilent standard procedures. The median foreground intensities were imported into R software and analyzed with BioConductor package Limma.

source_name: Lung tissue

label_protocol: Samples were amplified using T7 RNA polymerase method and the cRNAs were further labeled with Cy3 and Cy5 dye, according to the manufacturer's recommendations.

growth_protocol: Female BALB/c mice (6-8 weeks old) were housed in groups of four in stainless steel cages, bedded with aspen chip and were provided with standard mouse chow diet and tab water ad lib. 12 h dark/light cycle was used in the animal room temperature being 20-21 degree celcius and humidity of 40-45 %.

extract_protocol: Lung samples were homogenized in TRIsure reagent and total RNA extraction was performed following the instructions provided by the manufacturer. Quantity and quality of the samples was determined by NanoDrop spectrophotometer and Agilent Bioanalyzer 2100, respectively. Samples with RNA integrity number > 8 were selected and independent pools of two RNA samples were used for the analysis.

treatment_protocol: Mice were exposed to CuO, CuO COOH, CuO NH3 or CuO PEG at three doses, 2.5, 10 and 40 mg/mouse/administration via oropharyngeal aspiration on four consecutive days in a mouse model of asthma. Lung tissue samples were collected 24 h after the final exposure, stabilized in RNAlater overnight and stored thereafter at -70ºC.

value: BALB/c

tag: gender

value: Female

tag: sensitization

value: OVA/Alum

tag: challenge

value: OVA

tag: nanomaterial

tag: daily dose


title: PBS S5

description: PBS-challenged control, replicate 5

value: PBS


title: CuO PEG 10 S1

description: PBS-challenged, exposed to 10 μg/day of CuO PEG, replicate 1

value: CuO PEG


title: prostate cancer nucleus_ Replicate 2 [C47Y2]

data_processing:
The resulted Tagged Image File Format (tiffs) obtained through use of (Agilent) Scan Control Software 8.3 were analyzed with (Agilent) Feature Extraction 11.1 software. Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al., Mol Genet Genomics 2012.
Although hybridized with two-color microarrays, data were processed with our standard algorithm as resulted from a one-color microarray. Normalized to the median background subtracted signal of all valid features  in the corresponding channel. A NULL indicates that the feature was not considered because it is a control fetarure, OR is locally corrupted, OR has saturated pixels, OR the median of the foreground signal is less than 2x median of the background signal

tag: age


title: cancer free prostate resection margins_Replicate 1 [N47Y1]


title: CuO NH3 2.5 + OVA S1

description: OVA-challenged, exposed to 2.5 μg/day of CuO NH3, replicate 1

value: CuO NH3


title: cancer free prostate resection margins_Replicate 3 [N47Y3]


title: CuO NH3 10 S1

description: PBS-challenged, exposed to 10 μg/day of CuO NH3, replicate 1


title: CuO 10 S3

description: PBS-challenged, exposed to 10 μg/day of CuO, replicate 3

value: CuO


title: CuO NH3 10 + OVA S1

description: OVA-challenged, exposed to 10 μg/day of CuO NH3, replicate 1


title: CuO 2.5 S2

description: PBS-challenged, exposed to 2.5 μg/day of CuO, replicate 2


title: CuO COOH 10 S3

description: PBS-challenged, exposed to 10 μg/day of CuO COOH, replicate 3

value: CuO COOH


title: CuO 2.5 + OVA S3

description: OVA-challenged, exposed to 2.5 μg/day of CuO, replicate 3


title: CuO PEG 10 + OVA S1

description: OVA-challenged, exposed to 10 μg/day of CuO PEG, replicate 1


title: CuO 2.5 + OVA S1

description: OVA-challenged, exposed to 2.5 μg/day of CuO, replicate 1


title: PBS S3

description: PBS-challenged control, replicate 3


title: CuO COOH 10 S2

description: PBS-challenged, exposed to 10 μg/day of CuO COOH, replicate 2


title: CuO COOH 40 + OVA S3

description: OVA-challenged, exposed to 40 μg/day of CuO COOH, replicate 3


title: cancer free prostate resection margins_Replicate 2 [N47Y2]


