title: siControl_High_Ca_1

city: Bethesda

first: Maria

middle: I.

last: Morasso

address: Building 50, Room 1525 10 Center Drive

department: National Institute for Arthritis and Musculoskeletal and Skin Diseases

institute: National Institutes of Health

data_processing:
The raw reads were done by STAR.
Normalization and differential gene analysis were done using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: Gene count table

source_name: BALB/c neonatal mouse keratinocyte culture

growth_protocol: Primary murine keratinocytes were cultured in supplemented minimal essential medium (Gibco, Thermo Fisher Scientific Inc., Waltham, MA, USA) with 8% fetal bovine serum (FBS, Atlanta Biologicals, Flowery Branch, GA, USA) and 1% antibiotic (Penicillin Streptomycin Amphotericin B, Sigma), with Ca++ concentration of 0.05mM.

extract_protocol:
Total RNA from cells was extracted using RNeasy kit (Qiagen) according to the manufacturer’s instructions.
100 ng were used to prepare the libraries utilizing a Neoprep Library kit (Illumina).

treatment_protocol: A total of 1 million cells were seeded in each well of 6 well plates. 24 hours after seeding, the siRNA mix (Opti-Mem serum free media (GIBCO), 75pmol of siRNA (Dharmacon) and HiPerfect transfection reagent (Qiagen)) was added to cells. For SBSN, the siRNA used were Dharmacon, SMARTpool; siGENOME Sbsn siRNA M-054578-01-0005 and Control (mouse) SMARTpool; siGENOME Non-Targeting siRNA Pool #1. Each condition was done in triplicates. To induce keratinocyte differentiation, a final concentration of 0.12mM Ca++ was used. RNA was harvested 48hs after siRNA transfection.

tag: treatment

value: siControl

tag: batch

value: BALB/c


title: siSBSN_High_Ca_5

status: Public on May 31 2018

type: SRA

state: MD

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

value: siSbsn

tag: strain


title: siSBSN_High_Ca_6


title: wt_rep2_H3ChIPseq

city: Ithaca

first: Siu

middle: Sylvia

last: Lee

state: NY

address: 520 Campus road

institute: Cornell University

description: wtH3K4me3ChIP_pooled_bedgraph_forIGFview.bedgraph

library_source: genomic

data_processing:
Two replicate ChIP-Seq raw data were pooled. Raw data were first filtered by fastx_trimmer and fastq_quality_filter
bowtie2 was used to align reads to WS250 genome
PCR duplicate was removed by samtools and the data were converted to bam files
bamCoverage was used to generate bedgraph files
Genome build: WS250
Supplementary_files_format_and_content: bedgraph containing z-score in 50bp window

molecule: genomic DNA

organism: Caenorhabditis elegans

growth_protocol: L4 worms were cultured and harvested on NGM plates

extract_protocol:
Crosslinked protein-DNA complex were isolated with antibody.
ChIP-seqw libraries were prepared for sequencing using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB)

tag: genotype

tag: developmental stage

tag: chip antibody


title: siSBSN_High_Ca_4


title: N_H2

value: no siRNA


title: C_H2


title: siControl_High_Ca_3


title: C_H1


title: D_H2


title: wt_rep1_ribominusRNAseq

description:
total RNA after removing ribo-RNA
n2set9set26set9set26rnaseq.txt

data_processing:
Rawdata was filtered by fastq_quality_filter, adaptor was cut by cutadapt  and rRNA was  removed by bowtie2;
tophat2 was used to align reads to WS250 genome
cufflink was used to generate raw count for each gene
EdgeR was used to calculate the significant changed gene
Genome build: WS250
Supplementary_files_format_and_content: excel containing raw counts

extract_protocol:
RNA was extracted using Trizol reagent.
RNA libraries were prepared for sequencing using Ovation Human FFPE RNA-Seq Library Systems (NuGEN) kit


title: N_H1


title: D_H1


title: PVT1 primer R1 biological rep1 technical rep 2 in MCF7 UMI-4C

city: Stanford

first: Howard

middle: Y.

last: Chang

state: CALIFORNIA

address: 269 Campus Drive, CCSR 2130

institute: Stanford

data_processing:
Basecalls
analyzed using HiC-pro
Genome_build: Hg19
Supplementary_files_format_and_content: HiC-pro output describing interacting loops

organism: Homo sapiens

source_name: MCF7 cell line

growth_protocol: Cultured in DMEM with 10% FBS + 1% pen-strep.

extract_protocol:
described in doi:10.1038/nmeth.3922 (2016)
Truseq adaptor ligation/PCR

treatment_protocol: CRISPRi targeting PVT1 TSS

tag: cell line

value: CTACTCACAGCGCATCCCTA

value: GGGGACAAAATTGGAACTTACTGG


title: PVT1 primer R1 biological rep2 technical rep 1 in MCF7 UMI-4C


title: PVT1 primer R1 biological rep1 technical rep 1 in MCF7 UMI-4C


title: PVT1 primer R1 biological rep2 technical rep 2 in MCF7 UMI-4C


title: PVT1 primer F1 biological rep2 technical rep 2 in MCF7 UMI-4C

value: TTGCGGAAAGGATGTTGGC

value: CCCTGTGACCTGTGGAGACA


title: PVT1 primer F1 biological rep1 technical rep 2 in MCF7 UMI-4C


title: PVT1 targeting sgRNA R2 replicate 1 passage 0

description: targeted amplified DNA

data_processing:
Library strategy: targeted PCR
Basecalls
Counted using CRISPResso
Genome_build: Hg19
Supplementary_files_format_and_content: Allele frequency counted

source_name: MDA-MB-231 cells were transfected with Cas9-sgRNA ribonucleotide complex

growth_protocol: Cultured in DMEM supplemented with 10% FBS + 1% pen-strep.

extract_protocol:
Qiagen Blood and tissue kit
targeted PCR/nested PCR for Trueseq adaptor

treatment_protocol: 100 ug of Cas9 protein, 100 ug of sgRNA were transfected using  Amaxa Nucleofetor kit V program X-013 to 1 million of MDA-MD-231 cell.  Media was changed following day. Passaged every 2 days with 1:4 ratio

tag: passage


title: PVT1 primer F1 biological rep1 technical rep 1 in MCF7 UMI-4C


title: PVT1 targeting sgRNA R2 replicate 1 passage 30

description: targeted amplified DNA


title: MYC primer R2 biological rep1 technical rep 2 in MCF7 UMI-4C

value: GTTGCACAATGGCAGAGACC

value: CTCTAAGGGCCAATTTGTATTGTG


title: siControl_High_Ca_2


title: PVT1 targeting sgRNA R2 replicate 2 passage 20

description: targeted amplified DNA


title: MYC primer R2 biological rep1 technical rep 1 in MCF7 UMI-4C


title: MYC primer R2 biological rep2 technical rep 1 in MCF7 UMI-4C


title: PVT1 primer F1 biological rep2 technical rep 1 in MCF7 UMI-4C


title: PVT1 targeting sgRNA R2 replicate 1 passage 10

description: targeted amplified DNA


title: MYC primer F2 biological rep1 technical rep 1 in MCF7 UMI-4C

value: AGGCCGCTCTTACCTTTACT

value: TGCCAACTTCCTTCCCGAAAG


title: MYC primer F2 biological rep2 technical rep 1 in MCF7 UMI-4C


title: MYC primer F2 biological rep1 technical rep 2 in MCF7 UMI-4C


title: HeLa replicate 2

description: genomic DNA fragment

data_processing:
Basecalls
Trimming for Nextseq adaptor
Align using Bowtie2
Removing dupulicate using Picard
Peak calling using MACS2
Genome_build: Hg19
Supplementary_files_format_and_content: MACS2 output describing peak region and count

source_name: HeLa cell line

growth_protocol: HeLa cells were cultured in DMEM supplemented with 10% FBS + 1% pen-strep.

extract_protocol:
Qiagen MinElute column
Standard ATAC-seq protocol.

value: HeLa


title: HeLa replicate 1

description: genomic DNA fragment


title: PVT1 primer R1 biological rep1 technical rep 2 in MCF7 cell line

data_processing:
Library strategy: 4C-seq
Basecalls
analyzed using HiC-pro
Genome_build: Hg19
Supplementary_files_format_and_content: HiC-pro output describing intracting loops

growth_protocol: Cultured in DMEM (MDA-MB-231 or MCF-7) or McCoy's 5A supplemented with 10% FBS + 1% pen-strep.

treatment_protocol: non-treated


title: PVT1 primer R1 biological rep2 technical rep 2 in HCT116 cell line

source_name: HCT116 cell line


title: PVT1 primer R1 biological rep1 technical rep 1 in HCT116 cell line


title: PVT1 primer R1 biological rep1 technical rep 2 in HCT116 cell line


title: PVT1 primer R1 biological rep2 technical rep 1 in MDA-MB-231 cell line

source_name: MDA-MB-231 cell line


title: PVT1 primer R1 biological rep2 technical rep 2 in MDA-MB-231 cell line


title: PVT1 primer R1 biological rep2 technical rep 1 in HCT116 cell line


title: PVT1 primer R1 biological rep1 technical rep 1 in MCF7 cell line


title: PVT1 primer R1 biological rep2 technical rep 1 in MCF7 cell line


title: MYC primer R2 biological rep2 technical rep 2 in MCF7 UMI-4C


title: PVT1 primer F1 biological rep2 technical rep 2 in MDA-MB-231 cell line


title: PVT1 primer R1 biological rep2 technical rep 2 in MCF7 cell line


title: PVT1 primer R1 biological rep1 technical rep 2 in MDA-MB-231 cell line


title: MYC primer F2 biological rep2 technical rep 2 in MCF7 UMI-4C


title: PVT1 primer F1 biological rep2 technical rep 1 in MDA-MB-231 cell line


title: PVT1 primer F1 biological rep1 technical rep 1 in MDA-MB-231 cell line


title: PVT1 primer F1 biological rep2 technical rep 1 in MCF7 cell line


title: PVT1 primer F1 biological rep1 technical rep 2 in MCF7 cell line


title: PVT1 primer F1 biological rep1 technical rep 1 in MCF7 cell line


title: PVT1 primer F1 biological rep2 technical rep 2 in MCF7 cell line


title: PVT1 primer F1 biological rep1 technical rep 2 in MDA-MB-231 cell line


title: PVT1 primer F1 biological rep2 technical rep 1 in HCT116 cell line


title: PVT1 primer F1 biological rep1 technical rep 2 in HCT116 cell line


title: PVT1 primer F1 biological rep2 technical rep 2 in HCT116 cell line


title: PVT1 primer F1 biological rep1 technical rep 1 in HCT116 cell line


title: MYC primer R2 biological rep2 technical rep 1 in MDA-MB-231 cell line


title: MYC primer R2 biological rep1 technical rep 2 in MDA-MB-231 cell line


title: PVT1 primer R1 biological rep1 technical rep 1 in MDA-MB-231 cell line


title: MYC primer R2 biological rep1 technical rep 1 in MDA-MB-231 cell line


title: MYC primer R2 biological rep2 technical rep 2 in MDA-MB-231 cell line


title: sch9wild_wk00_af104

city: Boston

first: Andrew

middle: Ryan

last: Field

state: MA

address: 45 Shattuck St

department: BCMP

institute: Harvard Medical School

description:
10X RevA pipeline
single cell RNA

data_processing:
The "cellranger mkref" command was used with the (hg19) FANTOM lv3 (Hon et al, 2017) gene model to createthe reference used by "cellranger count" to align the reads and assign them to genes
The 10X supplied cellranger software version 2.0.0 was used. The "cellranger count" command was used with default parameters (and --expect-cells=3000), with the genome target of hg19 and a gene model derived from FANTOM
Genome_build: hg19, FANTOM lv3 (Hon et al, 2017) transcripts
Supplementary_files_format_and_content: gene-by-cell matrixin MatrixMarket format
Supplementary_files_format_and_content: barcodes.tsv  genes.tsv  matrix.mtx

source_name: Human embryonic stem cells

growth_protocol: The Eiraku et al., 2008 cortical organoid differentiation protocol was used with modifications. Human embryonic stem cells were grown in feeder-free conditions on vitronectin (ThermoFisher) with Essential-8 Flex media (ThermoFisher) and 10,000 cells per EB were aggregated using AggreWell-800 plates (Stem Cell Technologies) in Aggrewell media (Stem Cell Technologies) supplemented with 10 uM Y-27632 rock inhibitor (ATCC) and transferred to low attachment plates (Corning) on day 2. Media was supplemented with 500ng/mL DKK1 (Peprotech), 500 ng/mL NOGGIN (R & D Systemes), 10 uM SB431542 (Sigma), and 1 uM Cyclopamine V. californicum (VWR) for the first 18 days of differentiation. The media was changed to Neuralbasal (Invitrogen) supplemented with N2 (Gibco) and 1 uM Cyclopamine on day 18. Neurospheres were supplemented with 10ng/mL bFGF and 10ng/mL EGF to improve survivability in Neuralbasal media. After day 26, the media was switched to Neuralbasal/N2 media without any added factors.

