title: Kidney DNase-seq Rep 1

source_name: kidney tissue

extract_protocol:
25-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Digestions were checked by pulse field gel electrophoresis and material was pooled from 3 different DNase concentrations (extent of digestion matched between samples) in equimolar amounts following blunt-ending reactions. This was followed by ligation to adapters, MmeI digestion, streptavidin bead-based enrichment, 14 cycles of PCR amplification, and separation from linker-only bands on a gel.
C57BL/6 adult female mice were sacked and kidney dissected and stored in liquid nitrogen.  0.5-1.0g of frozen tissue (2 kidneys) was ground to fine powder in liquid nitrogen, resuspended in ice cold 20mL nuclei isolation buffer (NIB), filtered through Miracloth, spun down, resuspended in NIB with 0.5% Triton X-100, and centrifuged again to obtain nuclei pellet.

value: kidney


title: d7 Zic2 KD CGN RNA-seq Rep 1

status: Public on Feb 27 2015

type: SRA

city: Durham

first: Christopher

middle: L

last: Frank

state: NC

address: 101 Science Dr.

country: USA

institute: Duke University

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA v1.8
First 20bp of DNase-seq reads mapped to NCBI37/mm9 with BWA, RNA-seq mapped to NCBI37/mm9 with Tophat v2.0.8b; ChIP-seq mapped to NCBI37/mm9 with Bowtie v1.0.0; in all cases up to 2 mismatches were allowed
Putative PCR artifacts filtered from mapped DNase-seq and ChIP-seq prior to peak calls
DNase-seq peaks called with F-seq v1.84, ChIP-seq peaks called with MACS v1.4, FPKM expression values estimated by Cufflinks v2.0.2
Genome_build: mm9
Supplementary_files_format_and_content: DNase-seq .npf (narrow peak format with chromosome, start, stop, name, score, p-value) contain top 100,000 DHS peaks identified by F-seq ; RNA-seq Cufflinks text files contain gene FPKM abundances ; ChIP-seq .bed files contain all MACS peak calls and scores with default significance threshold.

molecule: total RNA

organism: Mus musculus

source_name: cultured cerebellar granule neurons

growth_protocol: Cerebellae from a litter of P7 mice were chopped into small pieces then digested at 37°C for 30 min in 10 U/ml papain (Worthington), 200g/ml L-cysteine (Sigma), and 250 U/ml DNase (Sigma) in PBS. The tissue was mechanically triturated in PBS with trypsin inhibitor and 250 U/ml DNase then centrifuged and resuspended in PBS/BSA. The cell suspension was passed through a cell strainer (Becton Dickinson), layered on a step gradient of 35% and 65% Percoll (Sigma), and centrifuged at 2500 rpm for 12 min at room temperature. Granule Neuron Precursors (GNPs) were harvested from the 35/65% interface, washed in PBS/BSA, resuspended in Neurobasal medium with B27 supplements and 2% fetal bovine serum and plated on poly-D-lysine coated dishes.

extract_protocol:
2μg of total RNA was used for standard TruSeq library preparation with polyA selection
RNA was isolated from P7, P14, or P60 C57BL/6 mouse cerebellar cortex or cultured mouse CGNs using the Absolutely RNA kit (Agilent). For in vivo samples, RNA from at least two cerebellae was pooled for each biological replicate, and in culture a single litter constituted a biological replicate of cultured CGNs.

tag: strain

tag: tissue

value: cultured cerebellar granule neurons

tag: developmental stage

value: GNP + 7DIV


title: d7 + BDNF CGN DNase-seq Rep 2

library_source: genomic

molecule: genomic DNA

extract_protocol:
15-30 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Digestions were checked by pulse field gel electrophoresis and material was pooled from 3 different DNase concentrations (extent of digestion matched between samples) in equimolar amounts following blunt-ending reactions. This was followed by ligation to adapters, MmeI digestion, streptavidin bead-based enrichment, 14 cycles of PCR amplification, and separation from linker-only bands on a gel.
Cell pellets were washed twice with 1xPBS and nuclei isolated by 0.1% NP-40 lysis

treatment_protocol: cultured in presence of BDNF (50 ng/ML added on +4DIV)


title: P7 Cerebellum RNA-seq Rep 3

source_name: whole cerebellum

growth_protocol: All animals were housed in groups of 4-5, given access to standard laboratory chow and water ad libitum and housed in a humidity and temperature-controlled room on a 14/10h light/dark cycle.

value: whole cerebellum

value: Postnatal day 7 (P7)


title: d7 CGN DNase-seq Rep 2


title: d0 CGN DNase-seq Rep 3

value: Granule Neuron Precursors (GNPs)


title: P60 Cerebellum RNA-seq Rep 3

value: Postnatal day 60 (P60)


title: P7 Cerebellum RNA-seq Rep 2


title: d3 CGN DNase-seq Rep 2

value: GNP + 3DIV


title: d0 CGN DNase-seq Rep 2


title: P60 Cerebellum DNase-seq Rep 3

extract_protocol:
15-30 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Digestions were checked by pulse field gel electrophoresis and material was pooled from 3 different DNase concentrations (extent of digestion matched between samples) in equimolar amounts following blunt-ending reactions. This was followed by ligation to adapters, MmeI digestion, streptavidin bead-based enrichment, 14 cycles of PCR amplification, and separation from linker-only bands on a gel.
C57BL/6Ncrl male and female mice at P7, P14, or P60 were deeply anesthetized with isofluorane and decapitated for brain harvesting. The cerebellar cortex was dissected, flash frozen, and stored at -80°C. Each cerebellum was dounced in 5mL 2M sucrose, 1mM MgCl2 and poured through a 100μM filter. Filtered tissue was ultracentrifuged in 15 mL of 2M sucrose, 1mM MgCl2 at 65,000 x g for 80 min. Supernatant was removed and the tight nuclear pellet was resuspended by pipetting in 1 mL buffer RSB from the DNase-seq protocol. Nuclei were quantified by hemocytometer, yielding approximately 5-10 million per adult cerebellum (~30 mg tissue).


title: P60 Cerebellum DNase-seq Rep 1


title: Heart DNase-seq Rep 1

source_name: heart tissue

extract_protocol:
25-50 million nuclei were digested with a range of recombinant DNase I enzyme (Roche) concentrations (between 1.2 and 12U) for 15 minutes at 37°C in 120uL 1X DNase buffer. Digestions were checked by pulse field gel electrophoresis and material was pooled from 3 different DNase concentrations (extent of digestion matched between samples) in equimolar amounts following blunt-ending reactions. This was followed by ligation to adapters, MmeI digestion, streptavidin bead-based enrichment, 14 cycles of PCR amplification, and separation from linker-only bands on a gel.
C57BL/6 adult female mice were sacked and heart dissected and stored in liquid nitrogen.  0.5-1.0g of frozen tissue (2 hearts) was ground to fine powder in liquid nitrogen, resuspended in ice cold 20mL nuclei isolation buffer (NIB), filtered through Miracloth, spun down, resuspended in NIB with 0.5% Triton X-100, and centrifuged again to obtain nuclei pellet.

value: heart

value: Adult


title: d7 + BDNF CGN DNase-seq Rep 1


title: P7 Cerebellum RNA-seq Rep 1


title: d7 + BDNF CGN DNase-seq Rep 3


title: d7 CGN DNase-seq Rep 3


title: P60 Cerebellum RNA-seq Rep 2


title: P14 Cerebellum DNase-seq Rep 2

value: Postnatal day 14 (P14)


title: d3 CGN DNase-seq Rep 3

value: GNP + 3 DIV


title: P7 Cerebellum DNase-seq Rep 3


title: NAc projector, experiment-2: NAc_537

city: Boston

first: Suzuko

last: Yorozu

state: Massachusettes

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

description: Experiment-2, NAc

data_processing:
Sequencing reads were aligned using Tophat version 2.0.10 against the Mus musculus UCSC version mm10 genome and the mm10 RefSeq transcriptome.
Genome_build: mm10
Supplementary_files_format_and_content: raw counts

source_name: Brain tissue (BLA), NAc-projector, Experiment-2

extract_protocol:
Total RNA was isolated using Arcturus PicoPure RNA isolation kit (Life Technologies).
Double stranded cDNA was generated from total RNA using a DNA-RNA chimeric primer mix and reverse transcriptase, and cDNA was amplified by the SPIA amplification process developed by NuGEN (Ovation RNA-Seq System V2 kit (Neugen)).
The amplified double stranded cDNA was fragmented to an average size of 200 bases using Covaris S-S series sonication system. The fragmented cDNA was end-repaired, and adaptors and barcodes were ligated before PCR-based library preparation using Ovation Ultralow DRMultiplex Systems (Nugen).

treatment_protocol: In order to label the BLA neurons projecting to the NAc or CeM, red retrobeads (Lumafluor Inc.) were injected into the NAc and CeM of the adult mice brains.  Two weeks after retrobeads injection, the retrobeads are traveled to the BLA, and the brain was quickly removed for acute 330 μm coronal brain slices for subsequent dissociation and isolation of retrobeads labeled BLA neurons. After dissociation of the retrobeads labeled BLA neurons, 30-60 retrobeads-positive neurons were isolated under a fluorescent dissecting microscope for subsequent RNA extraction.