title: OVA S3

description: OVA-challenged control, replicate 3


title: CuO 40 + OVA S2

description: OVA-challenged, exposed to 40 μg/day of CuO, replicate 2


title: CuO 2.5 S3

description: PBS-challenged, exposed to 2.5 μg/day of CuO, replicate 3


title: CuO PEG 40 S3

description: PBS-challenged, exposed to 40 μg/day of CuO PEG, replicate 3


title: CuO COOH 2.5 + OVA S3

description: OVA-challenged, exposed to 2.5 μg/day of CuO COOH, replicate 3


title: CuO 10 + OVA S3

description: OVA-challenged, exposed to 10 μg/day of CuO, replicate 3


title: CuO COOH 2.5 + OVA S2

description: OVA-challenged, exposed to 2.5 μg/day of CuO COOH, replicate 2


title: CuO COOH 10 + OVA S1

description: OVA-challenged, exposed to 10 μg/day of CuO COOH, replicate 1


title: CuO 40 S2

description: PBS-challenged, exposed to 40 μg/day of CuO, replicate 2


title: CuO COOH 2.5 S1

description: PBS-challenged, exposed to 2.5 μg/day of CuO COOH, replicate 1


title: CuO 10 S1

description: PBS-challenged, exposed to 10 μg/day of CuO, replicate 1


title: CuO 10 + OVA S1

description: OVA-challenged, exposed to 10 μg/day of CuO, replicate 1


title: CuO PEG 10 S3

description: PBS-challenged, exposed to 10 μg/day of CuO PEG, replicate 3


title: PBS S1

description: PBS-challenged control, replicate 1


title: CuO NH3 40 + OVA S1

description: OVA-challenged, exposed to 40 μg/day of CuO NH3, replicate 1


title: OVA S6

description: OVA-challenged control, replicate 6


title: CuO NH3 10 S4

description: PBS-challenged, exposed to 10 μg/day of CuO NH3, replicate 4


title: CuO NH3 2.5 S3

description: PBS-challenged, exposed to 2.5 μg/day of CuO NH3, replicate 3


title: CuO NH3 2.5 + OVA S3

description: OVA-challenged, exposed to 2.5 μg/day of CuO NH3, replicate 3


title: CuO PEG 40 S2

description: PBS-challenged, exposed to 40 μg/day of CuO PEG, replicate 2


title: CuO PEG 2.5 S2

description: PBS-challenged, exposed to 2.5 μg/day of CuO PEG, replicate 2


title: CuO COOH 40 S1

description: PBS-challenged, exposed to 40 μg/day of CuO COOH, replicate 1


title: CuO PEG 40 + OVA S1

description: OVA-challenged, exposed to 40 μg/day of CuO PEG, replicate 1


title: CuO NH3 10 S2

description: PBS-challenged, exposed to 10 μg/day of CuO NH3, replicate 2


title: CuO PEG 2.5 + OVA S2

description: OVA-challenged, exposed to 2.5 μg/day of CuO PEG, replicate 2


title: OVA S8

description: OVA-challenged control, replicate 8


title: CuO PEG 2.5 S1

description: PBS-challenged, exposed to 2.5 μg/day of CuO PEG, replicate 1


title: CuO NH3 40 + OVA S2

description: OVA-challenged, exposed to 40 μg/day of CuO NH3, replicate 2


title: CuO PEG 2.5 + OVA S1

description: OVA-challenged, exposed to 2.5 μg/day of CuO PEG, replicate 1


title: PBS S4

description: PBS-challenged control, replicate 4


title: PBS S6

description: PBS-challenged control, replicate 6


title: CuO PEG 10 + OVA S3

description: OVA-challenged, exposed to 10 μg/day of CuO PEG, replicate 3


title: CuO NH3 40 S1