extract_protocol: 10X Genomics Chromium single cell RNA-seq RevA and RevB as indicated

tag: time point

value: week 0


title: MYC primer R2 biological rep1 technical rep 2 in MCF7 cell line


title: MYC primer R1 biological rep2 technical rep 2 in MDA-MB-231 cell line

value: GCCTCTCGCTGGAATTACTAC

value: CCCCGAAAACCGGCTTTTATAC


title: MYC primer R1 biological rep1 technical rep 2 in MDA-MB-231 cell line


title: MYC primer R1 biological rep1 technical rep 1 in MDA-MB-231 cell line


title: sch9wild_wk02_af106

description:
10X RevB pipeline
single cell RNA

value: week 2


title: sch9wild_wk05_af102

description:
10X RevA pipeline
single cell RNA

value: week 5


title: sch9froz_wk01_af112

description:
10X RevB pipeline
single cell RNA

value: week 1


title: MYC primer R2 biological rep2 technical rep 1 in HCT116 cell line


title: MYC primer R1 biological rep2 technical rep 1 in MCF7 cell line


title: MYC primer R2 biological rep2 technical rep 2 in HCT116 cell line


title: MYC primer R2 biological rep2 technical rep 2 in MCF7 cell line


title: MYC primer R2 biological rep1 technical rep 1 in MCF7 cell line


title: MYC primer R2 biological rep1 technical rep 2 in HCT116 cell line


title: MYC primer R1 biological rep1 technical rep 2 in MCF7 cell line


title: MYC primer R2 biological rep2 technical rep 1 in MCF7 cell line


title: MYC primer R1 biological rep2 technical rep 1 in MDA-MB-231 cell line


title: sch9wild_wk05_af103

description:
10X RevA pipeline
single cell RNA


title: MYC primer R2 biological rep1 technical rep 1 in HCT116 cell line


title: MYC primer R1 biological rep1 technical rep 1 in MCF7 cell line


title: sch9wild_wk02_af107

description:
10X RevB pipeline
single cell RNA


title: EC109 shDHX9 #286

city: Singapore

first: Polly Leilei

last: Chen

address: #12-01, MD6, 14 Medical Drive

department: Department of Anatomy

country: Singapore

institute: Cancer Science Institute of Singapore NUS

description: strand-specific RNA-Seq

data_processing:
Reads with adapters, unknown bases more than 10% and low quality bases (<=5) more than 50% were removed using SAOPnuke software.
Clean reads were then mapped to reference genome (hg19) using bwa (v0.7.15-r1140). PCR duplicates were removed with samtools (v1.4.1). The reads with mapping quality score less than 20 were discarded.
Variants were called with an in-house variant caller (Perl script) from the samtools mpileup data.
Candidate editing sites were filtered as the following: SNPs from different databases (1000 Genomes Project, NHLBI GO Exome Sequencing Project (http://evs.gs.washington.edu/EVS/), dbSNP v138) were removed, sites within the first 6 bases of the reads were excluded. For sites not located in Alu elements, the candidates within the 4 bases of a splice junction on the intronic side, and those residing in the homopolymeric regions and in the simple repeats were all removed. Candidate variants located in the reads that map to the non-unique regions of the genome by using BLAT were also excluded. Only A-to-G editing sites based on the strand information were retained.
To obtain high confidence editing events, the candidate sites were required to be supported by at least 20 reads and both shDHX9 knockdown treatments to result in at least 5% change in the editing level in the same direction.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file include DHX9 knockdown specific high confidence editing events

source_name: human esophageal squamous carcinoma cells

extract_protocol:
Total RNA samples were extracted using Qiagen Rneasy Mini Kit.
Strand-specific cDNA library according to Illumina's TruSeq Stranded mRNA Library Prep Kit.

treatment_protocol: Human ESCC cells were treated with specific shRNAs for silencing DHX9.

tag: cell type

value: DHX9 knockdown


title: MYC primer R1 biological rep2 technical rep 2 in HCT116 cell line


title: MYC primer R1 biological rep2 technical rep 2 in MCF7 cell line


title: MYC primer R1 biological rep2 technical rep 1 in HCT116 cell line


title: EC109 shScr

description: strand-specific RNA-Seq

value: human esophageal squamous carcinoma cells

value: scramble shRNA treated


title: sch9froz_wk01_af111

description:
10X RevB pipeline
single cell RNA


title: EC109 shDHX9 #5

description: strand-specific RNA-Seq


title: MYC primer R1 biological rep1 technical rep 2 in HCT116 cell line


title: MYC primer R1 biological rep1 technical rep 1 in HCT116 cell line


title: MYC primer F2 biological rep2 technical rep 1 in MDA-MB-231 cell line


title: MYC primer F2 biological rep2 technical rep 2 in MDA-MB-231 cell line


title: PVT1 targeting sgRNA R3 rep1

data_processing:
Basecalls
QC using FASTQC
Trimming for Truseq adaptor
Align using Bowtie2
Mapping using Tophat2
Genome_build: Hg19
Supplementary_files_format_and_content: Tophat2 output describing raw counts and RPKM

source_name: MDA-MB-231 clonal cell line expressing dCas9-BFP-KRAB construct

extract_protocol:
Qiagen Rneasy Plus Mini kit
Standard Illumina protocols

treatment_protocol: lentivirus harboring mU6-sgRNA (control or PVT1 R2/R3). Selected by Puromycin 1 ug/ml for 4 days. Recovered for one day in media without Puromycin.

value: PVT1 Knockdown


title: MYC primer F2 biological rep2 technical rep 1 in MCF7 cell line


title: MYC primer F2 biological rep1 technical rep 2 in MCF7 cell line


title: PVT1 targeting sgRNA R3 rep2


title: MYC primer F2 biological rep1 technical rep 2 in MDA-MB-231 cell line


title: MYC primer F2 biological rep2 technical rep 1 in HCT116 cell line


title: MYC primer F2 biological rep1 technical rep 2 in HCT116 cell line


title: MYC primer F2 biological rep1 technical rep 1 in MDA-MB-231 cell line


title: control sgRNA rep2

value: wild type


title: MYC primer F2 biological rep2 technical rep 2 in MCF7 cell line


title: MYC primer F1 biological rep2 technical rep 2 in MDA-MB-231 cell line

value: CCCTCCTGCCTCGAGAAG

value: CTCAGAGGCTTGGCGGGAAAA


title: MYC primer F1 biological rep2 technical rep 2 in MCF7 cell line


title: PVT1 targeting sgRNA R2 rep1


title: PVT1 targeting sgRNA R2 rep1 passage 0

description: targeted amplified DNA

data_processing:
Library strategy: targeted PCR
Basecalls
QC using FASTQC
Trimming for Truseq adaptor
Removing reads with "N" base
analyzed using CRISPresso
Genome_build: Hg19
Supplementary_files_format_and_content: Allele frequency counted


title: MYC primer F1 biological rep2 technical rep 1 in MDA-MB-231 cell line


title: PVT1 targeting sgNRA R2 rep2


title: MYC primer F1 biological rep2 technical rep 1 in MCF7 cell line


title: PVT1 targeting sgRNA R2 rep2 passage 10

description: targeted amplified DNA


title: MYC primer F2 biological rep1 technical rep 1 in MCF7 cell line


title: control sgRNA rep1


title: MYC primer F2 biological rep2 technical rep 2 in HCT116 cell line


title: PVT1 targeting sgRNA R2 rep2 passage 0

description: targeted amplified DNA


title: PVT1 targeting sgRNA R2 rep1 passage 10

description: targeted amplified DNA


title: MYC primer F1 biological rep1 technical rep 1 in MCF7 cell line


title: MYC primer F1 biological rep1 technical rep 2 in MDA-MB-231 cell line


title: MYC primer F1 biological rep1 technical rep 1 in MDA-MB-231 cell line


title: MYC primer F1 biological rep2 technical rep 2 in HCT116 cell line


title: control sgRNA

description: targeted amplified DNA


title: MYC primer F1 biological rep2 technical rep 1 in HCT116 cell line


title: MYC primer F2 biological rep1 technical rep 1 in HCT116 cell line


title: HiChIP-H3K27ac-PVT1sgRNAR2-rep2

data_processing:
Library strategy: HiChIP
Basecalls
analyzed using HiC-pro
Genome_build: Hg19
Supplementary_files_format_and_content: HiC-pro output describing intracting loops

extract_protocol:
described in doi:10.1038/nmeth.3999 (2016)
Nextera

tag: antibody

value: Abcam, #ab4729


title: MYC primer F1 biological rep1 technical rep 2 in HCT116 cell line


title: MYC primer F1 biological rep1 technical rep 2 in MCF7 cell line


title: HiChIP-H3K27ac-PVT1sgRNAR3-rep1


title: MYC primer F1 biological rep1 technical rep 1 in HCT116 cell line


title: HiChIP-H3K27ac-PVT1sgRNAR2-rep1


title: HiChIP-H3K27ac-control sgRNA-rep2


title: HCT116 non-treated rep1

source_name: HCT116 cell line expressing dCas9-BFP-KRAB construct

growth_protocol: For MDA-MB231 and MCF7 cell line, Cultured in DMEM supplemented with 10% FBS + 1% pen-strep. HCT116 cell line was maintained with Mcoy's 5A media supplemented with 10% FBS + 1% pen-strep

treatment_protocol: For MDA-MB-231 or MCF7 cell line, lentivirus harboring mU6-sgRNA (control or PVT1 R2/R3). Selected by Puromycin 1 ug/ml for 4 days. Recovered for one day in media without Puromycin.


title: HiChIP-H3K27ac-PVT1sgRNAR3-rep2


title: HCT116 non-treated rep2


title: input-PVT1sgRNAR3-rep1

data_processing:
Basecalls
Trimming for Nextseq adaptor
Align using Bowtie2
Removing dupulicate using Picard
Peak calling using MACS2 substracted input peaks
Genome_build: Hg19
Supplementary_files_format_and_content: MACS2 output describing peak region and count

extract_protocol:
described in doi:10.1016/j.cell.2011.09.057 (2011)
NEB UltraII NEBnext ultra-II kit (NEB, #E7645)


title: nrx-1; nlg-1

city: Cordoba

first: Manuel

last: Ruiz-Rubio

address: Campus Rabanales s/n

department: Genetics

country: Spain

institute: University of Cordoba

data_processing:
Torrent Suite v4.2
The resulting fastq files were trimmed and mapped to the version WS220 of the C. elegans  genome by using TopHat to generate BAM files that were analyzed in SeqSolve under the default settings to perform a differential transcript expression analysis between the different strains (false discovery rate of 0.05). Reads displaying multiple mapping were filtered out  and only transcripts covered by more than 5 reads were tested. Seqsolve uses Cufflink s/Cuffdiff ( Trapnell et al. 2012 ) to quantify and identify transcripts with a significant level of expression between different conditions. In this analysis, expression values were normalized in FPKM (fragments per kilobase of exon per million fragments mapped).
Genome_build: WS220 version of C. elegans  genome
Supplementary_files_format_and_content: FPKM

source_name: whole L4 worms

growth_protocol: Wild type, nlg - 1  ( ok259 ) , nrx - 1  ( tm1961 ) and nlg - 1 ; nrx - 1  ( ok259; tm1961 ) mutants were synchronized at  L1 stage  by  bleaching  ( Porta de la Riva 2012 ) . Then L4  worms were harvested from NGM plates,  frozen with TRIReagent and total RNA purified  and treated with DNase I (Thermo Fisher Scientific) . RNA quality and integrity was  evaluated with the Experion Bioanalyzer (Bio - Rad).

extract_protocol:
L4  worms were harvested from NGM plates,  frozen with TRIReagent and total RNA purified  and treated with DNase I (Thermo Fisher Scientific) . RNA quality and integrity was  evaluated with the Experion Bioanalyzer (Bio - Rad).
Polyadenylated - RNA was purified from total RNA using Dynabeads mRNA DIRECT kit ( Thermo Fisher Scientific ). Purified mRNA was used for preparing cDNA (strand - specific) libraries using the Ion Total RNA - Seq  Kit v2 kit ( Thermo Fisher Scientific). These libraries were run through the Ion Personal Genome Machine® (PGM™) System using the Ion 318™ Chip Kit v2 (Thermo Fisher Scientific ).