tag: Sex

value: male

tag: tag

value: basolateral amygdala complex neurons


title: P14 Cerebellum DNase-seq Rep 3


title: NAc projector, experiment-2: NAc_538

description: Experiment-2, NAc


title: P7 Cerebellum DNase-seq Rep 2


title: P7 Cerebellum DNase-seq Rep 1


title: CeM projector, experiment-2: CeM_551

description: Experiment-2, CeM

source_name: Brain tissue (BLA), CeM-projector, Experiment-2


title: vcap_ash2l_veh

city: Ann Arbor

first: Marcin

middle: Piotr

last: Cieslik

state: Michigan

address: 500 S State St

department: Pathology

institute: University of Michigan

data_processing:
Basecalls performed using RTA 1.6.47.
Reads were aligned to the hg19 genome using Bowtie2 with all default settings.
Resulting BAM files were sorted and duplicates were removed using samtools.
Coverage profiles were calculated using bedtools genomecov as BedGraph files.
BedGraph files were converted to BigWig using BedGraphToBigWig from Kent Utils.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: Coverage profiles are normalized to sequencing depth.

organism: Homo sapiens

source_name: VCaP prostate cancer cells, vehicle, ASH2 ChIP

growth_protocol: Cells were grown in DMEM containing 10% FBS.

extract_protocol:
ChIP was performed using the HighCell ChIP kit following the manufacturer's protocol (Diagenode). ChIP DNA was isolated (IPure Kit, Diagenode) from samples by incubation with the antibody at 4°C overnight, followed by wash and reversal of cross-linking.
The ChIP-seq sample preparation for sequencing was performed according to the manufacturer’s instructions (Illumina). ChIP-enriched DNA samples (1-10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, E. coli DNA polymerase I large fragment (Klenow polymerase) and T4 polynuleotide kinase (New England BioLabs, NEB). A single A-base was added to fragment ends by Klenow fragment (3' to 5' exo minus; NEB) followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-modified DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (QIAGEN). Libraries were quantified with the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina Genome Analyzer IIx Sequencer (100 nucleotide read length).

treatment_protocol: For ASH2L ChIP-seq experiments, VCaP cells were grown in 5% charcoal-stripped serum containing media for 48hrs, followed by stimulation with 100nM R1881 for 12 hrs.

tag: cell line

value: VCaP

tag: cell type

value: vertebral metastatic lesion-derived prostate cancer cell line

tag: treatment

value: vehicle

tag: chip antibody

value: rabbit anti-ASH2 antibody (Bethyl Laboratories, A300-489A)


title: CeM projector, experiment-2: CeM_546

description: Experiment-2, CeM


title: P14 Cerebellum DNase-seq Rep 1


title: vcap_ash2l_r1881

description: RI1881 is an androgen receptor agonist: http://www.sigmaaldrich.com/catalog/product/sigma/r0908?lang=en&region=US

source_name: VCaP prostate cancer cells, R1881, ASH2 ChIP


title: NAc projector, experiment-2: NAc_541

description: Experiment-2, NAc


title: NAc projector, experiment-2: NAc_548

description: Experiment-2, NAc


title: P60 Cerebellum DNase-seq Rep 2


title: H3K4me3.MN.Δ5|6 [ChIP-Seq]

status: Public on Feb 26 2015

city: New York City

first: Danny

last: Reinberg

state: New York

address: 522 First Avenue, 2nd floor Rm 211

institute: NYU School of Medicine / HHMI

data_processing:
biological replicates fastq files were merged
mapped to mm9 with BOWTIE -m4 -v2
duplicate reads were filtered
1nt resolution bedgraphs were generated with the BEDtools bamToBed and genomeCoverageBed utilities after extending each read to 200
coverage was normalized to FP10M (fragments per 10 million reads sequenced)
bigWig files were generated with bedGraphToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: FP10M-normalized bigWigs

source_name: Differentiated motor neuron

growth_protocol: mESCs were grown in standard ESC medium containing Lif, 1 μM MEK1/2 inhibitor (PD0325901) and 3 μM GSK3 inhibitor (CHIR99021). ESCs were differentiated  in ANDFK medium (Advanced DMEM/F12 : Neurobasal (1:1) Medium, 15% Knockout Serum Replacement, Pen/Strep, 2 mM L-Glutamine, and 0.1 mM 2-mercaptoethanol) to initiate formation of embryoid bodies (Day 0). Medium was exchanged on Day 2 of differentiation. Patterning of embryoid bodies was induced by supplementing the media on Day 2 with 1 μM all-trans-Retinoic acid (RA, Sigma) and 0.5 μM smoothened agonist (SAG, Calbiochem).

extract_protocol:
Cells were lysed in ChIP buffer (50 mM Tris-HCl pH 7.9, 150 mM NaCl, 1% Triron X-100, 0.5% NP-40, 5 mM EDTA pH 8.0, 1 mM PMSF and protease inhibitor) and chromatin was sonicated to ~200 bp with a Diagenode Bioruptor
Libraries were prepared according to manufacturer’s instructions (Illumina). Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters. Fragments of 300±100 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR), using Q5 polymerase (NEB M0530).

tag: genotype

tag: ip antibody

tag: antibody source

value: Abcam #ab8580


title: EZH2.MN.WT [ChIP-Seq]

value: WT

value: in-house


title: HiC_mouse_liver, replicate 2

city: London

first: Suzana

last: Hadjur

address: 72 Huntley street

department: Cancer biology

country: United Kingdom

institute: Ucl

data_processing:
Read alignment was done by using Bowtie v0.12.8 with the parameters "-v 3 -a -m 1 --best --strata".
HiC data analysis was done using hicpipe v1.01 (Yaffe and Tanay, 2011)
genome_build: mm10,oryCun2,rheMac2,canFam3
Supplementary_files_format_and_content: HiCseq_summary' is a tab-delimited text file summarizing alignment results for all samples. All other processed data files are cis-interaction maps reporting observed and expected values for contacts between 50 Kb bins separated by up to 2 Mb. One processed data file is supplied for each replicate plus a merge of the two replicates for each species. The files are in a modified bed format (with header) in which the first three columns are the coordinate of the first bin (chrom1, start1, end1), the second three columns are the coordinates of the second bin (chrom2, start2, end2) and the last two columns are the expected and observed interaction counts.

source_name: Liver

extract_protocol:
After liver homogenisation, cells were immediately fixed with 1% formaldehyde before proceeding with Hi-C protocol.
Ligated material was sonicated, enriched for biotinylated ligation junctions and PE sequencing adapters were added according to Illumina standard protocols

value: primary liver cells

value: Young adult


title: HiC_mouse_liver, replicate 1


title: H3K27me3.ESC.WT [ChIP-Seq]

source_name: mESC

value: Abcam #ab6002


title: EZH2.MN.Δ5|6 [ChIP-Seq]


title: Pol2.MN.WT [ChIP-Seq]

value: Pol II

value: Santa Cruz #sc-899


title: CeM projector, experiment-2: CeM_547

description: Experiment-2, CeM


title: Pol2.MN.Δ5|6 [ChIP-Seq]


title: CTCF.ESC.Δ5|6 [ChIP-Seq]

value: CTCF

value: Millipore #07-729


title: H3K4me3.MN.Δ5|6:7|9 [ChIP-Seq]


title: CeM projector, experiment-2: CeM_542

description: Experiment-2, CeM


title: 4C.HOXA5-B.MN.WT

data_processing:
Library strategy: 4C-Seq
Fastq was demultiplexed and primer sequence was removed from each read
Reads were mapped to mm9 using 4cseqpipe (http://compgenomics.weizmann.ac.il/tanay/?page_id=99)
Median and 20/80% contact intensity across chr6:52075000-52250000 were calculated in 1kb bins using 4cseqpipe
Genome_build: mm9
Supplementary_files_format_and_content: Median and 20/80% contact intensity across chr6:52075000-52250000 were calculated in 2kb windows centered about 1kb bins. Medians across windows of increasing size from 2-50kb are also presented.

source_name: Differentiated Motor Neurons (Day 4 post RA/SAG)

extract_protocol:
10 million cells were trypsinized and crosslinked in 2% formaldehyde and 10% FBS in PBS for 10 min at room  temperature. The primary restriction enzyme used was DpnII. The secondary enzyme was Csp6I. Template DNA (1ug) was amplified using inverse primers containing barcoded illumina sequencing adapters on either end.
Libraries were constructed by adding barcoded illumine adapters to the 5’ end of each primer. PCR reactions were performed using the Expand Long Template PCR System (Roche), and 100-700bp DNA was gel purified and quantified before sequencing.