description: PBS-challenged, exposed to 40 μg/day of CuO NH3, replicate 1


title: CuO PEG 40 + OVA S2

description: OVA-challenged, exposed to 40 μg/day of CuO PEG, replicate 2


title: CuO NH3 10 + OVA S3

description: OVA-challenged, exposed to 10 μg/day of CuO NH3, replicate 3


title: CuO PEG 40 S1

description: PBS-challenged, exposed to 40 μg/day of CuO PEG, replicate 1


title: CuO COOH 40 S3

description: PBS-challenged, exposed to 40 μg/day of CuO COOH, replicate 3


title: CuO COOH 10 + OVA S3

description: OVA-challenged, exposed to 10 μg/day of CuO COOH, replicate 3


title: CuO NH3 2.5 S1

description: PBS-challenged, exposed to 2.5 μg/day of CuO NH3, replicate 1


title: CuO COOH 2.5 S3

description: PBS-challenged, exposed to 2.5 μg/day of CuO COOH, replicate 3


title: CuO COOH 40 S2

description: PBS-challenged, exposed to 40 μg/day of CuO COOH, replicate 2


title: CuO 10 + OVA S2

description: OVA-challenged, exposed to 10 μg/day of CuO, replicate 2


title: CuO 40 S1

description: PBS-challenged, exposed to 40 μg/day of CuO, replicate 1


title: CuO 40 S3

description: PBS-challenged, exposed to 40 μg/day of CuO, replicate 3


title: CuO PEG 2.5 + OVA S3

description: OVA-challenged, exposed to 2.5 μg/day of CuO PEG, replicate 3


title: CuO NH3 40 S3

description: PBS-challenged, exposed to 40 μg/day of CuO NH3, replicate 3


title: PBS S2

description: PBS-challenged control, replicate 2


title: CuO 2.5 S1

description: PBS-challenged, exposed to 2.5 μg/day of CuO, replicate 1


title: CuO COOH 2.5 + OVA S1

description: OVA-challenged, exposed to 2.5 μg/day of CuO COOH, replicate 1


title: OVA S7

description: OVA-challenged control, replicate 7


title: CuO 40 + OVA S3

description: OVA-challenged, exposed to 40 μg/day of CuO, replicate 3


title: OVA S2

description: OVA-challenged control, replicate 2


title: human macrophages treated with rhFGL2 [GCS61088]

first: Xinxin

last: Hou

address: 1200 Cailun Road

institute: Shanghai University of Traditional Chinese Medicine

hyb_protocol: Following fragmentation, 5.2 ug of cRNA were hybridized for 16 hr at 45℃ according to Affymetrix WT PLUS Reagent Kit User Manual using the GeneChip Hybridization Wash and Stain Kit. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using AGCC Scan Control Software on the Affymetrix Genechip Scanner 3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: human macrophages

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 500ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Primary collection and culture of human peripheral blood monocytes. Monocytes were further differentiated into macrophages (monocyte-derived macrophage, MDM) by incubation with M-CSF for 6 days. The macrophages were cultured in cell culture incubator.

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

treatment_protocol: The macrophages were culutred in RPMI-1640 with 10% FBS, rhFGL2 (1 µg/ml, Abnova) or the same volume of PBS (as control) were added for 24h, then the cells were placed on ice in the Trizol solution (GibcoBRL).