treatment_protocol: No treatments were applied

value: L4 worms

tag: genotype/variation

value: nrx-1; nlg-1


title: input-PVT1sgRNAR2-rep2


title: input-PVT1sgRNAR3-rep2


title: input-PVT1sgRNAR2-rep1


title: N2


title: H3K27ac-PVT1sgRNAR3-rep1


title: nrx-1


title: input-control sgRNA-rep2


title: nlg-1


title: input-control sgRNA-rep1


title: H3K27ac-PVT1sgRNAR2-rep1


title: H3K27ac-control sgRNA-rep2


title: H3K27ac-control sgRNA-rep1


title: H3K9me3-PVT1sgRNAR3-rep2

value: Abcam, #ab8898


title: H3K9me3-PVT1sgRNAR3-rep1


title: HiChIP-H3K27ac-control sgRNA-rep1


title: H3K9me3-PVT1sgRNAR2-rep1


title: H3K9me3-control sgRNA-rep2


title: H3K9me3-control sgRNA-rep1


title: input_rep1_ChIPseq

description: SET926GFPChIP_pooled_bedgraph_forIGFview.bedgraph

value: anti-GFP (abcam, ab290, lot:GR278073-1)


title: input_rep2_ChIPseq


title: H3K9me3-PVT1sgRNAR2-rep2


title: HA-PVT1sgRNAR3-rep2

value: Cell Signaling, #2367S


title: HA-PVT1sgRNAR3-rep1


title: H3K27ac-PVT1sgRNAR2-rep2


title: HA-PVT1sgRNAR2-rep2


title: SET-9/26GFP_rep2_ChIPseq

value: set-9::gfp set-26::gfp


title: HA-control sgRNA-rep2


title: SET-26GFP_rep2_ChIPseq


title: H3K27ac-PVT1sgRNAR3-rep2


title: SET-9GFP_rep2_ChIPseq


title: SET-26GFP_rep1_ChIPseq


title: SET-9/26GFP_rep1_ChIPseq


title: SET-9GFP_rep1_ChIPseq


title: HA-control sgRNA-rep1


title: HA-PVT1sgRNAR2-rep1


title: MCF7 control sgRNA rep2

source_name: MCF7 clonal cell lines expressing dCas9-BFP-KRAB construct


title: MDA-MB-231 PVT1 targeting sgRNA R3 rep2


title: MCF7 control sgRNA rep1

source_name: MCF7 clonal cell lines expressing dCas0-BFP-KRAB construct


title: MDA-MB-231 PVT1 targeting sgRNA R3 rep1


title: MDA-MB-231 PVT1 targeting sgRNA R2 rep1


title: MDA-MB-231 control sgRNA rep2


title: MDA-MB-231 control sgRNA rep1


title: JHHS1_S1

city: illkirch

first: jacques

last: h

address: 74, route du rhin

department: esbs

country: France

institute: strasbourg university

data_processing:
Reads were mapped onto the hg38 assembly of the Homo sapiens genome using Tophat 2.0.10  and bowtie version 2-2.1.0
From bam file, read counts are normalized and log2 transform using qlucore omics explorer version 3.2(45) as described in www.qlucore.com/DocumentBank/Qlucore White Paper Analyzing RNA-seq data E.pdf
Genome_build: hg38
Supplementary_files_format_and_content: read counts

source_name: Glioblastoma cancer stemcell TG1

growth_protocol: The cells were grown as described in

extract_protocol:
Total RNA was extracted with RNeasy® mini kit (Qiagen)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: growth

value: Proliferation

tag: growth protocol

value: Change medium twice a week


title: JHHS8_S2

source_name: Glioblastoma cancer stemcell TG1_C1


title: JHH17_S2

value: Quiescence

value: Medium pH 6.5


title: JHHS10_S2

value: No medium change during 9 days


title: JHHS3_S1

source_name: Glioblastoma cancer stemcell TG10


title: JHHS4_S2

source_name: Glioblastoma cancer stemcell TG10_C1


title: JHHS9_S1


title: JHHS14_S1


title: JHHS2_S2


title: JHH20_S1

value: Normal medium with SKF96365 (10 µM)


title: JHHS5_S1


title: JHHS12_S2

value: Medium pH 6.2


title: 20_9E

city: Vestec by Prague

first: Radek

last: Šindelka

address: Průmyslová 595

country: Czech Republic

institute: Institute of Biotechnology, Czech Academy of Science, v.v.i.

data_processing:
Ribosomal RNA sequences were removed using sortmerna (version 2) and the SILVA rRNA database (version 119). Low quality reads and adaptor sequences were removed using Trimmomatic PE. Reads were aligned against the reference Xenopus laevis genome  using STAR (version 2.4.2a).
Annotated reads were counted using htseq-count with the reference model XL9.1_annot_v1.8.1.primary.gff3
Normalized number of reads was generated by DESeq2 using precalculated sizeFactors based on RT-qPCR experiment.
Genome_build: Xla.v91.repeatMasked.fa (ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla9.1/)
Supplementary_files_format_and_content: Tab-delimited text files include non-normalized and DESeq2 normalized number of reads for each Sample

organism: Xenopus laevis

source_name: Oocyte

extract_protocol:
20 oocytes was mounted to OCT medium and sliced using cryostat. RNA was isolated using TRIzol and reprecipitated by 2.5M Lithium Chloride. 500 ng of total RNA was used for rRNA depletion. Illumina TruSeq RNA Sample Prep Kit was used with rRNA depleted RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: Stage 1

tag: biological replicate

tag: position

value: Vegetal pole


title: 20_9D

value: Vegetal


title: 20_9C

value: Equatorial


title: JHHS11_S1


title: 15Y29P5

city: Taiyuan

first: Ruifeng

last: Liu

state: Shanxi

address: No. 1 Dong San Dao Xiang

department: Institute of Dermatology

country: China

institute: Taiyuan City Centre Hospital

data_processing:
The reads were aligned to the reference genome/transcriptome with BWA-MEM software and circRNAs were detected and annotated with CIRI software
Genome_build: hg19
Supplementary_files_format_and_content: circRNA expression profiles

source_name: Mesenchymal stem cells

growth_protocol: Skin derived mesenchymal stem cells were cultured in DMDM/F12 medium and adherent cultured

extract_protocol:
Total RNA from each sample was used to prepare the circRNA sequencing library
5ug total RNA were pretreated to enrich circRNA using CircRNA Enrichment Kit (Cloud-seq Inc, USA). RNA libraries were constructed by using pretreated RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA). The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

tag: tissue

value: Skin-derived MSC

tag: passages

tag: status

value: Psoriasis


title: 14Z70P5

value: Normal


title: 14Z66P5


title: 15Y26P5


title: 15Z3P5


title: 15Y15P5


title: 20_8D


title: 20_8C


title: JHHS7_S1


title: JHHS6_S2

source_name: HA rimary astrocyte cell line


title: MDA-MB-231 PVT1 targeting sgNRA R2 rep2


title: Exp4_Th0

city: Turku

first: Imran

middle: Ahammad

last: Mohammad

state: Finland

address: Tykistokatu 6

department: Lymphocytes and Inflammation

country: Finland

institute: Turku center for Biotechnology

data_processing:
RNA-seq with pair end 100 nt read length was performed at the Turku Center for Biotechnology with HiSeq 2000 instrument using Illumina TruSeq® chemistry according to the manufacture’s instruction.
The RNA-seq data were mapped using Tophat (version 2.0.14) with default parameters to the mm10 mouse reference genome, UCSC mouse transcriptome from Illumina's Igenomes collection. Read counts were computed with HTSeq-count with options stranded false, feature type exon, sorted by name and mode union.  Negative binomial generalized log-linear model to the read counts for each gene was fitted and genewise statistical tests using pairwise experimental design was performed with Bioconductor edgeR package. The common Negative Binomial dispersion was estimated with the experimental design, the abundance-dispersion trend was estimated by Cox-Reid approximate profile likelihood, and the tagwise dispersions for the generalized linear models were empirical Bayes estimates with expression levels specified by a log-linear model. Genes that did not have more than 1 cpm (count per million) at least in four samples were filtered out of the analysis.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample

source_name: CD4 T cells

extract_protocol:
RNA was isolated from the cultured CD4 T cells using  RNeasy isolation kit (Qiagen).
Libraries were prepared according to the protocols of Illumina

treatment_protocol: Mouse splenocytes were isolated from 8–10-week-old C57BL/6 mice. CD4+CD62L+ T cell Isolation Kit II (Miltenyi Biotec, Bergisch Gladbach, Germany) was used to obtain naïve T cells. The cells were activated with plate bound anti-CD3 (1μg/mL, BD PharMingen, San Diego, CA) and anti-CD28 (1μg/mL) for all Th0, Th17 and iTreg conditions. For Th17 polarization, IL6 (30ng/ml, PeproTech, UK), TGFb1 (5ng/ml) and neutralizing antibodies anti-IL4 and anti-IFNγ (both at 10 μg/mL, BD PharMingen, San Diego, CA) were added. For iTreg conditions IL2 (10ng/ml, R&D system, Minneapolis, MN) and TGFb1 (10ng/ml) were used.

tag: treatment


title: 20_8B

value: Animal


title: 20_7D


title: 20_9B


title: Exp3_Th0


title: Exp4_Treg

value: Treg


title: Exp3_Th17


title: Exp4_Th17


title: Exp1_Th17


title: Exp2_Treg


title: Exp2_Th0


title: Exp1_Treg


title: 20_8E


title: 20_9A

value: Animale pole


title: 20_7B


title: Exp1_Th0


title: 20_7C


title: 20_7A


title: Wildtype control mouse  biological replicate 2

city: Madison

first: Akihiro

last: Ikeda

state: Wisconsin

address: 5322 Genetics Biotechnology Center, 425 Henry Mall

department: Medical Genetics

institute: University of Wisconsin-Madison

description: cds_exp.diff, cds.diff,  gene_exp.diff, isoform_exp.diff, promoters.diff, splicing.diff, tss_group_exp.diff

data_processing:
QC raw sequences with fastqc v0.10.1
trimmed 5' adaptor (cut 12 bases) with FASTX-toolkit v 0.0.14, fastx_trimmer package
QC trimmed sequences with fastqc v 0.10.1
mapped sequences with tophat v2.0.9
sorted by chromosome with samtools  sort v 0.1.19
determined differential expression with cuffdiff v2.1.1
Genome_build: UCSC mm10
Supplementary_files_format_and_content: cuffdiff plain text output files with log2 transformed differential expression, pval, and qvals

source_name: whole heart homogenate

extract_protocol:
Hearts were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.
Libraries were constructed using Illumina TruSeq mRNA Sample Prep Guide #15031047 Revision E with 1ug RNA per sample.

tag: strain

value: FVB/NJ and C57BL6/J

tag: age

value: 6 mo

value: whole heart

tag: genotype

value: WT


title: Tmem135 transgenic mouse biological replicate 3


title: Wildtype control mouse  biological replicate 1


title: Tmem135 transgenic mouse biological replicate 2


title: Tmem135 transgenic mouse biological replicate 1


title: Wildtype control mouse  biological replicate 3


title: 20_8A


title: Exp3_Treg


title: 20_7E


title: Hypothalamus Dlx1 IP

city: Gwangju

first: JANGHYUN

last: KIM

state: Gwangju

address: 33, YONGBONG-RO, BUK-GU, GWANGJU

department: Oral pathology

country: South Korea

institute: CNUDH

data_processing:
ChIP-seq reads were filtered for quality and trimmed using NGSGCToolkit v2.3.3
ChIP-seq reads were aligned to the mm10 genome assembly using BWA 0.7.15
peaks were called using MACS2 version 2.1.1 with the following setting: -p 0.001 -B --nomodel --extsize 200.
Genome_build: mm10
Supplementary_files_format_and_content: bw files were generated using bedGraphToBigWig

source_name: Mouse Hypothalamus

extract_protocol:
To perform the ChIP assays with mouse embryonic tissues, we dissected E16 hypothalamuses. The tissues were dissociated completely, fixed by 1% formaldehyde for 10 min at room temperature, and quenched by 125 mM glycine. Next, cells were washed with PBS and lysed with lysis buffer (0.5% SDS, 5 mM EDTA, 50 mM Tris-HCl, pH 8.0, Protease inhibitor cocktail) and were subjected to sonication using bioruptor. Supernatant was incubated with Dlx1 homemade antibody and protein A agarose beads to precipitate the hexamer/chromatin complex for overnight at 4°C.
ChIP-seq libraries were constructed with the llumina's instructions accompanying the DNA Sample Kit. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

value: E16 embryo brain

value: Mouse Hypothalamus

tag: chip antibody

value: Dlx1 made by Bora Lee


title: CRG-JK2-3-CHRONIC-2

city: MELBOURNE

first: SANGKYU

state: VICTORIA

address: 305 GRATTAN ST

department: RESEARCH

country: Australia

institute: PETER MACCALLUM CANCER CENTRE

data_processing:
Illumina CASAVA 1.8.2 was used for base calling and quality control was performed using RNA-SeQC v1.1.7
Adapters were trimmed using Cutadapt v1.7
Reads were mapped to the mouse reference genome (mm10) using TopHat2
HTSeq v0.5 was used to count the number of reads per gene
Limma-Voom method was applied for data normalisation and differential gene expression analysis
Genome_build: mm10
Supplementary_files_format_and_content: csv file includes normalized counts for each sample

growth_protocol: Eμ-Crlf2/Jak2R683G-pREBIR-shRenilla.713 or Eμ-Crlf2/Jak2R683G-pREBIR-shJak2.3323 cells were established in NSG mice for 10 days prior to shRNA induction by doxycycline treatment

extract_protocol:
Total RNA was extracted from (dsRed+/eBFP2+) sorted splenocytes using the NucleoSpin RNA isolation kit (Macherey-Nagel) as per manufacturer's instructions
RNA libraries were prepared for sequencing according to standard Illumina protocols (TruSeq RNA Sample Preparation Guide v2 Guide)

treatment_protocol: Doxycycline treated recipient mice of Eµ-Crlf2/Jak2R683G-pREBIR-shRenilla.713 or Eµ-Crlf2/Jak2R683G–pREBIR-shJak2.3323 cells were sacrificed at either 48 hr (acute knockdown) or 21 days (chronic knockdown) post shRNA induction and RNA-Seq was performed using total RNA isolated from dsRed+/eBFP2+ sorted splenocytes.