tag: bait name

tag: bait coordinate


title: H3K4me3.MN.WT [ChIP-Seq]


title: CTCF.MN.Δ5|6 [ChIP-Seq]


title: H3K27me3.MN.Δ5|6:7|9 [ChIP-Seq]


title: H3K27me3.MN.Δ5|6 [ChIP-Seq]


title: CTCF.MN.WT [ChIP-Seq]


title: 4C.HOXA5-A.MN.WT


title: 4C.HOXA5-A.MN.Δ5|6


title: CTCF.ESC.WT [ChIP-Seq]


title: H3K27me3.MN.WT [ChIP-Seq]


title: 4C.HOXA10.MN.WT


title: Day4.Δ5|6.b1 [RNA-Seq]

data_processing:
mapped to mm9 with BOWTIE -m40 -v2
reads were assigned to the ENSEMBL annotation using DEGseq
Normalized differential expression (taking into account biological replicates) was calculated using Deseq
Genome_build: mm9
Supplementary_files_format_and_content: Raw read count and RPKM matching the ENSEMBL annotation

source_name: Differentiating Motor Neurons (Day 4 post RA/SAG)

extract_protocol:
RNA was purified from cells with TRIzol (Invitrogen)
PolyA+ RNA was isolated using Dynabeads Oligo(dT)25 (Invitrogen) beads and converted into dsDNA using the dUTP method (Parkhomchuk et al., 2009). DNA was end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), and ligated to custom adapters. Fragments of 300±100 bp were size-selected and subjected to ligation-mediated PCR amplification (LM-PCR) using Q5 polymerase (NEB M0530) to generate strand-specific libraries.

tag: time point

value: Day 4


title: Day4.WT.b2 [RNA-Seq]


title: H3K27me3.ESC.Δ5|6 [ChIP-Seq]


title: Day4.Δ5|6:Δ7|9.b1 [RNA-Seq]


title: 4C.HOXA5-A.ESC.Δ5|6:7|9


title: Day4.WT.b1 [RNA-Seq]


title: 4C.HOXA5-A.ESC.WT


title: 4C.HOXA5-A.ESC.Δ5|6


title: Day0.Δ5|6:Δ7|9.b1 [RNA-Seq]

source_name: Differentiating Motor Neurons (Day 0)

value: Day 0


title: H2AK119Ub.MN.WT [ChIP-Seq]

value: Cell Signaling #8240


title: HiC_macaque_liver, replicate 2

organism: Macaca mulatta


title: HiC_macaque_liver, replicate 1


title: Day0.WT.b1 [RNA-Seq]


title: Day0.Δ5|6.b1 [RNA-Seq]


title: ESC.Δ5|6.b1 [RNA-Seq]

value: ESC


title: CHON1

city: West Haven

first: Koryu

last: Kin

state: CT

address: 840 West Campus Drive

department: EEB

institute: Yale University

data_processing:
Basecalls performed using CASAVA version 1.4
mRNA-seq reads were aligned to the human (GRCh37.69) cDNA builds using Tophat2 version 2.0.5
Number of times reads overlapped with known features (gene counts) was counted using HTSeq
transcripts per million (TPM) values were calculated according to Wagner et al (2012) Theor. Biosci.
Genome_build: GRCh37.69
Supplementary_files_format_and_content: SixCellTypes_RNAseq_counts_tpm.txt: tab-delimited text files include read counts, transcript lenghts used, and TPM values for each Sample
Supplementary_files_format_and_content: SixCellTypes_RNAseq_tpm_proteincoding.txt: tab-delimited text files include TPM values of protein coding genes for each Sample

source_name: chondrocytes

extract_protocol:
Cells grown in cluture were treated with trypsin and detached from flasks, and RNA was isolated using the RNeasy  Mini RNA extraction kit (QIAGEN)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: chondrocytes (ATCC:CRL-2847) grown in culture


title: DSC2

source_name: decidual stromal cells

value: in vitro decidualized endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture


title: 4C.HOXA10.MN.Δ5|6


title: MYO1

source_name: myometrial cells

value: myometrial cells grown in culture


title: MFB2

source_name: myofibrobalsts

value: myofibrobalsts (ATCC:CRL-2854) grown in culture


title: ESF2

source_name: endometrial stromal fibroblasts

value: endometrial stromal fibroblast (ATCC:CRL-4003) grown in culture


title: ESC.WT.b1 [RNA-Seq]

value: WT


title: CAGE_AdMateM_4d_testes_rep2

city: Bethesda

first: Brian

last: Oliver

state: MD

address: 50 South Drive

department: LBG

institute: NIDDK, NIH

data_processing:
We removed linkers and adapters from raw reads to extract the 27 nt CAGE tags.   Tags were aligned to the D. melanogaster (release 5) and D. pseudoobscura (release 3) genomes with StatMap (http://www.statmap-bio.org/) to estimate tag density at the CAGE tag start sites (termed as CAGE sites).  CAGE sites with >1 tag per million (TPM) were retained for further analysis.  See Chen ZX et al. Genome Res 2014, 24(7):1209-23.
To compare orthologous transcription start sites (TSS) among CAGE sites in D. melanogaster and D. pseudoobscura, we used the AUG codons of 1:1 orthologs in the two species derived from OrthoDB version 6 (Waterhouse et al. Nucleic Acids Res. 2013, 41 (Database issue): D358–65.).  We associated CAGE sites with the nearest downstream gene AUG codon within 5kb, and the CAGE sites with the highest TPM of the orthologous genes were classified as TSS of the genes.
Genome_build: Drosophila melanogaster Release 5, Drosophila pseudoobscura Release 3
Supplementary_files_format_and_content: BED files for CAGE sites corresponding to TSS of orthologous genes in D. melanogaster and D. pseudoobscura.  Column 1: chromosome; Column 2: CAGE site start (0-based coordinates); Column 3: CAGE site end (1-based coordinates); Column 4: the orthoDB ID for protein-coding gene following the CAGE peak; Column 5: TPM (tags per million) for the CAGE site; Column 6: strand; Column 7: distance between the CAGE site and its nearest downstream gene AUG codon.

organism: Drosophila melanogaster

source_name: dissected testes and reproductive tracts

growth_protocol: Flies were grown on standard cornmeal medium at 25°C.  Adults were aged 4 days for D. melanogaster and 5-8 days for D. pseudoobscura before dissection.

extract_protocol:
Total RNA was extracted from dissected testes, ovaries and carcasses of D. melanogaster and D. pseudoobscura adults using the RNeasy procedure (Qiagen, Valencia, CA).  See Chen ZX et al. Genome Res 2014, 24(7):1209-23.
The optimized CAGE library preparation protocol resulted in 27 nt tags that correspond to the 5’ ends of capped RNAs for sequencing on the Illumina platform.  See Chen ZX et al. Genome Res 2014, 24(7):1209-23.

value: Adult

tag: age

value: 4 days post eclosion

value: Male

tag: read length

value: 36 nt


title: Day4.Δ5|6.b2 [RNA-Seq]


title: Day0.WT.b2 [RNA-Seq]


title: 4C.HOXA5-B.MN.Δ5|6:7|9


title: MYO2


title: FDC1

source_name: follicular dendritic cells

value: follicular dendritic cells isolated and grown in culture


title: ESF1


title: MFB1


title: CAGE_AdMateF_4d_ovaries

source_name: dissected ovaries and reproductive tracts

value: Female


title: FDC2


title: CHON2


title: Day0.Δ5|6.b2 [RNA-Seq]


title: DSC1


title: EV2

city: Cleveland

first: Jihye

last: Kim

state: Ohio

address: 9500 Euclid Ave.

department: Quantitative Health Sciences

institute: Cleveland Clinic

description: mRNA

data_processing:
Alignment: TopHat v1.4.1 using default settings. hg19 (UCSC).
Expression levels: Cufflinks v1.3.0 and cuffdiff using default settings.
GSEA anlalysis with GeneSigDB v4.
Genome_build: GRCh37
Supplementary_files_format_and_content: Tab-delimited text file with FPKM values.

source_name: breast cancer cancer cell line, control

growth_protocol: 10^5 MCF12A cells stably over-expressing miR-424 or an empty vector (EV) control were grown in triplicate for 48 hours.

extract_protocol:
Total RNA was extracted and mRNA isolated using the miRNeasy Kit (Qiagen) according to manufacturer's instructions.
RNA libraries were prepared for sequencing using TruSEQ RNA Sample Prep v2 using standard Illumina protocols.

value: breast cancer cancer cell line

tag: stable expression

value: empty vector


title: CAGE_MixMF_4d_carcass

source_name: carcasses minus reproductive tracts

tag: tissue

value: carcasses minus reproductive tracts

value: Mixed


title: miR424_3

description: mRNA

source_name: breast cancer cancer cell line, over-expressing miR-424

value: miR-424 over-expressed


title: EV1

description: mRNA


title: CAGE_AdMateM_4d_testes_rep1

value: dissected testes and reproductive tracts

tag: developmental stage


title: IDC-Patient6

city: Kansas City

first: Hanan

last: Elsarraj

state: KS

address: 3901 Rainbow Blvd.