tag: subject status

value: healthy volunteer

tag: ethnicity

value: Chinese

value: Peripheral blood

value: monocyte-derived macrophage (MDM)

tag: treatment

value: rhFGL2 for 24hrs


title: CuO COOH 10 + OVA S2

description: OVA-challenged, exposed to 10 μg/day of CuO COOH, replicate 2


title: OVA S4

description: OVA-challenged control, replicate 4


title: CuO COOH 10 S1

description: PBS-challenged, exposed to 10 μg/day of CuO COOH, replicate 1


title: CuO 2.5 + OVA S2

description: OVA-challenged, exposed to 2.5 μg/day of CuO, replicate 2


title: human macrophages untreated [GCS61087]

tag: tissue

value: PBS for 24hrs


title: CuO COOH 40 + OVA S2

description: OVA-challenged, exposed to 40 μg/day of CuO COOH, replicate 2


title: PBS S7

description: PBS-challenged control, replicate 7


title: CuO NH3 2.5 + OVA S2

description: OVA-challenged, exposed to 2.5 μg/day of CuO NH3, replicate 2


title: CuO PEG 2.5 S3

description: PBS-challenged, exposed to 2.5 μg/day of CuO PEG, replicate 3


title: CuO PEG 10 S4

description: PBS-challenged, exposed to 10 μg/day of CuO PEG, replicate 4


title: CuO COOH 40 + OVA S1

description: OVA-challenged, exposed to 40 μg/day of CuO COOH, replicate 1


title: CuO COOH 2.5 S2

description: PBS-challenged, exposed to 2.5 μg/day of CuO COOH, replicate 2


title: CuO 10 S2

description: PBS-challenged, exposed to 10 μg/day of CuO, replicate 2


title: CuO 40 + OVA S1

description: OVA-challenged, exposed to 40 μg/day of CuO, replicate 1


title: CuO NH3 40 + OVA S3

description: OVA-challenged, exposed to 40 μg/day of CuO NH3, replicate 3


title: human macrophages treated with rhFGL2 [GCS61086]


title: sRNA treated root

city: Bhubaneswar

first: Birendra

middle: Prasad

last: Shaw

state: Odisha

address: Nalco Square, Besides Kalinga Hospital

country: India

institute: Institute of Life Sciences

description: sRNA treated root

data_processing:
NGS QC Toolkit Cutadapt and UEA Small-RNA Workbench were used to process the raw reads.
Adaptor-trimmed high quality reads were queried against the NCBI and Rfam databases to screen out and discard the abundant non-coding RNAs like tRNA, snoRNA, snRNA and others.
The unique reads were searched for the known sequences in the miRBase 21.0 for the identification of the conserved miRNAs.
The sRNA sequences were then mapped on rice genome for the identification of possible novel miRNAs and their precursors.
The basic criteria described in literature were followed for putative miRNA prediction, length of the precursors should be greater than the desired length of 60-ntlike hairpin formation, MFEI value of the precursors should be higher than 0.64, the miRNAs occupied only one of the arm of the concerned secondary structure, and others.
Genome_build: NCBI Build 4.0, Rfam
Supplementary_files_format_and_content: Excel shhet of known and novel miRNAs and the related information on their ientification

organism: Oryza sativa

source_name: Seedlings

growth_protocol: Seeds of Oryza sativa cv. Pokkali were germinated on wet filter paper and raised hydroponically in a light and temperature controlled plant growth chamber.

extract_protocol:
Total RNA was extracted from the individual samples using TRIzol reagent (Thermo Fischer Scientific) following manufacturer’s instructions. Only good quality RNA with RIN value above 7.0 was used for downstream processing. Total RNA (1 µg) from each sample was subjected to electrophoresis on denaturing polyacrylamide gel to separate out the sRNA fragments
Small RNAs recovered were ligated with 3’- and 5’- adaptors. The ligated sRNA products from each sample were reverse transcribed and PCR amplified to generate the sRNA libraries. The individual libraries were normalized to 2 nM with Tris-HCl as per TruSeq Small RNA Prep kit manual (Illumina).
The adapter libraries prepared were processed for single-end sequencing on HiSeq2000. The sequencing results were generated as FASTQ data using Illumina pipeline CASAVA 1.8 package.
Therefore, the current study was planned to see the expression profile of miRNAs in a salt-tolerant rice (Oryza sativa L. ssp indica) cultivar (cv.) Pokkali in presence and absence of NaCl and to check the response pattern of a few important salt-responsive miRNAs in a salt-sensitive rice cultivar Badami in order to identify the miRNAs and their targets that could be involved in the salt tolerance process