tag: strain background

value: Dox (21 days)

tag: replicate

value: Replicate 2


title: CRG-JK2-3-ACUTE-2

value: Dox (2 days)


title: CRG-JK2-3-CHRONIC-1

value: Replicate 1


title: CRG-JK2-3-ACUTE-4

value: Replicate 3


title: CRG-JK2-3-ACUTE-1


title: Hypothalamus input DNA

tag: cell type


title: CRG-REN-ACUTE-1

source_name: CRG-REN-ACUTE

tag: genotype/variation


title: CRG-REN-ACUTE-2


title: ATAC_TET3_3

city: Cambridge

first: Christel

last: Krueger

state: -- None --

address: Babraham Research Campus

country: United Kingdom

institute: Babraham Institute

data_processing:
Libraries were sequenced on the Illumina HiSeq 2500 platform.
(RNA-Seq) Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the mouse GRCm38 genome assembly using Tophat 2.0.12 (options -g2) guided by the gene models from the Ensembl v70 release. BAM files were imported to Seqmonk v36.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) .
(ATAC-Seq) Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the mouse GRCm38 genome assembly using Bowtie 2 v2.2.5 (default parameters) . BAM files were imported to Seqmonk v36.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) .
(ChIP-Seq) Reads were trimmed using Trim Galore v0.4.2 (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) using default parameters to remove the standard Illumina adapter sequence. They were mapped to the mouse GRCm38 genome assembly using Bowtie 2 v2.2.5 (default parameters) . BAM files were imported to Seqmonk v36.0. (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/) .
Genome_build: GRCm38
Supplementary_files_format_and_content: (RNA-Seq) Quantitated RNA-Seq data file is tab delimited and contains the following columns: (1) gene name (Ensembl) ; (2) Chromosome; (3) Start; (4) End; (5) Strand; (6) ID (Ensembl) (7) Description (Ensembl) ; (8-16) log2 RPM value.
Supplementary_files_format_and_content: (ChIP-Seq) Quantitated ChIP-Seq data file is tab delimited and contains the following columns: (1) Chromosome; (2) Start; (3) End; (4-12) log2 RPM value per 500 bp tile.
Supplementary_files_format_and_content: (ATAC-Seq) Quantitated ATAC-Seq data file is tab delimited and contains the following columns: (1) Chromosome; (2) Start; (3) End; (4-9) log2 RPM value per 500 bp tile.

growth_protocol: E14 mouse embryonic stem cells were grown under standard serum/LIF conditions (DMEM 4,500 mg/l glucose, 4 mM L-glutamine, 110 mg/l sodium pyruvate, 15% fetal bovine serum, 1 U/ml penicillin, 1 mg/ml streptomycin, 0.1 mM nonessential amino acids, 50 mM b-mercaptoethanol, and 103 U/ml LIF).

extract_protocol:
(RNA-Seq)Prior to RNA isolation cell lines carrying different Tet3 constructs were enriched for cells with TET3 expression by flow sorting for GFP fluorescence using a BD Influx High-speed Cell Sorter. RNA was isolated using Qiagen RNeasy Micro columns and treated with DNaseI (Ambion).
(ChIP-Seq)Chromatin immunoprecipitation was performed as described in (Schmidt et al. 2009). ES cell lines expressing different TET3 isoforms  were cross-linked and harvested. 10 ug of a TET3 antibody developed with Millipore (ABE290) was used per precipitation, and cross-linked, sonicated nuclear material was used as input control.
(ATAC-Seq)ATAC-seq was performed according to the original protocol (Buenrostro et al., 2015) with the following modifications. 10,000 cells were treated with 0.5μl Tn5 transposase in a total volume of 20 μl for 30 minutes at 37 degrees.
(RNA-Seq)Indexed RNA-Seq libraries were constructed from 500 ng total RNA using theTruSeq Stranded Total RNA Library Prep Kit for Illumina with Ribo-Zero Gold.
(ChIP-Seq)Sequencing libraries from precipitated DNA were prepared using the Diagenode MicroPlex Library Preparation Kit.
(ATAC-Seq)Sequencing libraries were prepared according to the original protocol (Buenrostro et al., 2015).  A total of 15 PCR cycles  and two rounds of Ampure Bead clean-up were performed.

value: E14 embryonic stem cell (ESC)


title: Exp2_Th17


title: ATAC_TET3_2


title: ATAC_CTR_3

value: GFP


title: ATAC_CTR_2


title: ATAC_CTR_1


title: ChIP_Input


title: ChIP_TET3-trunc_3

value: TET3 (Millipore ABE290, LN:RA1205021)


title: ChIP_TET3-trunc_2


title: ChIP_TET3-CXXC_1


title: ChIP_TET3-CXXC_2


title: ChIP_TET3-CXXC_3


title: ChIP_TET3-trunc_1


title: CRG-JK2-3-CHRONIC-4


title: RNA_CTR_2

description:
total RNA rRNA depleted
RPM_log2_RNA-Seq.txt


title: ChIP_TET3_1


title: RNA_CTR_3


title: CRG-REN-ACUTE-4


title: RNA_TET3-trunc_3


title: RNA_CTR_1


title: ATAC_TET3_1


title: RNA_TET3_1


title: RNA_TET3_2


title: RNA_TET3-trunc_2


title: RNA_TET3_3


title: orang_iPSC_w5_af057

description:
af057
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

data_processing:
Paired-end Illumina reads were trimmed from the 3’ end of read1 and read2 to 100x100bp for human and rhesus libraries and 80x80bp for chimpanzee and orangutan based on sequence quality. Bowtie2 v2.2.1 was used with the “--very-sensitive” parameter to filter reads against the repeatMasker library for each respective species which were removed from further analysis.
STAR v2.5.1b was used to map RNA-seq reads to hg19 (human, Genome Reference Consortium GRCh37, 2009), panTro4 (chimpanzee, CGSC Build 2.1.4, 2011), ponAbe2 (orangutan, WUSTL Pongo_albelii-2.0.2, 2007), and rheMac8 (rhesus macaque, Baylor College of Medicine HGSC Mmul_8.0.1, 2015) respective to the origin species. STAR was run with the default parameters with the following exceptions: --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.04, --alignIntronMin 20, --alignIntronMax 1000000, and --alignMatesGapMax 1000000. STAR alignments were converted to genomic position coverage with the bedtools command genomeCoverageBed -split.
DESeq2 v1.14.1 was used to provide basemean expression values and differential expression analysis across the time course in each species using FANTOM5 lv3 (Hon et al., 2017) transcript annotations (lifted to other species by transMap). Total gene coverage for a gene was converted to read counts by dividing the coverage by N+N (100+100 for human and rhesus and 80+80 for chimpanzee and orangutan) since each paired-end NxN mapped read induces a total coverage of N+N across its genomic positions.
Cufflinks v2.0.2 suite was used to assemble transcript predictions of potentially unannotated lncRNAs in each species and the Cuffmerge tool was used to combine these annotations with FANTOM5 transcripts.
Cufflinks-assembled and merged transcript sets were then projected through the cactus alignment to each of the other three genomes (hg19, panTro4, ponAbe2, and rheMac8, respectively).
RSEM v1.3.0 was used to provide TPM expression values for Cufflinks generated transcripts.
Genome_build: hg19, panTro4, ponAbe2, and rheMac8
Supplementary_files_format_and_content: *tsv, *txt: Tab-delimited text files include either basemean values (DESeq) or TPM values (RSEM) for each time point in each of the respective species.

organism: Pongo abelii

source_name: Induced pluripotent stem cells

growth_protocol: The Eiraku et al., 2008 protocol was optimized for use with human ESCs, rhesus ESCs, chimpanzee iPSCs, and orangutan iPSCs. Human H9 and rhesus LyonESC1 embryonic stem cells were cultured on mouse embryonic fibroblasts with KSR-8 media (KO DMEM/F-12 + 20% KOSR, 1% NEAA, 1% GlutaMAX, 1% Pen-strep, and 0.1mM 2-mercaptoethanol supplemented with 8ng/mL bFGF). Embryonic stem cells were manually lifted from MEF feeders and allowed to self-form into embryoid bodies on low attachment plates (Corning) in KSR media. Chimpanzee and orangutan induced pluripotent stem cells were grown in feeder-free conditions on matrigel (Corning) with mTeSR-1 (Stem Cell Tech) or vitronectin (ThermoFisher) with Essential-8 Flex media (ThermoFisher), respectively, and 10,000 cells per EB were aggregated using AggreWell-800 plates (Stem Cell Technologies) in Aggrewell media (Stem Cell Technologies) supplemented with 10 uM Y-27632 rock inhibitor (ATCC) and transferred to low attachment plates (Corning) on day 2. Both methods supplemented the respective media with 500ng/mL DKK1 (Peprotech), 500 ng/mL NOGGIN (R & D Systemes), 10 uM SB431542 (Sigma), and 1 uM Cyclopamine V. californicum (VWR) for the first 18 days of differentiation. The media was changed to Neuralbasal (Invitrogen) supplemented with N2 (Gibco) and 1 uM Cyclopamine on day 18. At this time, chimpanzee and orangutan neurospheres were also supplemented with 10ng/mL bFGF and 10ng/mL EGF to improve survivability in Neuralbasal media. After day 26, all cultures were grown in Neuralbasal/N2 media without any added factors. Total RNA was extracted at weekly time points for each species. This timeline was adjusted accordingly in rhesus, harvesting on days 6, 11, 17, 22, and 28, to account for differences in gestational timing.

extract_protocol:
Trizol + RNeasy or Direct-zol cleanup, followed by ribozero rRNA depletion.
Strand-specific dUTP followed by TruSeq DNA library prep kit.

tag: cell line

tag: time point

value: week 5


title: orang_iPSC_w4_af052

description:
af052
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

value: week 4


title: orang_iPSC_w5_af058

description:
af058
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: orang_iPSC_w3_af051

description:
af051
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

value: week 3


title: orang_iPSC_w4_af056

description:
af056
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: orang_iPSC_w3_af055

description:
af055
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: ChIP_TET3_2


title: orang_iPSC_w1_af049

description:
af049
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

value: week 1


title: orang_iPSC_w2_af054

description:
af054
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

value: week 2


title: orang_iPSC_w2_af050

description:
af050
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: S1330 rep3

city: Beijing

first: Hui

last: Jiang

address: NO.8 Zhonguancun South Street

institute: China Insititute of Veterinary Drug Control

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2 mapping to reference genome
count counting
Genome_build: GRCm38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: Macrophage Line RAW264.7

growth_protocol: The mouse macrophage cell line RAW264.7 was propagated in Dulbecco’s modified Eagle’s medium (DMEM) with 10% fetal bovine serum.