department: Pathology and Laboratory Medicine

institute: University of Kansas Medical Center

description:
Sample name: IDC12
Invasive ductal carcinoma (IDC), biopsied from patient No.6

data_processing:
Paired Fastq sequence files were imported to CLC Genomics Workbench (version 7.5)and mapped to the human reference genome (hg19)
Ensembl database (GRCh37.74.gtf) was used for gene annotation…
Total number of reads mapped to the gene is used as the total counts for the gene, and the values were transformed by adding 1 followed by log2 transformation.
Transformed data was quantile normalized before the analysis of differential gene expression between two groups (DCIS vs IDC).
Empirical analysis of differential gene expression was performed between two groups (DCIS vs IDC) using ‘Exact Test"
Genome_build: human reference genome (hg19)
Supplementary_files_format_and_content: Excel file of all genes and of BCL9 normalized values

source_name: Patient 6

extract_protocol:
Total RNA was prepared using (All prep Qiagen Kit) according to the manufacturers protocol
Libraries were prepared according to illumina TruSeq RNA Sample Prep. (LT) Protocol

tag: individual

value: Patient 6

tag: sample type

value: DCIS-IDC tandem lesion

value: IDC cells


title: EV3

description: mRNA

tag: cell line


title: HiC_dog_liver, replicate 2

organism: Canis lupus familiaris

source_name: Liver

tag: cell type

value: primary liver cells

value: Young adult


title: IDC-Patient3

description:
Sample name: IDC3
Invasive ductal carcinoma (IDC), biopsied from patient No.3

source_name: Patient 3

value: Patient 3


title: IDC-Patient5

description:
Sample name: IDC5
Invasive ductal carcinoma (IDC), biopsied from patient No.5

source_name: Patient 5

value: Patient 5


title: IDC-Patient2

description:
Sample name: IDC2
Invasive ductal carcinoma (IDC), biopsied from patient No.2

source_name: Patient 2

value: Patient 2


title: CAGE_Dpse_Testes_Reproductive_Tract

organism: Drosophila pseudoobscura

value: Adult

value: 5-8 days post eclosion

tag: Sex

value: Male

value: 36 nt


title: DCIS-Patient6

description:
Sample name: DCIS12
Ductal carcinoma in situ (DCIS), biopsied from patient No.6

value: DCIS cells


title: IDC-Patient1

description:
Sample name: IDC1
Invasive ductal carcinoma (IDC), biopsied from patient No.1

source_name: Patient 1

value: Patient 1


title: DCIS-Patient4

description:
Sample name: DCIS4
Ductal carcinoma in situ (DCIS), biopsied from patient No.4

source_name: Patient 4

value: Patient 4


title: HiC_rabbit_liver, replicate 1

organism: Oryctolagus cuniculus


title: DCIS-Patient5

description:
Sample name: DCIS5
Ductal carcinoma in situ (DCIS), biopsied from patient No.5


title: CAGE_Dpse_Ovaries_Reproductive_Tract

value: dissected ovaries and reproductive tracts

value: Female


title: HiC_dog_liver, replicate 1


title: CAGE_Dpse_M_Carcass_Rep_Tract

value: carcasses minus reproductive tracts


title: DCIS-Patient3

description:
Sample name: DCIS3
Ductal carcinoma in situ (DCIS), biopsied from patient No.3

value: DCIS-IDC tandem lesion


title: miR424_2

description: mRNA

value: breast cancer cancer cell line

value: miR-424 over-expressed


title: DCIS-Patient2

description:
Sample name: DCIS2
Ductal carcinoma in situ (DCIS), biopsied from patient No.2


title: miR424_1

description: mRNA


title: IDC-Patient4

description:
Sample name: IDC4
Invasive ductal carcinoma (IDC), biopsied from patient No.4

value: IDC cells


title: testis_20wks_1

status: Public on Feb 25 2015

city: Berlin

first: Xintian

middle: Arthur

last: YOU

address: Robert-Roessle-str. 10

country: Germany

institute: Max-Delbrueck-Center for Molecular Medicine

description:
Sample 33
rRNA depleted
processed data file: mouse_TPM.txt, mouse_circRNA_TPM.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 or rn5.0 whole genome using Tophat2 v2.0.6 with parameters -N 6 --read-edit-dist 6 --segment-mismatches ---transcriptome-index=index, where the transcriptome-index is build on Ensembl annotation verion 67 for mouse and version 72 for rat
Fragments Per Kilobase of gene transcripts per million mapped reads (FPKM) were calculated using Cufflinks version 2.2.1 with parameter -u. Then FPKMs were converted to TPM following the protocol from Bo Li et at., BMC Bioinformatics, 2009
CircRNAs are identified and then quantified using the acfs pipeline available at https://code.google.com/p/acfs/
Genome_build: mm9 and rn5.0
Supplementary_files_format_and_content: tab-delimited text files include TPM values for TTO and circRNAs in mouse and rat samples
Supplementary_files_format_and_content: bed files for circRNAs in mouse and rat

source_name: Testis

extract_protocol:
TRIZOL (Invitrogen) extraction
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: 20 weeks

value: Testis


title: testis_20wks_2

description:
Sample 34
rRNA depleted
processed data file: mouse_TPM.txt, mouse_circRNA_TPM.txt


title: lung_20wks_1

description:
Sample 31
rRNA depleted
processed data file: mouse_TPM.txt, mouse_circRNA_TPM.txt

source_name: Lung

value: Lung


title: liver_20wks_2

description:
Sample 30
rRNA depleted
processed data file: mouse_TPM.txt, mouse_circRNA_TPM.txt

value: Liver


title: heart_20wks_1

description:
Sample 27
rRNA depleted
processed data file: mouse_TPM.txt, mouse_circRNA_TPM.txt

source_name: Heart

value: Heart


title: brain_20wks_2

description:
Sample 26
rRNA depleted
processed data file: mouse_TPM.txt, mouse_circRNA_TPM.txt

source_name: Brain

value: Brain


title: HiC_rabbit_liver, replicate 2

value: primary liver cells

value: Young adult


title: brain_20wks_1

description:
Sample 25
rRNA depleted
processed data file: mouse_TPM.txt, mouse_circRNA_TPM.txt


title: lung_20wks_2

description:
Sample 32
rRNA depleted
processed data file: mouse_TPM.txt, mouse_circRNA_TPM.txt


title: P30_rep2

description:
Sample 18
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 or rn5.0 whole genome using Tophat2 v2.0.6 with parameters -N 6 --read-edit-dist 6 --segment-mismatches ---transcriptome-index=index, where the transcriptome-index is build on Ensembl annotation verion 67 for mouse and version 72 for rat
Fragments Per Kilobase of gene transcripts per million mapped reads (FPKM) were calculated using Cufflinks version 2.2.1 with parameter -u. Then FPKMs were converted to TPM following the protocol from Bo Li et at., BMC Bioinformatics, 2009
CircRNAs are identified and then quantified using the acfs pipeline available at https://code.google.com/p/acfs/
Genome_build: mm9 and rn5.0
Supplementary_files_format_and_content: tab-delimited text files include TPM values for TTO and circRNAs in mouse and rat samples
Supplementary_files_format_and_content: bed files for circRNAs in mouse and rat
Supplementary_files_format_and_content: mouse_TPM.txt: abundance measurements for mRNAs and lincRNAs
Supplementary_files_format_and_content: mouse_circRNA_TPM.txt: abundance measurements for circRNAs
Supplementary_files_format_and_content: mouse_circRNA_MEA.bed: bed file for highly-confident circRNAs
Supplementary_files_format_and_content: mouse_circRNA_CBR.bed: bed file for less-confident circRNAs
Supplementary_files_format_and_content: rat_TPM.txt: abundance measurements for mRNAs and lincRNAs
Supplementary_files_format_and_content: rat_circRNA_TPM.txt: abundance measurements for circRNAs
Supplementary_files_format_and_content: rat_circRNA_MEA.bed: bed file for highly-confident circRNAs
Supplementary_files_format_and_content: rat_circRNA_CBR.bed: bed file for less-confident circRNAs
Supplementary_files_format_and_content: PacBio_CCS.fa: Only the Circular Consensus (CCS) Reads were used to support the circular structure and the full-length sequence of the circRNAs

source_name: Hippocampus


title: liver_20wks_1

description:
Sample 29
rRNA depleted
processed data file: mouse_TPM.txt, mouse_circRNA_TPM.txt


title: P10_rep2

description:
Sample 17
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: P10_rep1

description:
Sample 13
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: E18_rep2

description:
Sample 15
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: P1_rep1

description:
Sample 12
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: P30_rep1

description:
Sample 14
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: Neuropil_1

description:
Sample 9
rRNA depleted, acute 500µm slices microdissected as described in Cajigas, I.J., et al., The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imaging. Neuron, 2012. 74(3): p.453-66.
mouse_TPM.txt, mouse_circRNA_TPM.txt

source_name: Hippocampal CA1

value: 4 weeks


title: P1_rep2

description:
Sample 16
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: E18_rep1

description:
Sample 11
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: Somata_1

description:
Sample 10
rRNA depleted, acute 500µm slices microdissected as described in Cajigas, I.J., et al., The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imaging. Neuron, 2012. 74(3): p.453-66.
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: Homogenate

description:
Sample 7
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: Synaptosome

description:
Sample 8
rRNA depleted, synaptosomes purified as in Dunkley et al., 2008
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: DCIS-Patient1

description:
Sample name: DCIS1
Ductal carcinoma in situ (DCIS), biopsied from patient No.1

value: Patient 1

value: DCIS cells


title: CAGE_Dpse_F_Carcass_Rep_Tract

value: Adult

value: 5-8 days post eclosion

value: Female

value: 36 nt


title: Testis_14wks

description:
Sample 6
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt

value: 14 weeks


title: Liver_14wks

description:
Sample 3
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: Lung_14wks

description:
Sample 4
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: Heart_14wks

description:
Sample 5
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: Brain_14wks_2