treatment_protocol: On 9th day of germination the seedlings were treated with 1.5 % NaCl through root in the morning. The seedlings not receiving NaCl treatment served as control. Shoot and root of the seedlings were harvested after 9 h for extraction of RNA

tag: cultivar

value: cv. Pokkali

tag: seedling part

value: Submerged part of the seedlings

value: Root tissue

tag: maturity

value: 9 days


title: sRNA control root

description: sRNA control root


title: CuO NH3 2.5 S2

description: PBS-challenged, exposed to 2.5 μg/day of CuO NH3, replicate 2

tag: strain

value: BALB/c

value: Female

value: OVA/Alum


title: CuO PEG 10 + OVA S2

description: OVA-challenged, exposed to 10 μg/day of CuO PEG, replicate 2

value: OVA

value: CuO PEG


title: RNAseq_plusdox_rep1

city: Minneapolis

first: Lauren

last: Mills

state: MN

address: 420 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

description:
Doxycycline-inducible embryonic stem cells.
D4_plus_dox_1_CCGTCC
processed data file: Day4_NoDox_vs_Dox.xlsx

data_processing:
ChIP-seq analysis: Each sample’s reads were aligned to the mouse (mm10) genome using Bowtie2 followed by removal of PCR duplicates using Samtools. Peak calling was performed using MACS with the following parameters: --bw 300 -p 1e-3. To identify the list of high confidence mouse Sox7 peaks we performed 4 independent ChIP-seq experiments and, using the bedtools intersect function, only common regions between 2 experiments were further considered. In addition, the Sox7 peak list was filtered (intersect –v option) for sites overlapping to peaks detected in the uninduced control ChIP-seq and input sample. Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS using the Kent tool Wig-to-BigWig.
ATAC-seq analysis: Reads were aligned to the mouse genome (mm10) using Bowtie2 with the following parameters: -q -I 38 -X 2000 --local --dovetail --no-mixed --no-discordant. Aligned reads were filtered for PCR duplicates using Samtools and then processed with MACS 1.4 with the following parameters: --nomodel --nolambda --keep-dup all --call-subpeaks -p 1e-4 -w –S. Bigwig files for visualization on IGV were generated by converting the wig files obtained from MACS using the Kent tool Wig-to-BigWig. ATAC-seq reads overlapping to Pax3 peaks were retrieved using the R Bioconductor package and then used to generate density maps with Seqminer. To identify differentially accessible peaks, we used the BEDTools intersect function: the common regions (-f 0.5 -F 0.5 -e options) for the dox-induced samples were intersected (-v -f 0.2 options) with the combined list of control peaks (from non-induced cells).
Mouse RNA-seq analysis: FASTQ files were trimmed for quality using trimmomatic and aligned to the mm10 genome using HISAT2. Raw counts per gene were assigned using subread featurecounts and used as input for differential gene expression analysis in edgeR via the CLC genomics workbench.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: ChIP-seq: Processed files represent list of peaks 1) identified by MACS in each replicate; 2) Sox7 peaks detected indox-induced samples after removing peaks called in non-induced samples and input; 3) Sox7 peaks overlapping to Gata4 sites.
Supplementary_files_format_and_content: ATAC-seq: Processed files contain 1) the list of peaks identified by MACS in each replicate and 2) the list of CPC +dox and EPC +dox specific accessible loci.
Supplementary_files_format_and_content: RNA-seq: Processed file contains tab-delimited expression values following analysis using EdgeR.