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
HiSeq Sequencing Protocol

treatment_protocol: Infected with brucella strains at a 200 multiplicity of infection

tag: infection

value: infected with brucella

tag: infective strain

value: Brucella suis 1330 strain


title: S2 rep3

value: Brucella suis S2 strain


title: S1330 rep1


title: orang_iPSC_w0_af053

description:
af053
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

value: week 0


title: orang_iPSC_w1_el022

description:
el022
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: orang_iPSC_w0_af048

description:
af048
Processed data file: ponAbe2.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: S2 rep2


title: chimp_iPSC_w5_af047

description:
af047
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

organism: Pan troglodytes


title: chimp_iPSC_w5_af041

description:
af041
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: RNA_TET3-trunc_1


title: rhesus_ESC_w5_fj080

description:
fj080
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt

organism: Macaca mulatta

source_name: embryonic stem cells

value: LYON-1 ESC


title: chimp_iPSC_w4_af046

description:
af046
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: rhesus_ESC_w4_fj122

description:
fj122
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: chimp_iPSC_w4_af045

description:
af045
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: rhesus_ESC_w4_fj121

description:
fj121
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: rhesus_ESC_w5_fj079

description:
fj079
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: chimp_iPSC_w3_af038

description:
af038
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: rhesus_ESC_w3_fj120

description:
fj120
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: chimp_iPSC_w3_af044

description:
af044
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: rhesus_ESC_w3_fj119

description:
fj119
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: chimp_iPSC_w2_af036

description:
af036
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: S1330 rep2


title: rhesus_ESC_w1_fj115

description:
fj115
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: S2 rep1


title: rhesus_ESC_w1_fj116

description:
fj116
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: rhesus_ESC_w0_fj114

description:
fj114
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: rhesus_ESC_w2_fj117

description:
fj117
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: rhesus_ESC_w0_fj113

description:
fj113
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: chimp_iPSC_w0_af033

description:
af033
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: rhesus_ESC_w2_fj118

description:
fj118
Processed data file: rheMac8.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: chimp_iPSC_w2_af043

description:
af043
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: D-A004A replicate 1

first: Wei

last: Wei

address: Chaoyang District, Beichen West Road, Campus #1, No.2

department: State Key Lab of Plant Genomics

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to soybean whole genome using Tophat software (http://ccb.jhu.edu/software/tophat/).
Reads per kilo bases per million reads (RPKM) were calculated.
Genome_build: Glycine max (https://phytozome.jgi.doe.gov/pz/portal.html)
Supplementary_files_format_and_content: Excel files containing RPKM value of each sample

organism: Glycine max

source_name: leaf

growth_protocol: The seeds were germinated on soil in sunlight greenhouse.

extract_protocol:
Total RNA was extracted using RNeasy mini kit (QIAGEN company).
Library were prepared according to the protocol of RNA-Seq RNA sample Prep Kit (Illumina)

treatment_protocol: Two-week-old soybean seedlings were dehydrated in air for 6h, the trifoliates were harvested for RNA extraction.Well-watered plants were also harvested for RNA extraction.

tag: transgenic line

tag: condition

value: dehydrated


title: D-Null replicate 2


title: chimp_iPSC_w1_af035

description:
af035
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: Null replicate 2

value: well watered


title: B010C replicate 2


title: D-A005B replicate 2


title: A005B replicate 2


title: Null replicate 1


title: D-A005B replicate 1


title: B010C replicate 1


title: D-A004A replicate 2


title: chimp_iPSC_w1_af034

description:
af034
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: D-Null replicate 1


title: D-B010C replicate 1


title: A004A replicate 1


title: A004A replicate 2


title: A005B replicate 1


title: CanS carcass

status: Public on May 30 2018

city: Cold Spring Harbor

first: Yixin

last: Zhao

state: NEW YORK

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

description: Small RNAs

data_processing:
For RNA seq, raw data from RNA-seq were mapped to the D. melanogaster genome (r6.04), and normalized using Tophat (Trapnell, et al. 2009) and SeqMonk version 1.36.0 (http://www.bioinformatics.babraham.ac.uk/projects/seqmonk/). The expression level of each gene was calculated in Reads Per Kilobase per Million (RPKM) and log2 transformed.
For small RNA seq, sequenced reads were trimmed for adaptor sequence, masked for low-complexity or low-quality sequence, and collapsed to the fasta format. The expression of mature miRNA was then measured using the Mapper and Quantifier modules of miRDeep2 version 2.0.0.7 (Friedlander, et al. 2012) with default parameters, normalized by the total reads matching all the miRNA precursors per library, and scaled as Reads Per Million (RPM).
Genome_build: FlyBase Drosophila melanogaster r6.04
Supplementary_files_format_and_content: gene expression, miRNA expression and fasta files include clean reads and raw read count;

organism: Drosophila melanogaster

source_name: CanS carcass

growth_protocol: Fruit flies were cultured under 25℃

extract_protocol:
Tissues were dissected on dry ice, and RNA was harvested using Trizol reagent.
Libraries were prepared according to Illumina's instructions

value: Canton-S

value: 3-5d adult

tag: tissue

value: carcass

tag: molecule subtype

value: Small RNAs


title: CanS ovaries

description: Small RNAs

source_name: CanS ovaries

value: ovaries


title: chimp_iPSC_w0_af032

description:
af032
Processed data file: panTro4.RSEM.gene_expression.txt
Processed data file: deseq_baseMean_allF2.txt


title: D-B010C replicate 2


title: Z56 testes

description:
Small RNAs
miR-313-5p_target

source_name: Z56 testes

value: testes


title: Z56 ovaries

description:
Small RNAs
miR-313-3p_target

source_name: Z56 ovaries


title: Overexpressor HSFA1b-RFP Heat stress rep3

city: Colchester

first: Philip

middle: M

last: Mullineaux

state: Essex

address: Wivenhoe Park

department: Environmental and Plant Bioscience Research Group

institute: University of Essex

data_processing:
Raw short reads files were obtained in fastq format
Illumina adapters and low quality as well as overrepresented Illumina TruSeq primer sequences were trimmed from fastq files using in-house made programs
Quality-trimmed RNA-seq reads were aligned to the Arabidopsis thaliana genome (TAIR10) using the aligner GSNAP with the known splices options for RNA-seq (5 mismatches allowed).
Transcript assembly, absolute expression analysis (Fragments per kilobase exon model; FPKM) and differential expression analysis were carried out using Cufflinks and Cuffdiff (Trapnel et al 2008) using the geometric library normalization method with threshold q ≤ 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: text files containing FPKM s with p-values, q-values, and fold changes and separate text file containing normalized FPKM values from each replicate

organism: Arabidopsis thaliana

source_name: Leaves

growth_protocol: Arabidopsis thaliana Col-0 ecotype was obtained from the European Arabidopsis Stock Centre and 35S:HSFA1b-RFP/Col-0 plants have been described previously (Bechtold et al 2013 J. Exp. Bot. 64: 3467). Plants were grown in a controlled environment chamber under the following conditions: 8/16 hours light/dark cycles, temperature 23°C, relative humidity 60% (growth vapour pressure deficit was 1kPa), light intensity of 120 µmols m-2 s-1. Three Arabidopsis seed was sown onto a wetted soil mix (Scotts Levingtons F2+S compost) in pots (5.5 cm diameter x 5.5 cm deep) and stratifed for 2 days at 4°C before transfer to the growth conditions. Seedlings were thinned to one per pot and grown until 5 weeks after germination.

extract_protocol:
Plants were harvested immedaitely at the end of the stress and snap frozen in liquid nitrogen. Plant material was ground in liquid nitrogen to a fine powder uisng a mortar and pestle. RNA extraction was carried out using TRI-reagent (Life Technologies Inc.) according to the manufacturer's instructions, with the following modifications: Each sample was homogenised in 1ml of TRI-reagent, vortexed for 2 min and 200 µl chlorofrom added, vortexed and the phases separated by centrifugation (18,400 x g for 20 min). Nucleic acid was precipitated from the aqueous phase (500 µl) by adition of an equal volume of isopropanol. The nucleic acid pellet was dissovled in 30 µl sterile water and genomic DNA was removed using the DNA-free kit (Ambion Inc.) according to the manufacturer's instructions.
Libraries were constructed using Illumina TruSeq RNA library preparation kit at The Genome Analysis Centre (TGAC, Norwich, UK)

treatment_protocol: Plants were subjected to heat stress treatment at 37°C for 30 minutes with relative humidity of 86% to maintain the vapour pressure deficit at 1 kPa.

tag: ecotype

value: Columbia 0

value: 5 weeks

value: wild type

tag: treatment

value: heat stress


title: Overexpressor HSFA1b-RFP Heat stress rep2

tag: age


title: Overexpressor HSFA1b-RFP Non-stress rep3

tag: genotype

value: no stress


title: Tame_fox_basal_forebrain_ID541

last: Clark

address: 227 Biotech Building

institute: Cornell University

description:
Illumina RNA-seq
processed data file: fox_forebrain_read_counts_by_gene.txt.gz

data_processing:
Illumina CASAVA 1.8.2 software was used for basecalling.
Illumina reads QC was performed using FastQC software. Adapter containing reads were trimmed by Trimmomatic.
De novo assembly of the fox brain transcripts were performed with all 1.8 billion RNA-seq reads by Trinity. rRNA and mtDNA reads were filtered out by custom scripts before the assembly. Among the 321,151 assembled transcripts, short repetitive contigs due to gene families and repetitive sequences were removed by repeat masking and BLAT within them. The transcripts were then annotated by blasting against dog Ensembl transcripts. The RNA-seq reads were mapped to the transcript contig sets by BWA with a maximum of 4 mismatches. Uniquely mapped read counts were summarized on annotated transcripts using BEDTools. Differentially expressed genes between tame and aggressive individuals in the two brain tissues were detected by edgeR package in Bioconductor at 5% FDR level (false discovery rate, q-value<0.05). Normalization and expression levels estimation (FPKM: Fragments Per Kilobase-pair of exon Model) were also calculated using edgeR.
Genome_build: Dog Ensembl CanFam3/Ens68
Supplementary_files_format_and_content: gzipped tab-delimited text file includes the raw read counts for expressed genes annotated with a dog Ensembl gene ID.

molecule: polyA RNA

organism: Vulpes vulpes

source_name: 1.5 year adult tame fox right basal forebrain

extract_protocol:
Total RNA samples were extracted from all 48 brain samples with Qiagen RNeasy Lipid Tissue Mini Kit (Qiagen, CA). QIAzol Lysis Reagent was used to remove excessive lipids in the brain tissue.  A260/A280 absorption ratios and RNA concentrations were measured by NanoDrop ND-1000 Spectrophotometer (Thermo Scientific, DE).
RNA-seq libraries were constructed from 1.5 µg total RNA using Illumina TruSeq RNA Sample Preparation Kits v2 according to manufacture protocols (Illumina Inc., CA), and sequenced on an Illumina HiSeq2000 instrument.

tag: developmental stage

value: 1.5 year adult

value: Right basal forebrain

tag: Sex

value: male


title: Aggr_fox_basal_forebrain_ID595

source_name: 1.5 year adult aggressive fox right basal forebrain


title: Aggr_fox_basal_forebrain_ID540


title: Aggr_fox_basal_forebrain_ID539


title: Aggr_fox_basal_forebrain_ID537


title: Aggr_fox_basal_forebrain_ID534


title: Aggr_fox_basal_forebrain_ID536


title: Non-stress rep3


title: Non-stress rep2


title: Aggr_fox_basal_forebrain_ID529


title: Heat stress rep2


title: Heat stress rep1


title: Aggr_fox_basal_forebrain_ID538


title: Overexpressor HSFA1b-RFP Non-stress rep1


title: Aggr_fox_basal_forebrain_ID532


title: Non-stress rep1


title: Aggr_fox_basal_forebrain_ID533


title: Overexpressor HSFA1b-RFP Non-stress rep2


title: Aggr_fox_basal_forebrain_ID531


title: 35S_control_NS_rep2

description: 35S_no_stress_PE_summits.bed, 35S_no_stress_PE_peaks.xls, 35S_no_stress_PE_peaks.narrowPeak

data_processing:
Basecalls performed using CASAVA version 1.8.2
Illumina adapters and low quality as well as overrepresnted illumina TruSeq primer sequences were trimmed from fastq files using in-house made programs
Quality-trimmed ChIP-seq reads were aligned to the Arabidopsis thaliana genome (TAIR10) using the aligner GSNAP with the following options -t 6 -A sam -m 0.01 -d Arabidopsis_thaliana
Conversion of SAM files to BAM followed by filtering unmapped reads, sorting and indexing were performed using samtools
peaks were called using MACS2 with the following settings: -f BAMPE -g 1.2e8 -q 0.05 -B –trackline
Genome_build: TAIR10
Supplementary_files_format_and_content: BED files containing ChIP-seq narrow peaks and peak summits, excel spreadsheet files containing all peaks with p-values, q-values, and fold enrichments

growth_protocol: Arabidopsis thaliana Col-0 ecotype plants were grown in a controlled environment at the following conditions: 8/16 hours light/dark cycles, temperature 23C, relative humidity 60%, light intensity of 120 micro mole / meter second

extract_protocol:
Plants were crosslinked in 1% formaldehyde solution using the vacuum infiltration method, nuclei were isolated then lysed, extracted chromatin was sheared using sonication, DNA-HSFA1b complexes were captured using antibodies specific to the tag proteins. DNA-HSFA1b-antibody complexes were then purified using protein A-sepharose beads.
Libraries were constructed using Illumina TruSeq ChIP-seq library preparation kit at The Genome Analysis Centre (TGAC, Norwich, UK)

treatment_protocol: Plants were subjected to heat stress treatment at 37C for 30 minutes with relative humidity of 86% to maintain the vapour pressure deficit (VPD) at 1 kilo pascal.