description:
Sample 2
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: heart_20wks_2

description:
Sample 28
rRNA depleted
processed data file: mouse_TPM.txt, mouse_circRNA_TPM.txt


title: HL60_VitD_14d_positive_control.50ng_1

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

data_processing:
Sequencing was performed on the Illumina HiSeq 2000 system using the standard 100bp paired-end configuration.
Raw sequence reads were trimmed using Trimmomatic (Bolger et al., 2014) version 0.32 with the following parameters: HEADCROP:6 ILLUMINACLIP:<Illumina_adapter_file>:2:10:4:1:true SLIDINGWINDOW:4:1 MAXINFO:16:0.40 MINLEN:16)
Trimmed reads were aligned against the human genome (hg19/GRCh37) and/or the mouse genome (mm10/GRCm38) using the Bismark Bisulfite Mapper (Krueger and Andrews 2011), version v0.12.2, parameter: –bowtie2). Duplicate reads were discarded and DNA methylation calls were extracted.
Reads containing fewer than three cytosines outside a CpG context that have been converted to thymines were discarded, which effectively removes unconverted and contaminating DNA fragments.
Genome_build: hg19/GRCh37 - mm10/GRCm38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: The genome-wide CpG methylation report is tab-delimited, uses 1-based genomic coordinates and is in the following format: <chromosome>  <position>  <strand>  <count methylated>  <count non-methylated>  <C-context>  <trinucleotide context>

extract_protocol:
Direct extraction of DNA following the steps of the EZ DNA methylation Direct Kit as described in the methods section in Farlik et al.
A novel method to perform library preparation from single cells as described in the methods section of Farlik et al.

tag: treatment

value: Vitamin D

tag: replicate


title: HL60_VitD_14d.1_7

value: 1 cell


title: HL60_VitD_14d.1_10


title: HL60_VitD_14d.4_6

value: 4 cells


title: HL60_VitD_14d.1_8


title: HL60_VitD_14d.1_11


title: HL60_VitD_14d.4_2


title: HL60_VitD_14d.4_3


title: CCE_ATRA_7d.1_deep

source_name: CCE

value: CCE

value: ATRA

value: deep


title: HL60_VitD_14d.4_1


title: HL60_VitD_14d.4_5


title: HL60_VitD_14d.4_4


title: KBM7.1_1


title: KBM7.4_2


title: KBM7.4_3


title: KBM7.1_3


title: KBM7.1_2


title: KBM7.4_1


title: K562_Aza_96h.1_SC2

value: Azacytidine


title: K562.1_SC3


title: K562_Aza_96h.1_SC3


title: K562_Aza_48h.1_SC3


title: rpn_BIC12h_rep2

description:
Sample 24
rRNA depleted
rat_TPM.txt, rat_circRNA_TPM.txt

organism: Rattus norvegicus

source_name: Primary hippocampal neuron culture

value: Sprague Dawley

value: DIV 28

tag: treatment protocol

value: bicuculline (Tocris, 40,μM), treated for 12h

tag: growth protocol

value: Dissociated hippocampal neurons prepared as in Aakalu, G., et al., Dynamic visualization of local protein synthesis in hippocampal neurons. Neuron, 2001. 30(2):p. 489-502.


title: K562_Aza_96h.1_SC1


title: rpn_BIC12h_rep1

description:
Sample 23
rRNA depleted
rat_TPM.txt, rat_circRNA_TPM.txt

value: bicuculline (Tocris, 40  μM), treated for 12h


title: K562_positive_control.50ng_1


title: K562_Aza_48h.1_SC2


title: rpn_ctrl_rep2

description:
Sample 22
rRNA depleted
rat_TPM.txt, rat_circRNA_TPM.txt

value: H20 control


title: K562_Aza_48h.1_SC1


title: rpn_ctrl_rep1

description:
Sample 21
rRNA depleted
rat_TPM.txt, rat_circRNA_TPM.txt


title: Neuropil_2

description:
Sample 19
rRNA depleted, acute 500µm slices microdissected as described in Cajigas, I.J., et al., The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imaging. Neuron, 2012. 74(3): p.453-66.
rat_TPM.txt, rat_circRNA_TPM.txt

value: 4 weeks


title: Somata_2

description:
Sample 20
rRNA depleted, acute 500µm slices microdissected as described in Cajigas, I.J., et al., The local transcriptome in the synaptic neuropil revealed by deep sequencing and high-resolution imaging. Neuron, 2012. 74(3): p.453-66.
rat_TPM.txt, rat_circRNA_TPM.txt


title: K562.1_7


title: K562_Aza_96h.1_5


title: K562_Aza_48h.1_4


title: K562.1_8


title: HL60_VitD_14d.1_5


title: K562.1_6


title: negative_control_hg.0_4

value: 0 cells


title: negative_control_hg.0_5


title: HL60_VitD_14d.1_3


title: K562_Aza_48h.1_6


title: K562_Aza_96h.1_6


title: K562_Aza_96h.1_7


title: HL60_VitD_14d.1_6


title: cross_control.0_4

value: 0 cell


title: HL60_VitD_14d.1_1


title: G18_100

city: Perth

first: Sulev

last: Koks

state: Western Australia

address: 90 South Street

department: Centre for Molecular Medicine and Innovative Therapeutics

country: Australia

institute: Murdoch University

data_processing:
Color-space base calling
Mapping, alignment with Lifescope
Lifescope transcriptome workflow
Genome_build: hg19
Supplementary_files_format_and_content: counts data

source_name: heart

growth_protocol: tissue sample from the right atrial appendage

extract_protocol:
RNALater and mirVana miRNA Isolation Kit
RNA was amplified with Ovation RNA-Seq System V2 Kit (NuGen, Emeryville, CA, USA) and the output double stranded DNA was used to prepare SOLiD 5500 W System DNA fragment library according to manufacturer’s protocols (Thermo Fisher Scientific Inc, Waltham, MA, USA). The barcoding primers in library preparation and fragment sequencing chemistry was applied (75 bp in forward directions). In case of 12 samples per flowchip lane approximately 33 million mappable reads were expected per one sample, which would be enough for successful whole transcriptome expression pattern analysis.

treatment_protocol: After induction of anesthesia and intubation of the trachea, patients were randomly allocated to receive either 40% or > 96% oxygen for 60 minutes.