source_name: differentiating mES cells

growth_protocol: Mouse ES cell differentiation was achieved by diluting cells to 10,000 cells/ml in EB differentiation medium following incubation at 37°C as hanging drops in non-adherent Petri dishes (10μl/drop equivalent to 100 cells). EB differentiation medium: IMDM supplemented with 15% FBS, 1% Penicillin/Streptomycin, 2mM Glutamax, 50 μg/ml Ascorbic acid, 4.5 mM Monothioglycerol and 200μg/ml iron-saturated transferrin. After 2 days, EBs were recovered by flushing plates with PBS, resuspended in EB medium and incubated in an orbital shaker at 80 RPM, 37°C. Transgene induction was achieved by adding doxycycline for 24 hrs (Sigma-Aldrich) to day 3 EBs cultures (final concentration 1µg/ml). Medium was replaced every two days through the differentiation protocol. At day 4, EBs were disaggregated and single cells were incubated for 20 minutes with PDGFRα-PE and FLK1-APC conjugated antibodies. PDGFRα+FLK1- cells were sorted using FACSAriaII (BD biosciences). The dox inducible cell line A2lox-Sox7-Myc derived from E14Tg2a (parental) were used to make all EBs.

extract_protocol:
ChIP-seq: Day 4 EBs were prepared for ChIP from doxycycline treated (24 hrs) and untreated (control) conditions. Day 4 EBs were dissociated with trypsin/EDTA solutionvat 37°C for 1.5 min with gentle shaking and reaction was inhibited by adding 10% FBS/PBS. Washed cells were treated with 1% formaldehyde (Pierce) to crosslink protein-DNA complexes (10 min at RT) followed by quenching with glycine. Cell pellets were incubated sequentially in lysis buffers 1, 2, 3 supplemented with protease inhibitors (complete-mini protease inhibitor cocktail (Roche)) for 10 min each at 4°C (LB1: 50mM HEPES KOH, pH7.5, 140mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP40, 0.25% Triton X-100; LB2: 10mM Tris-HCl, pH 8, 200mM NaCl, 1mM EDTA, 0.5 mM EGTA; LB3: 10mM Tris-HCl, pH 8, 100mM NaCl, 1mM EDTA, 0.5mM EGTA, 0.1% sodium deoxycholate, 0.5% N-lauroylsarcosine) and then sonicated for four cycles with a probe tip sonicator at 18% power for 1 min with intervals of 10 s ON-10 s OFF to reach an average chromatin size of 300bp. After shearing, samples were centrifuged for 10 min at 16,000g and snap-frozen in liquid nitrogen if not processed immediately. For each ChIP, 25mg of chromatin was precleared for 4 hr at 4°C with 15µl of BSA-blocked Protein A-conjugated sepharose beads (GE healthcare) and then supplemented with 1/10 volume of 10% Triton X-100. Immunoprecipitation was performed by overnight incubation with normal mouse IgG (5µg - Millipore) or anti-myc antibody (5µg clone 9E10 – Roche). Immune complexes were recovered by incubation with 15µl of BSA-blocked Protein A-conjugated sepharose beads for 4 hr at 4°C and then washed five times with RIPA wash buffer (50mM HEPES KOH, pH7.5, 500mM LiCl, 1 mM EDTA, 1% NP40, 0.25% Triton X-100 and 0.7% sodium deoxycholate) and one time with TEN buffer (10mM Tris-HCl, pH 8, 1mM EDTA and 50mM NaCl). Immunoprecipitated chromatin was recovered by incubating beads with 200µl of elution buffer (50mM Tris-HCl, pH 8, 10mM EDTA and 1% SDS) for 20 min at 65°C. Chromatin from immunoprecipitation and input (equivalent to 1% of starting material) was reverse crosslinked overnight at 65°C, then diluted 1:1 with TE (10mM Tris-HCl, pH 8, and 1mM EDTA) supplemented with 4µl of RNaseA (20mg/ml – ThermoFisher) and incubated for 2 hr at 37°C followed by Proteinase K treatment (4µl of 20mg/ml) for 30 min at 55°C. DNA was purified using Phenol-chloroform-isoamyl alcohol extraction, precipitated, washed, and dissolved in 50µl H2O.
ChIP-seq libraries were generated using the NEBNext DNA library prep kit (NEB) and AMPure XP beads (Beckman Coulter) for all the purification and size selection steps. 10ng or less of DNA were processed following manufacturer's instructions.
ATAC-seq: 50,000 freshly sorted cells from differentiated ES cultures were washed with 200 µl of cold PBS then resuspended in 100 µl of cold lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630), spun at 500 g for 10 minutes at 4°C and resuspended in 50 µl of the transposition reaction mix. Transposition occurred at 37°C for 30 minutes, after which transposed DNA was purified using a Qiagen MinElute Kit and eluted in 10µl Elution Buffer. Final libraries were generated by primer extension of the transposed DNA followed by PCR amplification using Illumina-compatible adapter-barcodes.
RNA-seq: d4 EBs were collected and RNA was prepared using the Purelink RNA mini kit (ThermoFisher).
RNA-seq libraries were generated using the TruSeq stranded kit and dual-index adapter-barcodes following manufacturer's instructions.