tag: antibody

value: Anti-RFP (Abcam, ab62341)


title: Overexpressor HSFA1b-RFP Heat stress rep1


title: Heat stress rep3


title: Aggr_fox_basal_forebrain_ID530


title: 35S_control_NS_rep1


title: Tame_fox_basal_forebrain_ID491


title: 35S:HSFA1b_HS_rep2

description: 35S_heat_stress_PE_summits.bed, 35S_heat_stress_PE_peaks.xls, 35S_heat_stress_PE_peaks.narrowPeak


title: Tame_fox_basal_forebrain_ID490


title: 35S:HSFA1b_HS_rep1


title: 35S:HSFA1b_NS_rep2


title: Tame_fox_basal_forebrain_ID489


title: 35S:HSFA1b_NS_rep1


title: 35S_control_HS_rep2


title: 35S_control_HS_rep1


title: Tame_fox_basal_forebrain_ID487


title: Tame_fox_basal_forebrain_ID488


title: NP_control_HS_rep2

description: native_heat_stress_summits.bed, native_heat_stress_peaks.xls, native_heat_stress_peaks.narrowPeak

value: Anti-GFP (Abcam, ab290)


title: NP_control_HS_rep1


title: NP:HSFA1b_NS_rep2

description: native_no_stress_summits.bed, native_no_stress_peaks.xls, native_no_stress_peaks.narrowPeak


title: NP:HSFA1b_HS_rep1


title: Tame_fox_basal_forebrain_ID492


title: Tame_fox_basal_forebrain_ID486


title: NP:HSFA1b_NS_rep1


title: Tame_fox_basal_forebrain_ID484


title: NP_control_NS_rep1


title: Tame_fox_basal_forebrain_ID482


title: Tame_fox_basal_forebrain_ID485


title: Tame_fox_basal_forebrain_ID483


title: NP_control_NS_rep2


title: NP:HSFA1b_HS_rep2


title: Aggr_fox_prefrontal_cortex_ID240

description:
Illumina RNA-seq
processed data file: fox_cortex_read_counts_by_gene.txt.gz

source_name: 1.5 year adult aggressive fox right prefrontal cortex

value: Right prefrontal cortex


title: Aggr_fox_prefrontal_cortex_ID237


title: Aggr_fox_prefrontal_cortex_ID239


title: Aggr_fox_prefrontal_cortex_ID238


title: Aggr_fox_prefrontal_cortex_ID236


title: Aggr_fox_prefrontal_cortex_ID235


title: Aggr_fox_prefrontal_cortex_ID234


title: Aggr_fox_prefrontal_cortex_ID233


title: Aggr_fox_prefrontal_cortex_ID230


title: Aggr_fox_prefrontal_cortex_ID232


title: Tame_fox_prefrontal_cortex_ID192

source_name: 1.5 year adult tame fox right prefrontal cortex


title: Aggr_fox_prefrontal_cortex_ID231


title: Aggr_fox_prefrontal_cortex_ID229


title: Tame_fox_prefrontal_cortex_ID190


title: Tame_fox_prefrontal_cortex_ID189


title: Tame_fox_prefrontal_cortex_ID191


title: Tame_fox_prefrontal_cortex_ID188


title: Tame_fox_prefrontal_cortex_ID181


title: Tame_fox_prefrontal_cortex_ID187


title: Tame_fox_prefrontal_cortex_ID183


title: Tame_fox_prefrontal_cortex_ID184


title: Tame_fox_prefrontal_cortex_ID185


title: Tame_fox_prefrontal_cortex_ID186


title: Control replicate 1

description:
Gene expression in testes
2a_1

source_name: Control

tag: strain background

value: Control


title: Tame_fox_prefrontal_cortex_ID182


title: Control replicate 2

description:
Gene expression in testes
2a_2

tag: genotype/variation

value: 3-5d adult


title: Dm310s KO replicate 1

description:
Gene expression in testes
2b_1

source_name: Dm310s KO

value: Dm310s mutant


title: Dm310s KO replicate 2

description:
Gene expression in testes
2b_2


title: rspd-WT-2

city: Smithville

first: Jianqiang

last: Bao

state: Texas

address: 1808 Park Road 1C (P.O. Box 389), Smithville  TX 78957

department: Epigenetics and Molecular Carcinogenesis

institute: University of Texas MD Anderson Cancer Center

description:
WT4_2
RNA-Seq (poly A selection)
Processed data file: DESeq_counts.txt

data_processing:
Basecalling was done by Illumina analysis pipeline CASAVA (version 1.8.2).
The reads were mapped to mouse genome (mm10) by TopHat (version 2.0.10).
The number of fragments in each known gene from RefSeq database (downloaded from UCSC Genome Browser on July 17, 2015) was enumerated using htseq-count from HTSeq package (version 0.6.0).
Genes with less than 10 fragments in all the samples were removed, and then the normalized fragment count for each gene was calculated by R/Bioconductor package DESeq (version 1.16.0).
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: DESeq_counts.txt: The first column is gene symbol. The other columns are normalized expression values (estimated by DESeq) for all the samples.

source_name: round spermatids

growth_protocol: Each isolated spermatid sample was freshly purified from eight whole testes in the mice through the centrifugal elutriation. Purified cells were washed three times by the 1X PBS and immediately snap-frozen at -80oC until RNA extraction.

extract_protocol:
Trizol method followed by the DNase I digestion to remove the potential genomic DNA.
TruSeq RNA Library Prep Kit v2 (Illumina).

treatment_protocol: No treatment.

tag: strain/background

value: WT

tag: cell type

value: round spermatids

tag: tissue source

value: Testis


title: mpo_RNAseqnuclear_-+mif(NRas+)_1

city: Oxford

first: Tatjana

last: Sauka-Spengler

state: Oxfordshire

address: Radcliffe Department of Medicine

department: University of Oxford

institute: MRC Weatherall Institute of Molecular Medicine

description: mpo BAC driving biotin ligase, bactin driving Avi-Rangap (active biotagging of neutrophil nuclei) with melanocyte-specific LexPR driving mCherry_Nras oncogene (active in presence of mifepristone)

data_processing:
Reads were mapped using STAR (v.2.4.2a) to danRer10 and read counts were obtained using subreads FeatureCounts
Genome_build: danRer10
Supplementary_files_format_and_content: counts

organism: Danio rerio

extract_protocol:
For nuclei isolation, zebrafish embryos were anaesthetised with 0.01% Tricaine and embryos dissected to separate the head from the trunk and tail. Heads were washed in hypotonic buffer H (20 mM HEPES (pH 7.9), 15 mM MgCl2, 10 mM KCl, 1 mM DTT, and 1 X Complete protease inhibitor) and subsequently resuspended in 500 μL of buffer H. Embryos were transferred to a Dounce homogenizer and dissociated by 10 strokes with the loose fitting pestal A and incubated on ice for 5 minutes. Further dissociation was carried out by 10 strokes with tight fitting pestal B, every 5 minutes for 15 minutes. Nuclei were collected by centrifugation (2000 g, 4 °C) and resuspended in 1 mL buffer NDP (10 mM HEPES (pH 7.9), 40 mM NaCl, 90 mM KCl, 0.5 mM EDTA, 0.5 mM spermidine, 0.15 mM spermine, 1 mM dithiothreitol and 1 X Complete protease inhibitor). For nuclei purification, nuclei were incubated with 5 mg of M-280 streptavidin-coated dynabeads with rotation for 30 minutes at 4 °C. A flow-based system based on the previously published protocol by was used to capture the nuclei bound on the streptavidin beads. A 10 mL seriological pipette (VWR, cat # 8913-898) attached to a 1 mL micropipette tip (Rainin reach pipet tip, cat # RT-L1000S), both pre-treated with NPB/BSA for 30 minutes, and added to a MiniMACS separator magnet (OctoMACS Separator, Miltenyl Biotec, cat # 130-042-109). A two-way stopcock (Biorad cat # 732-8102) was connected to the end of the 1mL micropipette tip via a piece of Tygon tubing (Fisher Scientific, cat # 8220) and the flow-rate set to ~0.75 mL/min. The nuclei beads suspension was diluted by addition of 9 mLs of nuclei pulldown buffer with 0.01 % Triton X-100 (NPBt) and added to the slow-flow setup. The tip was subsequently removed from the stand and the nuclei-beads released from the tip by slowly pipetting 1 mL of NPBt in and out of the tip. The solution was then diluted again to 10 mL with NPBt and added again to the slow-flow setup. Nuclei-beads were eluted in 1 mL of NPBt as described above and the NPBt removed using a magnetic stand (DynaMag TM-2 magnet, Invitrogen, cat # 12321D). Nuclei-beads were then processed for RNA extraction.
RNA extraction and DNAse treatment were carried out using the RNAqueous®-Micro Kit (Life Technologies, cat # AM1931). RNA integrity was checked with a RNA pico chip (Agilent Technologies, cat # 5067-1513) using the Agilent 2100 Bioanalyzer.
cDNA was synthesized and amplified from 100 pg – 1 ng of input RNA using SMART-seqTMv4 ultra low input kit for RNA (Clontech laboratories, cat #’s 634888, 634889, 634890, 634891, 634892, 634893, and 634894). Sequencing libraries were prepared using the Nextera XT DNA library preparation kit and sequencing performed on a NextSeq platform using a NextSeq™ 500 High Output Kit for the generation of 80 base pair paired end reads (150 cycles) (Illumina, cat # FC-404-1002).

treatment_protocol: Incrossed larvae were treated with 1 μM from 24 hpf

tag: strain

tag: development

value: 5 days post fertilization

value: neutrophil

value: In Vivo Biotinylated Nuclei

value: 1 μM mifepristone added to embryo water from 24 hpf

tag: amplification

tag: strand

value: reverse

tag: assay

value: RNA-seq


title: rspd-WT-1

description:
WT4_1
RNA-Seq (poly A selection)
Processed data file: DESeq_counts.txt


title: mpo_RNAseqnuclear_+mif(NRas+)_2

tag: tissue


title: mpo_RNAseqnuclear_-mif(cntrl)_2

description: mpo BAC driving biotin ligase, bactin driving Avi-Rangap (active biotagging of neutrophil nuclei) with melanocyte-specific LexPR driving mCherry_Nras oncogene (inactive in absence of mifepristone)

tag: treatment


title: espd-WT-1

description:
WT2_1
RNA-Seq (poly A selection)
Processed data file: DESeq_counts.txt

source_name: elongating spermatids

value: elongating spermatids


title: espd-WT-2

description:
WT2_2
RNA-Seq (poly A selection)
Processed data file: DESeq_counts.txt


title: rspd-KO-1

description:
KO4_1
RNA-Seq (poly A selection)
Processed data file: DESeq_counts.txt

value: cKO


title: mpo_RNAseqnuclear_-mif(cntrl)_1


title: rspd-KO-2

description:
KO4_2
RNA-Seq (poly A selection)
Processed data file: DESeq_counts.txt


title: espd-KO-2

description:
KO2_2
RNA-Seq (poly A selection)
Processed data file: DESeq_counts.txt


title: espd-KO-1

description:
KO2_1
RNA-Seq (poly A selection)
Processed data file: DESeq_counts.txt


title: CTCFL ChIP-seq (p19 control)

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

country: Germany

institute: Justus-Liebig-University Giessen

description: ChIP-seq

data_processing:
Quality control of FASTQ files was done using FastQC.
Removal of low quality reads was done using fastx_toolkit-0.06
Reads were aligned to a pre-compiled index of the mouse hg19 genome using Bowtie (options: -k 1 -m 1) 0.12.5.
Duplicate reads were removed with Samtools' rmdup function.
Samtools was used to convert aligned reads to BAM format.
MACS 1.4 was used to call peaks at default settings
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq peaks are supplied as BED and coverage vectors as bigwig files

source_name: mouse embryonic carcinoma cells

growth_protocol: Cells were kept in DMEM supplemented with 2 μg/ml Doxycycline.

extract_protocol:
Chromatin was isolated and sheared using BioRuptor (Diagenode). ChIPs were performed using a One-Day Protocol as described by Nelson et al. (2006 / Nature Protocols / DOI: 10.1038/nprot.2006.27
Sequencing libraries were prepared from 10 ng of immunoprecipitated DNA with the Illumina ChIPSeq DNA Sample Prep Kit according to Illuminas’ instructions

treatment_protocol: For induction the cells were grown for 48h in DMEM without Doxycycline.