value: heart; right atrial appendage

tag: oxygen percentage

value: M


title: G14_100


title: K562.4_7


title: G13_40

value: F


title: cross_control.0_2


title: HL60_VitD_14d.1_2

value: Vitamin D

value: 1 cell


title: cross_control.0_3


title: K562.4_6

value: 4 cells


title: G12_40


title: K562_Aza_48h.1_5


title: K562.4_2


title: K562.4_3


title: HL60_positive_control.50ng_1


title: HL60_VitD_120h.1_4


title: G10_40


title: G9_100


title: G8_40


title: G11_100


title: G16_40


title: G6_40


title: HL60_VitD_120h.1_3


title: G15_40


title: G4_40


title: HL60_VitD_120h.1_2


title: HL60_VitD_120h.4_6


title: G3_100


title: G2_40


title: G5_40


title: HL60.4_8


title: HL60_VitD_120h.4_7


title: HL60_VitD_120h.4_5


title: HL60.4_6


title: HL60.4_7


title: HL60.4_5


title: HL60_VitD_48h.1_4


title: M7_40


title: M6_100


title: M8_100


title: HL60.4_deep

value: deep


title: M4_40


title: G7_100


title: HL60_VitD_120h.4_8


title: M3_40


title: HL60_VitD_48h.1_3


title: M1_40


title: M2_100


title: HL60.4_4


title: HL60_VitD_48h.1_2


title: HL60.4_3


title: HL60_VitD_48h.1_1


title: HL60.4_1


title: HL60.1_4


title: HL60.4_2


title: HL60.1_3


title: CCE_EB_14d.4_1

value: CCE

value: EB


title: HL60.1_1


title: CCE_EB_7d.4_2


title: CCE_EB_14d.4_3


title: CCE_EB_14d.4_2


title: HL60.1_2


title: CCE_2i_120h.1_11


title: CCE_EB_7d.4_1


title: M5_100


title: CCE_2i_120h.1_10


title: K562_Aza_96h.4_1

value: Azacytidine


title: K562_Aza_48h.4_2


title: CCE_2i_120h.1_9


title: K562.4_1


title: CCE_ATRA_14d.4_3

value: ATRA


title: CCE_2i_120h.1_7


title: CCE_ATRA_14d.4_1


title: cross_control.0_15


title: CCE_ATRA_7d.4_1


title: CCE_2i_120h.1_6


title: CCE_2i_120h.1_5


title: K562_Aza_96h.1_4


title: cross_control.0_16


title: CCE_2i_120h.1_2


title: K562_Aza_96h.1_2


title: K562_Aza_48h.1_2


title: cross_control.0_14


title: K562_Aza_96h.1_3


title: cross_control.0_13


title: cross_control.0_12


title: cross_control.0_11


title: K562.1_3


title: K562_Aza_48h.1_1


title: cross_control.0_10


title: cross_control.0_8


title: cross_control.0_9


title: cross_control.0_6


title: K562.1_2


title: cross_control.0_7


title: CCE_ATRA_14d.4_2


title: negative_control_hg.0_3


title: cross_control.0_5


title: 32D.4_11


title: K562_Aza_96h.1_1


title: negative_control_hg.0_2


title: 32D.4_10


title: 32D.4_7


title: 32D.4_9


title: CCE_2i_120h.1_4


title: 32D.4_8


title: CCE_2i_120h.1_3


title: K562.19_1

value: 19 cells


title: K562.19_2


title: 32D.4_5


title: 32D.4_6


title: 32D.4_3


title: K562.10_2

value: 10 cells


title: 32D.4_1


title: K562.50_2

value: 50 cells


title: CCE.4_19


title: CCE.4_20


title: K562.10_1


title: CCE.4_18


title: CCE.4_17


title: K562.20_1

value: 20 cells


title: CCE.4_16


title: CCE.4_15


title: K562.50_1


title: CCE.4_13


title: CCE.4_14


title: CCE.4_12


title: CCE.4_11


title: CCE.4_9


title: negative_control_mm.0_5

value: 0 cells


title: K562.500_1

value: 500 cells


title: 32D.4_4


title: 32D.4_2


title: K562.100_1

value: 100 cells


title: cross_control.0_1


title: K562.2_1

value: 2 cells


title: negative_control_mm.0_4


title: K562_positive_control.1k_3

value: 1k cells


title: CCE_positive_control.50ng_2


title: CCE.1_SC1


title: K562_positive_control.1k_2


title: CCE.1_7


title: P30_rep2 [PacBio]

description:
Sample 18
rRNA depleted
mouse_TPM.txt, mouse_circRNA_TPM.txt


title: CCE.1_6


title: KBM7.3125ng_1


title: K562_positive_control.100k_1

value: 100k cells


title: CCE.1_3

value: 1 cell


title: Sample_998-L

city: Ames

first: Andrew

middle: J

last: Severin

email: severin@iastate.edu, csiva@iastate.edu

state: IA

address: 2200 Osborn Drive

department: Office of Biotechnology

institute: Iowa State University

description: Post-weaning pig growth and gene expression

data_processing:
Illumina Casava1.7 software used for basecalling.
GSNAP was used for aligning the reads to the reference genome
HTSeq was used to get the raw counts for the gene (GTF file Ensembl gene set version 70)
Quasi-seq was used to normalize (upper quarltile) and call DGE
Genome_build: Sus scrofa genome build 10.2 (Ensembl release 70)
Supplementary_files_format_and_content: Text and raw counts for the gene experssion

organism: Sus scrofa domesticus

source_name: longissimus dorsi muscle

growth_protocol: Over a 3.5 d period 1,500 pigs (Danbred 600 × Newsham NC32) were farrowed at commercial farm, a total of 1,054 pigs were randomly selected from this farrowing group, weaned, and transported to a commercial wean-to-finish barn. Nine pigs from each of the lowest 10th percentile (low tADG) and the 60th-70th percentile (high tADG) for tADG were used to create nine pairs of pigs, with pairs derived from litters of the same size and from sows of the same parity. These nine pairs (18 total pigs) were transported approximately 45 min to the Iowa State University Diagnostic Laboratory where they were euthanized via captive-bolt stunning followed by exsanguination. Samples of subcutaneous backfat between the 8th and last ribs and longissimus dorsi muscle (LM) and were rapidly collected, frozen in liquid nitrogen, and stored at -80°C for later isolation of RNA

extract_protocol:
Total RNA was isolated and purified from LM and adipose tissues using Ambion MagMAX total RNA isolation kits (Life Technologies, Carlsbad, CA) per manufacturer’s instructions. Quality and quantity of RNA were determined by using a Nanodrop ND- 1000 (Thermo Scientific, Wilmington, DE) and an Agilent 2100 Bioanalyzer (Agilent Technologies, Inc., Santa Clara, CA).
RNA sequencing libraries were prepared using TruSeq RNA Sample Prep Kits (Illumina Inc., San Diego, CA) and samples sequenced by 2 × 100 bps paired-end sequencing on an Illumina HiSeq 2000 instrument at the Iowa State DNA facility

tag: breed

value: Danbred 600 X Newsham NC71

value: 16-17 days old

value: weaning


title: CCE.1_5

value: CCE


title: KBM7.625ng_1


title: CCE.4_10

value: 4 cells


title: Sample_991-L

value: Danbred 600 X Newsham NC70

tag: age


title: CCE.1_2


title: CCE_2i_120h.4_8


title: KBM7_positive_control.50ng_3


title: Sample_911-L

value: Danbred 600 X Newsham NC68


title: CCE_2i_120h.4_6


title: CCE.1_SC2


title: CCE_2i_120h.4_5


title: CCE_EB_14d.1_3

value: EB


title: Sample_889-L

value: Danbred 600 X Newsham NC66


title: KBM7_positive_control.50ng_2


title: CCE_EB_14d.1_2


title: Sample_835-L

value: Danbred 600 X Newsham NC65


title: KBM7_positive_control.50ng_1


title: CCE_EB_7d.1_4


title: KBM7.25ng_1


title: CCE_EB_7d.1_3


title: CCE_EB_7d.1_2


title: KBM7.100ng_1


title: CCE_EB_7d.1_1


title: Sample_735-L

value: Danbred 600 X Newsham NC64


title: Sample_731-L

value: Danbred 600 X Newsham NC63


title: CCE_2i_48h.4_12


title: Brain_14wks_1

description:
Sample 1
oligo-dT beads
mouse_TPM.txt, mouse_circRNA_TPM.txt

molecule: polyA RNA

value: 14 weeks


title: CCE_2i_48h.4_11


title: Sample_659-L

value: Danbred 600 X Newsham NC62


title: CCE_2i_48h.4_10


title: Sample_656-L

value: Danbred 600 X Newsham NC61


title: KBM7.125ng_1


title: CCE_2i_48h.4_9


title: CCE_2i_120h.4_7


title: Sample_572-L

value: Danbred 600 X Newsham NC60


title: CCE_ATRA_14d.1_3

value: ATRA

value: 1 cell


title: CCE_ATRA_14d.1_4


title: CCE_ATRA_14d.1_1


title: CCE_ATRA_7d.1_3


title: Sample_491-L

value: Danbred 600 X Newsham NC59

value: 16-17 days old


title: CCE_2i_120h.4_4

value: CCE


title: CCE_ATRA_7d.1_1


title: CCE_ATRA_7d.1_2


title: Sample_391-L

value: Danbred 600 X Newsham NC58

value: weaning


title: Sample_242-L

value: Danbred 600 X Newsham NC57


title: CCE_2i_120h.4_3

value: 4 cells


title: CCE_2i_48h.4_8


title: CCE_2i_120h.4_1


title: CCE_2i_48h.4_7


title: CCE_2i_48h.4_5


title: Sample_186-L

value: Danbred 600 X Newsham NC55


title: CCE_2i_48h.4_6


title: Sample_176-L

value: Danbred 600 X Newsham NC54


title: CCE.4_8


title: Sample_114-L

value: Danbred 600 X Newsham NC53


title: CCE.4_7


title: Sample_77-L

value: Danbred 600 X Newsham NC52


title: CCE.4_5


title: CCE.4_6


title: CCE_2i_96h.1_1


title: Sample_998-BF

source_name: subcutaneous adipose (black fat)

value: Danbred 600 X Newsham NC51


title: CCE.1_1


title: CCE_2i_48h.1_1


title: CCE_2i_96h.4_4


title: CCE_2i_120h.4_2


title: Sample_991-BF

value: Danbred 600 X Newsham NC50


title: CCE_2i_48h.1_2


title: CCE_2i_96h.4_2


title: Sample_231-L

value: Danbred 600 X Newsham NC56


title: Sample_911-BF

value: Danbred 600 X Newsham NC48


title: CCE_2i_48h.4_2


title: CCE_2i_96h.4_3


title: Sample_889-BF

value: Danbred 600 X Newsham NC46


title: CCE_2i_48h.4_3


title: Sample_735-BF

value: Danbred 600 X Newsham NC44


title: CCE.4_2


title: CCE_2i_96h.4_1


title: negative_control_mm.0_2

value: 0 cells


title: Sample_835-BF

value: Danbred 600 X Newsham NC45

value: 16-17 days old


title: Sample_659-BF

value: Danbred 600 X Newsham NC42


title: 32D.1_2

value: 1 cell


title: Sample_491-BF

value: Danbred 600 X Newsham NC39

value: weaning


title: 32D.2_1

value: 2 cells


title: Sample_391-BF

value: Danbred 600 X Newsham NC38


title: 32D.10_1

value: 10 cells


title: 32D.50_1

value: 50 cells


title: Sample_242-BF

value: Danbred 600 X Newsham NC37


title: CCE_positive_control.50ng_1

value: CCE


title: Sample_231-BF

value: Danbred 600 X Newsham NC36


title: Sample_186-BF

value: Danbred 600 X Newsham NC35


title: Sample_114-BF

value: Danbred 600 X Newsham NC33


title: Sample_176-BF

value: Danbred 600 X Newsham NC34


title: CCE.4_1

value: 4 cells


title: Thymus Satb1 ChIP-seq (TKS238B)

city: San Francisco

first: Hunter

last: Richards

state: CA

address: 513 Parnassus Ave., HSW 863

department: Orofacial Sciences

institute: UCSF

data_processing:
Raw ChIP-seq data was aligned to mouse reference genome release mm9 using bowtie v1.0.0 with the following parameters set: --chunkmbs 1024 --best --strata -n 3 -m 1
Fragment size was estimated from strand cross-correlation plots created by MaSC (v1.2.1) and MACS2 (predictd; v2.1.0.20140616). This estimate (248 bp) was used in the model building step for peak-calling with MACS.
Candidate peaks were called using MACS (v1.4.3) keeping peaks ranked below a p-value threshold of 1x10^-5. The options --nomodel and --shiftsize=124 (half fragment size) were used to override automatic model building. For downstream analysis only peaks having an FDR < 1% and Fold Enrichment > 4 were kept.
Genome_build: NCBI37/mm9
Supplementary_files_format_and_content: bigWig tracks of coverage profiles were generated using the wigToBigWig utility from UCSC. The bigWig track of MACS peaks was created using a custom Perl script.