tag: cell line

value: A2lox-Sox7-Myc (derived from E14Tg2a)

tag: doxycycline-treatment

value: 12 hours

tag: purification

value: Unsorted

value: Day 4 EB


title: RNAseq_plusdox_rep2

description:
Doxycycline-inducible embryonic stem cells.
D4_plus_dox_2_GTCCGC
processed data file: Day4_NoDox_vs_Dox.xlsx

tag: cell type


title: sRNA treated shoot

description: sRNA treated shoot

value: Aerial part of the seedlings

value: Shoot tissue


title: sRNA control shoot

description: sRNA control shoot


title: CuO NH3 10 + OVA S2

description: OVA-challenged, exposed to 10 μg/day of CuO NH3, replicate 2

tag: gender

tag: sensitization

value: CuO NH3


title: NT1

city: Cambridge

first: Kevin

last: Chalut

address: Tennis Court Road

department: Stem Cell Institute

institute: University of Cambridge

data_processing:
1. Trimmomatic adaptor clipping for TruSeq-HT adapters.
2. Hisat2 alignment to rat genome Rn6 paired end
3. Stringtie
4. Bowtie
Genome_build: RN6
Supplementary_files_format_and_content: All processed data files are supplied in the GTF format.

source_name: Cultured neonate OPCs stiff hydrogel

growth_protocol: MACs sorted OPCs cultured  in FGF and PDGF

extract_protocol:
Zymo Directzol RNA microkit
SMARTer Stranded Total RNA-pico Input Mammalian Kit

treatment_protocol: OPCs were cultured on laminin coated hydrogels of differing stiffness

value: Cultured neonate OPCs stiff hydrogel


title: NT3


title: RNAseq_nodox_rep2

description:
Doxycycline-inducible embryonic stem cells.
D4_no_dox_2_ATGTCA
processed data file: Day4_NoDox_vs_Dox.xlsx

value: Not treated


title: NT2


title: NO3

source_name: Cultured neonate OPCs soft hydrogel

value: Cultured neonate OPCs soft hydrogel


title: ATACseq_EPC_plusdox_rep2

description: Doxycycline-inducible embryonic stem cells.

value: PDGFRalpha-FLK1+ sorted


title: RNAseq_nodox_rep1

description:
Doxycycline-inducible embryonic stem cells.
D4_no_dox_1_AGTTCC
processed data file: Day4_NoDox_vs_Dox.xlsx


title: CuO PEG 10 S2

description: PBS-challenged, exposed to 10 μg/day of CuO PEG, replicate 2

tag: challenge

value: PBS

tag: nanomaterial


title: ATACseq_EPC_plusdox_rep1