tag: cell line

value: p19 cells

tag: stable integrate

value: pBI-EGFP-FLAG-mCtcfl and pTA-N

value: Cells were kept in DMEM supplemented with 2 μg/ml Doxycycline, for induction the cells were grown for 48h in DMEM without Doxycycline

value: CTCFL S6


title: Input DNA (p19 control)

description: ChIP-seq


title: CTCFL ChIP-seq (3T3) 2

description: ChIP-seq

source_name: mouse fibroblast cells

value: NIH3T3 cells


title: CTCF ChIP-seq (3T3) 2

description: ChIP-seq

value: CTCF N2.2


title: CTCFL ChIP-seq (3T3) 1

description: ChIP-seq


title: CTCF ChIP-seq (3T3) 1

description: ChIP-seq


title: CTCF ChIP-seq (p19 control)

description: ChIP-seq


title: npl6∆ - 10 generations

city: Berkeley

first: Tina

middle: Lynn

last: Sing

state: California

address: Barker Hall, Rm 616, University of California, Berkeley

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Reads were mapped using TopHat from the Tuxedo protocol using the web-based Galaxy platform
Mapped reads were assembled into transcripts using Cufflinks from the Tuxedo protocol using the web-based Galaxy platform
Assembled transcripts and mapped reads were combined with Cuffmerge from the Tuxedo protocol using the web-based Galaxy platform
Differentially expressed genes were identified with CuffDiff from the Tuxedo protocol using the web-based Galaxy platform
Genome_build: SacCer3
Supplementary_files_format_and_content: gene_differential_expression

organism: Saccharomyces cerevisiae

source_name: Obtained from tetrad dissection of a rsc heterozygote

growth_protocol: Strains from experiment 1 were grown to logarithmic phase in YPD media. Strains from experiment 2 were grown to saturation in YPGR media, washed, and grown in YPGR or YPD for an additional 10 generations in logarithmic phase, as indicated.

extract_protocol:
RiboPure-Yeast Kit (Ambion)
Polyadenylated RNA was captured by oligoDT beads (illumina) and prepped for sequencing on a HiSeq 2500 (Illumina)

tag: experiment number

value: npl6delta - 10 generations


title: htl1∆ - GALpr-HTL1 - YPD 10 generations

value: htl1delta - GALpr-HTL1 - YPD 10 generations


title: WT - GALpr-HTL1 - YPGR

value: WT - GALpr-HTL1 - YPGR


title: rsc2∆ - 10 generations

value: rsc2delta - 10 generations


title: WT - GALpr-HTL1 - YPD 10 generations

value: WT - GALpr-HTL1 - YPD 10 generations


title: htl1∆ - GALpr-HTL1 - YPGR

value: htl1delta - GALpr-HTL1 - YPGR


title: rsc1∆ - 10 generations

value: rsc1delta - 10 generations


title: WT - 10 gerenations

value: WT - 10 gerenations


title: htl1∆ - 10 generations

value: htl1delta - 10 generations


title: rtt102∆ - 10 generations

value: rtt102delta - 10 generations


title: shLUC-H3K9me3_TTAGGC

city: Stanford

first: Stephen HK

last: WONG

address: G2035 SIM1 Bldg

department: Pathology

institute: Stanford University

description: antibody: Anti-H3K9me3

data_processing:
RNA-seq libraries were constructed using Illumina’s TruSeq Stranded mRNA LT Kit and sequenced at Centrillion Genomics Technologies (http://www.centrilliontech.com).  RAW fastq files were mapped by bowtie2 to the human hg19 genome assembly.  Mapped files (BAM) were subjected to read counting using R-bioconductor package (GenomicAlignments: summarizeOverlaps function).  Expression matrix (prior normalization) was then used for differential expression calculations and statistical modeling using R-bioconductor package (DESeq2).
ChIP-seq samples were analyzed as follows: i) Reads mapped by BWA to human genome assembly hg19; ii) Peaks called and differential peaks analyzed by MAC2; iii) peaks were viewed by genome browser IGV; iv) density plot and heatmap were generated using the program ngsplot.
Genome_build: hg19

source_name: RCH-ACV E2A-PBX1+ human cell line

growth_protocol: RPMI R10

extract_protocol:
Trizol for total RNA
Manufacture prototol for RNAseq library; customized protocol for ChIP-seq (Wong et al., 2015, Cancer Cell)

value: E2A-PBX1+ B-ALL cell line


title: T138-B

city: Freiburg

first: Manching

last: Ku

address: Mathildenstrasse 1

department: Hematology and Oncology

institute: Medical Center - University of Freiburg

description:
supplementary file column: NT2357Fplus
Replicate 2 of T138 T cell

data_processing:
Basecalls performed using CASAVA version 1.8.2
Reads were quality filtered and adapter trimmed using bbmap v36.27 with the following options: ktrim=r k=28 mink=13 hdist=1, minlen=25.
Filtered reads were aligned to the moue genome using RNA-STAR v2.5.2b with the following options:  --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --sjdbScore 1
Reads were quanitifed using Homer v4.8 using the analyzeRepeats.pl script with the following options: -count exons -strand - -condenseGenes
Normalized abundance calculated from EdgeR called by Homer v4.8 using the script getDiffExpression.pl
Genome_build: mm10
Supplementary_files_format_and_content: Tab deliminated text file of the matrix table encompassing normalized abundance measurements from EdgeR for each sample (column) of each gene (row)

source_name: Foxp3-positive CD4-positive T cells isolated from T138 mouse

extract_protocol:
Foxp3-positive and CD4-positive T cells were FACS-sorted and RNA was isolated using RNA Nucleospin XS kit, treated with Dnase (Machery-Nagel)
RNA was processed into RNA-Seq libraries using Truseq Stranded mRNA-Seq sample prep kit(Illumina) following manufacturer’s instructions

treatment_protocol: no treatment

tag: strain/genotype

value: T-cell

tag: cd4 status

value: positive

tag: foxp3 status

tag: model

tag: derivation

value: nuclear transfer


title: WT-B

description:
supplementary file column: WTM1Fplus
Replicate 2 of wildtype T cell

source_name: Foxp3-positive CD4-positive T cells isolated from wild-type mouse

tag: cell type

value: wildtype


title: T138-A

description:
supplementary file column: NT2300Fplus
Replicate 1 of T138 T cell


title: T143-C

description:
supplementary file column: T14313_Fplus
Replicate 3 of T143 T cell

source_name: Foxp3-positive CD4-positive T cells isolated from T143 mouse


title: T143-B

description:
supplementary file column: T14312_Fplus
Replicate 2 of T143 T cell


title: T143-A

description:
supplementary file column: T14311_Fplus
Replicate 1 of T143 T cell


title: sh216-input_CGATGT

description: antibody: Anti-H3K9me3


title: Young fasted intestinal stem cells

first: Maria

last: Mihaylova

address: 9 Cambridge Center

institute: Whitehead Institue

data_processing:
Single-end, 40 base reads generated by Illumina HiSeq 2000 were subjected to quality control analysis using the FastQC program (Babraham Bioinformatics, UK), which revealed overall good quality of the sequencing libraries.
The reads were then mapped to the genome of Mus musculus (GRCm38; mm10) using RNA-Seq alignment software, STAR, with default parameters and Ensembl 81 gene annotations for the splice junction database.
Reads aligning to individual genes were counted using htseq-count (Anders et al., 2015) in “union” mode with Ensembl 81 gene annotations.
Read counts of different samples were normalized using the “geometric means” scaling method implemented in the DESeq R package (Anders and Huber, 2010).
Genome_build: GRCm38 (mm10)
Supplementary_files_format_and_content: Each tab-delimited text file (one per sample) includes the raw read count for each Ensembl Gene ID.
Supplementary_files_format_and_content: The tab-delimited text file "Normalized_gene_counts.txt" (linked as Series-level supplementary file) includes the normalized read count for each Ensembl Gene ID in each sample.

source_name: intestinal stem cells

extract_protocol:
Intestinal stem cells were sorted directly into Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: experimental context

value: fasting

tag: age

value: 4 month

value: intestinal stem cells (GFP high)

tag: cell age

value: young


title: sh216-H3K9me3_TGACCA

description: antibody: Anti-H3K9me3


title: Young fed intestinal stem cells

tag: strain

value: fed ad libitum (standard chow)


title: shRNA.ctr-RCH-ACV-C

tag: shRNA knockdown


title: WT-C

description:
supplementary file column: WTM2Fplus
Replicate 3 of wildtype T cell


title: shRNA.ctr-RCH-ACV-A


title: shRNA.ctr-697-C

source_name: 697 E2A-PBX1+ human cell line


title: shLUC-input_ATCACG

description: antibody: Anti-H3K9me3


title: shRNA.ctr-697-B


title: shRNA.ctr-697-A


title: shRNA2-RCH-ACV-C


title: shRNA2-RCH-ACV-A


title: WT-A

description:
supplementary file column: WT3Fplus
Replicate 1 of wildtype T cell


title: shRNA2-697-C


title: shRNA1-RCH-ACV-C


title: shRNA2-697-B


title: shRNA2-697-A


title: shRNA1-RCH-ACV-B


title: shRNA1-RCH-ACV-A


title: shRNA1-697-C


title: shRNA.ctr-RCH-ACV-B


title: GFPplus

description: gene expression of single nuclear transferred T cells

data_processing:
Data processing: The Cell Ranger Single Cell Software Suite v1.3 was used to perform sample demultiplexing, barcode processing, and single cell 3' gene counting (https://support.10xgenomics.com/single-cell/software/pipelines/latest/what-is-cell-ranger). Cell Ranger commands used to produce this aggregated dataset:
cellranger count (--cells=3000 ...)
cellranger aggr --id=AGG001 --csv=cellranger-aggregation.csv --normalize=mapped
Genome_build: mm10
Supplementary_files_format_and_content: Tab-deliminated text file of matrix table containing normalized expression values (UMI/cell). Each row corresponds to a gene and each column corresponds to an individual cell.

source_name: Foxp3-positive CD4-positive T cells from Wild-type mice

extract_protocol:
Foxp3-positive and CD4-positive T cells were FACS-sorted from wild-type NOD mice. Single cells were diluted to 1000 cells /ul in 0.04% BSA/PBS
Chromium Single-cell 3’ RNA-Seq library (v1) generation was carried according to 10X Genomics protocols


title: shRNA1-697-A


title: shRNA2-RCH-ACV-B


title: WT.Low.Whole.Rep1.F2

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

description:
F2.Low1-WT-1nuc_S3.R1.fastq.gz
processed data file: WT.Low.Whole.Rep1.bw

data_processing:
Demultiplexing: demultiplexing of raw sequencing data was done using bcl2fastq v2.16.0.10.
Alignment: tracks were aligned to mouse genome assembly NCBI36 using bowtie v0.12.5 with command-line parameters -m 1 --best. Paired-end data were joined into matching fragments.
Track Generation: aligned fragment records were pooled across technical repeats, then MNase-seq tracks for whole-nucleosome particle sequencing runs were generated by taking the central 140 bp region of each aligned fragment, then binning centered fragments in non-overlapping, contiguous 10 bp bins.  Tag counts per bin were normalized to the number of millions of reads sequenced, to correct for lane or sample biases, and to the average fragment size, to correct for fragment size variability between the high and low MNase-seq. A similar procedure was undertaken for sub-nucleosome sequencing runs, except that the entire fragment and not the central 140 bp was used.
Genome_build: mm8
Supplementary_files_format_and_content: BigWigs: for each sample, aligned fragments from two technical replicates (flowcells) were pooled and the composite pool was made into a track. We additionally pooled tags from two biological replicates for the sub-nucleosomal data (low MNase digestion, mutant and WT) to make Low1.2-FoxAdel-0-5nuc.Fragments.merge.shorter80.bw and Low1.2-WT-0-5nuc.Fragments.merge.shorter80.bw.

growth_protocol: No special protocols for rearing mice; animal use was approved by an IACUC committee.