source_name: thymus

extract_protocol:
For ChIP-seq using anti-SATB1 (abcam, ab109122), 4x10^7 C57BL/6J thymocytes were freshly prepared and washed with PBS containing 0.5 mM PMSF and were subjected to crosslinking by incubation for 10 min in 5 mM HEPES pH 7.5, 10 mM NaCl, 0.1 mM EDTA, 0.05 mM EGTA, 1% formaldehyde at 23 °C. The reaction was stopped by addition of glycine to 0.125 M. Cells were then immediately washed in ice-cold PBS containing 0.5 mM PMSF and lysed by incubation for 10 min on ice in 1 ml of 50 mM HEPES pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% TritonX-100 containing protease inhibitor (Roche). Nuclei were pelleted and lysed by resuspending in 10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA and 0.5 mM EGTA containing protease inhibitor (Roche). Pelleted chromatin was resuspended in 400 μl of 10 mM Tris pH 8.0, 300 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% TritonX-100, 0.1% sodium deoxycholate and 0.5% N-laurylsarcosine, and was sonicated using a model XL2000 ultrasonic cell disruptor (MICROSON) so that relatively large fragments (1-10 kbp) were included. Sonicated chromatin was incubated overnight at 4 °C with anti-SATB1 antibody that was preconjugated with magnetic beads (Dynabeads). Immunoprecipitated DNA was then purified after vigorous washing of immunoprecipitates and reversal of crosslinks by overnight incubation at 65 °C in 50 mM Tris pH 8.0, 10 mM EDTA, 1% SDS.
Input DNA and ChIP DNA (10-20 ng) were subjected to sonication (Bioruptor, UCD-200) on low power for 20 cycles (30 sec. on and 30 sec. off). Library construction was conducted as follows: 1) End repair by T4 DNA polymerase, Klenow DNA polymerase and T4 kinase; 2) A-tailing by Klenow exo-; 3) Adaptor ligation using Illumina TruSeq adaptors (Illumina) and T4 DNA ligase; 4) 10 cycles of PCR amplification by AccuPrime DNA Taq polymerase (Invitrogen) and TruSeq primers; 5) purification of final products by size selection (200-1000 bp) using SPRI beads (Thermo Fisher). Libraries were sequenced to 50 bp read length on a HiSeq2000 (Illumina).

value: thymocyte

tag: chip antibody

value: Satb1 (AbCam ab109122)

value: 6 weeks


title: Thymus input control ChIP-seq (TKS238A)


title: Sample_77-BF

value: Danbred 600 X Newsham NC32

value: 16-17 days old


title: Sample_731-BF

value: Danbred 600 X Newsham NC43

value: weaning


title: CB.3

status: Public on Feb 24 2015

city: Chapel Hill

first: J

middle: Mauro

last: Calabrese

address: 120 Mason Farm Road

department: Pharmacology

institute: UNC-Chapel Hill

data_processing:
Variant sequence data was obtained from the Sanger Institute (http://www.sanger.ac.uk/resources/mouse/genomes/).
Reads were aligned to mm9 or an in silico constructed version of the Cast genome using Bowtie.
SNP-containing reads were extracted using custom scripts.
Genome_build: mm9
Supplementary_files_format_and_content: BED files were generated from mm9 alignments, and reported read ends reflect an average fragment size of 100bp for corresponding libraries. Snp files contain snp-overlapping read locations, snp-overlapping base, and snp-overlapping read allele.

source_name: F1 Hybrid CB.3 Trophoblast stem cells

growth_protocol: TSCs were grown under standard conditions (Quinn J, Kunath T, Rossant J. Methods Mol Med. 2006; PMID: 16251740). To eliminate feeder cell contamination of TSC RNA and chromatin preparations, TSC cultures grown on sub-lethally irradiated feeders were trypsinized and pre-plated for 40 minutes before transferring to new plates. TSC cultures were then split an additional 1x before harvesting.

extract_protocol:
Trizol
Strand-specific RNA-Seq prepped with mRNA-Seq kit from KAPA Biosciences

tag: data type

value: RNA-Seq

tag: parent-of-origin

value: CAST/EiJ mother X C57BL/6J father

tag: passage number


title: BC.2

description: Strand-specific RNA-Seq prepped with mRNA-Seq kit from KAPA Biosciences

source_name: F1 Hybrid BC.2 Trophoblast stem cells

value: C57BL/6J mother X CAST/EiJ father


title: BC.3

source_name: F1 Hybrid BC.3 Trophoblast stem cells


title: negative_control_mm.0_3

value: 0 cells


title: Sample_656-BF

value: Danbred 600 X Newsham NC41

tag: developmental stage


title: CB.2

source_name: F1 Hybrid CB.2 Trophoblast stem cells


title: Sample_572-BF

value: Danbred 600 X Newsham NC40


title: 32D.1_1

value: 1 cell


title: Heat Stress Sample 5 43oC

city: Newark

first: Carl

last: Schmidt

state: DE

address: 531 South College Ave

department: Dept. of Animal and Food Sciences

institute: University of Delaware

description: Established cell line from a liver carcinoma in a male white leghorn chicken.

data_processing:
CASAVA
Erange for RNA-SEQ alignment and qualitation
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Feb. 2004 (galGal2) assembly
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

organism: Gallus gallus

source_name: LMH Chicken Hepatocellular Carcinoma Cell Line

growth_protocol: LMH cells were grown according to the recommendations of ATCC.

extract_protocol:
Cells were removed from the flask by trypsin digestions and collected by centrifugation at either control or heat stress temperatures. RNA was isolated using the Qiagen mini-prep protocol.
Libraries were constructed using the Illumina RNA-seq kit

treatment_protocol: Cells were grown for 2.5 hours at either control (37oC) or heat stress (43oC) temperatures.

value: LMH Chicken Hepatocellular Carcinoma

value: heat stressed at  43oC


title: Heat Stress Sample 4 43oC


title: Heat Stress Sample 2 43oC


title: Heat Stress Sample 3 43oC


title: FB035_LG+Prlo

first: Matthew

middle: Bonser

last: Johnson

state: Massachusetts

address: 300 Longwood Ave.

department: Genetics and Genomics

institute: Boston Children's Hospital

description: Outer radial glial cells, replicate 3

data_processing:
base-calling with Illumina CASAVA 1.8.2
alignment to the human reference genome and UCSC Known Genes transcriptome with tophat v2.0.6
gene expression level estimation and differential expression analysis performed with cufflinks v2.0.2
Genome_build: hg19
Supplementary_files_format_and_content: cufflinks gene-level fpkm tracking file format, contains gene-level expression estimates for each condition summarized across the three biological replicates

source_name: mid-fetal cerebral cortex

extract_protocol:
Tissue samples were dissociated with trypsin, immunolabeled, and FACS sorted, and RNA purified from sorted cell populations, all using standard kits and protocols.
Illumina TruSeq v2 paired-end mRNA library protocol

tag: gestational age (weeks)

tag: facs population

value: LeX+ Glast+ Prominin-low


title: FB035_LG+Prhi

description: Apical radial glial cells, replicate 3

value: LeX+ Glast+ Prominin-high


title: Control Sample 6  37oC

tag: cell line

value: normal temperature at 37oC


title: FB033_LG-Pr-

description: Neurons, replicate 2

value: LeX/Glast/Prominin-negative


title: FB033_LG+Prhi

description: Apical radial glial cells, replicate 2


title: Control Sample 5  37oC


title: Control Sample 4  37oC


title: FB033_LG+Prlo

description: Outer radial glial cells, replicate 2


title: FB032_LG-Pr-

description: Neurons, replicate 1


title: Control Sample 3  37oC


title: Control Sample 2  37oC


title: FB032_LG+Prlo

description: Outer radial glial cells, replicate 1


title: Control Sample 1   37oC


title: BRD2 +GATA1

status: Public on Feb 23 2015

city: Philadelphia

first: Aaron

middle: James

last: Stonestrom

state: PA

address: 315 ARC 3615 Civic Center Blvd

department: Hematology

institute: Children's Hospital of Philadelphia

data_processing:
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm9 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2  --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Wiggle files were converted to bigWig using wigToBigWig
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file with read coverage

source_name: GATA1 null erythroblasts

growth_protocol: G1E cells were grown in IMDM +20% FBS, glutamine, penicillin/streptomycin, MTG, and Epoetin alpha in a standard tissue culture incubator at 37 degree with 5% CO2.