extract_protocol:
Two weeks after AAV-Cre injection, which was previously shown to yield efficient deletion (Lee et al., 2014), livers were perfused with 45 ml of 37°C Liver Perfusion Medium (Life technologies, 17701-038), followed by 45 ml of 37°C Liver Digestion Medium (Life technologies, 17703-034) at a speed of 5 ml /min.  The perfused liver was excised, washed with SST (150 mM NaCl, 15 mM Na citrate, 10 mM Tris [pH 7.4]), and minced using cell scrapers to release the hepatocytes.  The hepatocytes were filtered through a 100 mm cell strainer into a 50 ml conical tube, which was then filled up to 50 ml with SST.  Hepatocytes were centrifuged at 50 g for 3 min at 4°C to pellet only hepatocyte cells.  The supernatant was aspirated and the pellet was resuspended in 50 ml SST.  Hepatocytes were centrifuged at 50 g for 3 min at 4°C.  The SST wash was repeated.  Hepatocytes were resuspended in 5 ml RSB (10 mM Tris [pH7.4], 10 mM NaCl, 3 mM MgCl2, 10 mM sodium butyrate, 0.5 mg/ml aprotinin, 0.5 mg/ml leupeptin, 1 mg/ml pepstatin) plus 0.5% NP40 and were swollen on ice for 5 min.  Liver and spleen from C3H mice were minced with scalpels in SST (150 mM NaCl, 15 mM Na Citrate, 10 mM Tris [pH 7.4]) on ice and washed with SST in 30 ml Corex tubes three times.  The tissue was resuspended in RSB (10 mM Tris [pH7.4], 10 mM NaCl, 3 mM MgCl2 with 10 mM sodium butyrate, 0.5 mg/ml aprotinin, 0.5 mg/ml leupeptin, 1 mg/ml pepstatin) and 0.5% NP40, and was swollen on ice for 5 min (liver) or 10 min (spleen).  The tissue was homogenized with a glass Teflon pestle in a glass homogenizer and a portion was observed under the microscope to confirm nuclear isolation. The nuclear suspension was filtered through a 100 mm cell strainer and pelleted by centrifugation at 1.4 K rpm for 7 min at 4°C in 15 ml Corex tubes with a swinging bucket rotor.  The pellet was washed in RSB plus 0.5% NP40 and pelleted by centrifugation at 900 rpm for 10 min at 4°C in 15 ml Corex tubes with a swinging bucket rotor; this wash step was repeated once.  The nuclear pellet was re-suspended in RSB and adjusted to O.D. A260 of 1 for liver and 0.68 for spleen.  CaCl2 (3 mM final) was added, the nuclear suspension was pre-warmed for 1.5 min at 37°C, and was treated with MNase (Worthington Biochemicals) at 0 U/ml for control, 0.5 or 1 U/ml for low digestion and 20 U/ml for high digestion for 2 min at 37°C.  Quench control (“Q” sample) to assess endogenous nucleases was without MNase and CaCl2 and was not warmed.  The reactions were stopped by adding an equal volume of 2x TNESK (20 mM Tris [pH7.4], 200 mM NaCl, 2 mM EDTA, 2% SDS, 0.2 mg/ml Proteinase K), and incubated overnight at 37 °C.  DNA was purified using phenol-chloroform extraction followed by ethanol precipitation.  The nucleic acid was digested with 10 ng/ml of RNase for 20 min at 37°C and DNA was purified using phenol-chloroform extraction followed by ethanol precipitation.  50 ug samples of low MNase and 10 ug samples of high MNase were run on 6% polyacrylamide gels (TBE).  The mono-nucleosomal DNA was excised from the 140 bp~200 bp size range and sub-nucleosomal DNA was excised from 25-140 bp size range.  The gel was sliced into small pieces, put in 2 vol of diffusion buffer (500 mM ammonium acetate, 10 mM magnesium acetate, 1 mM EDTA, 0.1% SDS), and rotated overnight. The supernatant was filtered through Whatman GF/C and ethanol precipitated.  DNA was purified using QIA EX II (QIAGEN) for sub-nucleosomal DNA and AMPure XP (Beckman) beads for mono-nucleosomal DNA. Mono-nucleosomal DNA from low MNase digestion averaged 1.5~2.5% of bulk DNA. Mono-nucleosomal DNA from high MNase digestion averaged 25~30% of bulk DNA.  The percent of mononucleosomal DNA of bulk DNA was estimated based on the amount of mononucleosomal DNA recovered from a preparative PAGE gel, multiplied by 1.25 (PAGE gel extraction recovers about 80% of sample in our hands) compared to the amount of bulk DNA loaded onto to the PAGE gel.
We prepared multiplexed libraries from two biological replicates of low and high MNase digested mono-nucleosomal DNA from WT liver, low and high MNase digested mono/sub-nucleosomal DNA from FoxA1/FoxA2 flox;AAV-Cre and WT;AAV-Cre.  The standard Illumina multiplexing library preparation protocol was employed with the following changes: 1) All QIAGEN purification steps were substituted with AMPure XP bead (Beckman) purifications. 2) For MNase digested mono-nucleosomal DNA, gel purification following adapter ligation was substituted with AMPure XP bead purification in order to remove excess adapters. 3) 10 ng of adapter ligated DNA was used as a template for PCR, wth 10 PCR cycles for MNase DNA, and 12 PCR cycles for ChIP DNA. 4) Gel purification after PCR was substituted with AMPure XP beads purification in order to remove excess primers.  The DNA libraries were assessed using an Agilent Technologies 2100 Bioanalyzer.  MNase-seq libraries from FoxA1/FoxA2 flox;AAV-Cre and WT;AAV-Cre were were sequenced as 37-bp paired-end by Illumina NextSeq500.

treatment_protocol: The FoxA2loxP and FoxA1loxP alleles have been reported previously (Gao et al., 2008; Sund et al., 2000). Two FoxA1loxP/loxP;FoxA2loxP/loxP mice (Li et al., 2011) and two wild type mice were anaesthetized with isofluorane and injected with AAV expressing Cre recombinase (AAV-Cre) under the control of the Tbg (also known as Serpina7) promoter (Lee et al., 2014) for liver-specific deletion of FoxA1loxP/loxP;FoxA2loxP/loxP alleles.

tag: strain background

tag: genotype/variation

value: WT

value: adult

value: liver

tag: mnase digestion

value: Low

tag: particle size

value: Whole Nucleosome

tag: biological replicate

tag: technical replicate


title: Mutant.Low.Whole.Rep2.F2

description:
F2.Low2-FoxAdel-1nuc_S10.R1.fastq.gz
processed data file: Mutant.Low.Whole.Rep2.bw

value: FoxA1,FoxA2 Deletion

tag: tissue


title: WT.Low.Sub.Rep2.F1

description:
F1.Low2-WT-0-5nuc_S2.R1.fastq.gz
processed data file: WT.Low.Sub.Rep2.bw;
Low1.2-WT-0-5nuc.Fragments.merge.shorter80.bw

value: Sub-Nucleosomal


title: Mutant.Low.Whole.Rep1.F2

description:
F2.Low1-FoxAdel-1nuc_S9.R1.fastq.gz
processed data file: Mutant.Low.Whole.Rep1.bw


title: WT.High.Whole.Rep2.F2

description:
F2.High2-WT-1nuc_S6.R1.fastq.gz
processed data file: WT.High.Whole.Rep2.bw

value: High


title: WT.High.Whole.Rep1.F2

description:
F2.High1-WT-1nuc_S5.R1.fastq.gz
processed data file: WT.High.Whole.Rep1.bw


title: WT.Low.Sub.Rep2.F2

description:
F2.Low2-WT-0-5nuc_S2.R1.fastq.gz
processed data file: WT.Low.Sub.Rep2.bw;
Low1.2-WT-0-5nuc.Fragments.merge.shorter80.bw


title: WT.Low.Whole.Rep2.F2

description:
F2.Low2-WT-1nuc_S4.R1.fastq.gz
processed data file: WT.Low.Whole.Rep2.bw


title: WT.Low.Whole.Rep2.F1

description:
F1.Low2-WT-1nuc_S4.R1.fastq.gz
processed data file: WT.Low.Whole.Rep2.bw


title: Mutant.High.Whole.Rep1.F2

description:
F2.High1-FoxAdel-1nuc_S11.R1.fastq.gz
processed data file: Mutant.High.Whole.Rep1.bw


title: Mutant.Low.Sub.Rep2.F2

description:
F2.Low2-FoxAdel-0-5nuc_S8.R1.fastq.gz
processed data file: Mutant.Low.Sub.Rep2.bw;
Low1.2-FoxAdel-0-5nuc.Fragments.merge.shorter80.bw


title: WT.Low.Sub.Rep1.F2

description:
F2.Low1-WT-0-5nuc_S1.R1.fastq.gz
processed data file: WT.Low.Sub.Rep1.bw;
Low1.2-WT-0-5nuc.Fragments.merge.shorter80.bw


title: Mutant.Low.Sub.Rep1.F1

description:
F1.Low1-FoxAdel-0-5nuc_S7.R1.fastq.gz
processed data file: Mutant.Low.Sub.Rep1.bw;
Low1.2-FoxAdel-0-5nuc.Fragments.merge.shorter80.bw


title: Mutant.Low.Whole.Rep1.F1

description:
F1.Low1-FoxAdel-1nuc_S9.R1.fastq.gz
processed data file: Mutant.Low.Whole.Rep1.bw


title: WT.Low.Sub.Rep1.F1

description:
F1.Low1-WT-0-5nuc_S1.R1.fastq.gz
processed data file: WT.Low.Sub.Rep1.bw;
Low1.2-WT-0-5nuc.Fragments.merge.shorter80.bw


title: WT.Low.Whole.Rep1.F1

description:
F1.Low1-WT-1nuc_S3.R1.fastq.gz
processed data file: WT.Low.Whole.Rep1.bw


title: WT.High.Whole.Rep2.F1

description:
F1.High2-WT-1nuc_S6.R1.fastq.gz
processed data file: WT.High.Whole.Rep2.bw


title: Mutant.Low.Sub.Rep2.F1

description:
F1.Low2-FoxAdel-0-5nuc_S8.R1.fastq.gz
processed data file: Mutant.Low.Sub.Rep2.bw;
Low1.2-FoxAdel-0-5nuc.Fragments.merge.shorter80.bw


title: shRNA1-697-B

value: E2A-PBX1+ B-ALL cell line


title: Mutant.High.Whole.Rep1.F1

description:
F1.High1-FoxAdel-1nuc_S11.R1.fastq.gz
processed data file: Mutant.High.Whole.Rep1.bw


title: Mutant.High.Whole.Rep2.F1

description:
F1.High2-FoxAdel-1nuc_S12.R1.fastq.gz
processed data file: Mutant.High.Whole.Rep2.bw


title: WT.High.Whole.Rep1.F1

description:
F1.High1-WT-1nuc_S5.R1.fastq.gz
processed data file: WT.High.Whole.Rep1.bw


title: iKOX-5_plus_ATc3

city: Lille

first: Mathieu

last: Gissot

address: 1, rue du Pr. calmette

institute: CNRS

description: RHΔhxgprtΔku80 TATi; teto7SAG4:AP2X-5-3HA:DHFR-TS

data_processing:
Clusters were generated on a flow cell within a cBot using the Cluster Generation Kit (Illumina), and libraries were sequenced as 50-bp reads on a HiSeq 2000 using a Sequence By Synthesis (SBS) technique (Illumina).
Image analysis and base calling were performed using the HiSeq Control Software and Real-Time Analysis component. Demultiplexing was performed using Illumina’s conversion software (bcl2fastq 2.17). The quality of the data was assessed using FastQC from the Babraham Institute and the Illumina software Sequence Analysis Viewer (SAV). Potential contaminants were investigated with the FastQ Screen software from the Babraham Institute.
RNASeq reads were aligned to the Toxoplasma gondii genome (ToxoDB-25_TgondiiGT1_Genome.fasta from the ToxoDB Toxoplasma Genomics Resource, downloaded on 08/31/15) with a set of gene model annotations (ToxoDB-25_TgondiiGT1.gff from the ToxoDB Toxoplasma Genomics Resource, downloaded on 08/31/15) using the splice junction mapper TopHat 2.0.13. Final read alignments having more than three mismatches were discarded. Gene counting was performed using HTSeq-count 0.6.1p1 (union mode). Because the data come from a strand-specific assay, the read must be mapped to the opposite strand of the gene. Before statistical analysis, genes with less than 15 reads (combining all the analyzed samples) were filtered out. Differentially expressed genes were identified using the Bioconductor package edgeR 3.6.7. The data were normalized using the Relative Log Expression (RLE) normalization factors. Genes with adjusted p-values less than 5% (according to the FDR method from Benjamini-Hochberg) were declared differentially expressed.
Genome_build: ToxoDB-25_TgondiiGT1_Genome.fasta from the ToxoDB Toxoplasma Genomics Resource, downloaded on 08/31/15
Supplementary_files_format_and_content: tab-delimited text file include  read values for each genes

organism: Toxoplasma gondii

source_name: intracellular parasite grown on HFF

growth_protocol: Intracellular parasite were grown 30h on HFF under ATc treatment for both WT and iKD strains.

extract_protocol:
Total RNA was extrated using TRIzol reagent according to manufacturer’s protocol.
Library preparation was performed using the TruSeq Stranded mRNA Sample Preparation kit (Illumina) according to the manufacturer’s instructions. Libraries were validated using a Fragment Analyzer and quantified by qPCR (ROCHE LightCycler 480).

value: iKD TgAP2X-5

tag: genotype


title: Mutant.Low.Sub.Rep1.F2

description:
F2.Low1-FoxAdel-0-5nuc_S7.R1.fastq.gz
processed data file: Mutant.Low.Sub.Rep1.bw;
Low1.2-FoxAdel-0-5nuc.Fragments.merge.shorter80.bw


title: iKOX-5_plus_ATc2


title: Tatiwt_plus_ATc3

description: RHΔhxgprtΔku80 TATi

value: wild type

value: RHdeltahxgprtdeltaku80 TATi


title: iKOX-5_plus_ATc1


title: Tatiwt_plus_ATc1

description: RHΔhxgprtΔku80 TATi


title: Tatiwt_plus_ATc2

description: RHΔhxgprtΔku80 TATi