extract_protocol:
Chromatin immunoprecipitation was performed as described (Kadauke et al. Cell 2012). Cells were fixed in 1% formaldehyde for 10 minutes with gentle shaking at room temperature. Sonication employed a Diagenode Bioruptor (High signal, 30 seconds on/30 seconds off, for 30 minutes). IPs were performed using protein A/G sepharose beads. Beads were washed in high salt buffer and eluted in buffer containing bicarbonate and SDS. Crosslinks were reversed by heating to 65 degrees overnight. DNA was purified on Qiagen miniprep columns.
Libraries were prepared using the protocol as outlined for Illumina's TruSeq ChIP Sample Prep Kit ( IP-202-1012), except that the libraries were size selected using Agencourt SPRIselect beads for an average size of ~300-325bp prior to PCR amplification. Library quality was assessed using the Aglient Bioanalzyer 2100 and libraries were sequenced on the Illumina HiSeq2000.

treatment_protocol: 10mM JQ1 was added to a final concentration of 250nM. 10mM E2 was added to a final concentration 100nM.

tag: cell type

value: GATA1 null erythroblasts

tag: gata1 transgene

value: 100nM estradiol for 24 hours

tag: antibody

value: Bethyl BRD2 A302-583A


title: FB032_LG+Prhi

description: Apical radial glial cells, replicate 1


title: Heat Stress Sample 6 43oC

tag: treatment


title: FB035_LG-Pr-

description: Neurons, replicate 3


title: HA BRD2 +GATA1 r1

description: Cell express HA tagged BRD2

value: HA (homemade)


title: BRD2 -GATA1


title: HA BRD2 +GATA1 r2

description: Cell express HA tagged BRD2


title: Mbd3_rep

first: Joan

last: Conaway

state: MO

institute: Stowers Institute

description: Chromatin IP of Mbd3; Replicate 2

data_processing:
[ChIP-seq] Alignments were extended to a total fragment length of 150 bases in the orientation of the read alignment.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
RNA-seq alignments were done using TopHat v2.0.9 with bowtie1 v0.12.9, using -g 1 option and allowing up to two mismatches.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

source_name: ES cell culture

growth_protocol: Mouse embryonic stem cells V6.5 were cultured on irradiated mouse embryonic fibroblast (MEF) feeder layers in 0.1% gelatin-coated tissue culture flask. Cells were grown in DMEM (D6546, Sigma) supplemented with 15% ES-certified fetal bovine serum, 2 mM L-glutamine, 0.1 mM nonessential amino acids, 0.1 mM β-mercaptoethanol, and ecombinant LIF. For ChIP and RNA analysis, cells were grown for one passage off feeders on tissue culture plates for 30 minutes.

extract_protocol:
For ChIP-Seq, 5×107 ES cells (V6.5) were used per immunoprecipitation according to previously described protocols (Lee et al., 2006). ChIP-Seq libraries were prepared with Illumina's kit.For RNA-seq, ES cells (V6.5) were infected with lentivirus carrying either Non-targeting shRNA, Zic2, Mbd3 or Mta2 shRNA in the presence of 8 ug/ml of polybrene. 24 hours later, ES cells were selected with 2 ug/ml of puromycin for additional 48 hours and then were grown one passage off feeders for 30 min before harvesting. Total RNA was isolated with the RNeasy (74106 Qiagen) kit, treated with DNase I (M0303L NEB), and re-purified with RNeasy. For total RNA-seq analyses, total RNA was depleted of ribosomal RNA using Ribozero (Illumina) before library preparation performing Tru-seq sample prep (Illumina).
ChIP-seq and RNA-seq libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: embryonic stem cell

value: Mbd3 (Bethyl, A302-528A)


title: RNA_shZic3_rep2

description:
Ribosomal RNA-depleted total RNA
RNAseq after Zic3-RNAi; Replicate 2

data_processing:
[RNA-seq] Reads were aligned using Ensembl 67 GTF mouse annotations using TopHat v2.0.9 and Bowtie v0.12.9.  Alignments were not extended.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
RNA-seq alignments were done using TopHat v2.0.9 with bowtie1 v0.12.9, using -g 1 option and allowing up to two mismatches.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: http://genome.ucsc.edu/goldenPath/help/bigWig.html

tag: shRNA


title: RNA_shZic3_rep1

description:
Ribosomal RNA-depleted total RNA
RNAseq after Zic3-RNAi; Replicate 1


title: Chd4_rep

description: Chromatin IP of Chd4; Replicate 2

value: Chd4 (Abcam, ab70469)


title: Zic3

description: Chromatin IP of Zic3

value: Zic3 (Abcam, ab80966)


title: S12_H3K27AC_C

city: New York

first: Li

last: Shen

state: NY

address: 1425 Madison Ave

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Bowtie 0.12.9 defaults
diffReps 1.54 --mode n --pval 0.001
ChromHMM 1.1 defaults
Genome_build: mm9
Supplementary_files_format_and_content: TAB delimited text file of chromatin differential sites
Supplementary_files_format_and_content: BED file of condition specific enhancer sites

source_name: mouse saline NAc H3K27ac ChIPseq

extract_protocol:
following regulation qiagen kit protocol for RNA/DNA isolation
following illumina kit protocol for library prep

treatment_protocol: seven daily cocaine ip injection at 20mg/kg bodyweight

tag: tissue

value: nucleus accumbens

tag: strategy

value: ChIP-seq

value: Saline


title: S8_H3K27AC_A


title: S10_H3K27AC_B


title: Heat Stress Sample 1 43oC

value: LMH Chicken Hepatocellular Carcinoma


title: C_Input

source_name: mouse cocaine NAc ChIP input

value: input

value: Cocaine


title: S_Input

source_name: mouse saline NAc ChIP input


title: C7_H3K27AC_D

source_name: mouse cocaine NAc H3K27ac ChIPseq


title: C9_H3K27AC_E


title: C11_H3K27AC_F


title: 5hmC.S18

source_name: mouse saline control NAc 5hmC capture seq

value: 5hmC capture


title: 5hmC.S20


title: 5hmC.S16


title: 5hmC.C17

source_name: mouse cocaine NAc 5hmC capture seq


title: 5hmC.C19


title: 5hmC.Cb

source_name: mouse cerebellum input 5hmC seq


title: 5hmC.C15


title: GATA1 +JQ1 rep2

description: #533 GATA1 +JQ1 rep2

data_processing:
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm9 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2  --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle and peaks called using MACS with parameters --format BAM --gsize 1870000000 --tsize 36 --bw 120 --mfold 12 --wig --space 1
Filter blacklist regions from peaks, and convert the *peaks.xls file from MACs to broadpeak format (see UCSC Genome Browser for format specs)
Genome_build: mm9
Supplementary_files_format_and_content: bigWig file with read coverage, mapped reads in bam format

source_name: G1E_GATA1 +JQ1

value: GATA1 null erythroblasts (G1E)

tag: treated with

value: 100nM estradiol + 250nM JQ1 for 24 hours

value: GATA-1 Antibody (N6)

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot #


title: BRD4 G1E rep2

description: #423 BRD4 G1E rep2

source_name: G1E_BRD4 G1E

tag: chip antibody

value: Bethyl

value: Lot# 1


title: BRD4 +GATA1 rep1

description: #424 BRD4 +GATA1 rep1

source_name: G1E_BRD4 +GATA1

value: 100nM estradiol for 24 hours


title: BRD4 +GATA1 rep2

description: #425 BRD4 +GATA1 rep2


title: BRD4 G1E rep1

description: #422 BRD4 G1E rep1


title: GATA1 +JQ1 rep1

description: #532 GATA1 +JQ1 rep1


title: GATA1 control rep2

description: #531 GATA1 control rep2

source_name: G1E_GATA1 control


title: GATA1 control rep1

description: #530 GATA1 control rep1


title: RNA_shMta2_rep2

description:
Ribosomal RNA-depleted total RNA
RNAseq after Mta2-RNAi; Replicate 2

data_processing:
Base-calling and quality filtering, default settings, Illumina Casava 1.8
Reads were aligned using Bowtie v0.12.9, allowing unique reads only and up to three mismatches of a 50bp seed length.
[ChIP-seq] Alignments were extended to a total fragment length of 150 bases in the orientation of the read alignment.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Peak detection was done using MACS, version 1.4.2 (Zhang, Y. et al, 2008) using the indicated criteria.
[RNA-seq] Reads were aligned using Ensembl 67 GTF mouse annotations using TopHat v2.0.9 and Bowtie v0.12.9.  Alignments were not extended.  UCSC bigWig files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
RNA-seq alignments were done using TopHat v2.0.8 with bowtie1 v0.12.9, allowing uniquely mapping reads only and allowing up to two mismatches. Differential expression analysis was done using Cuffdiff v1.3.0.
Genome_build: UCSC mm9
Supplementary_files_format_and_content: BIGWIG (http://genome.ucsc.edu/goldenPath/help/bigWig.html)

value: embryonic stem cell


title: RNA_shMbd3_rep2

description:
Ribosomal RNA-depleted total RNA
RNAseq after Mbd3-RNAi; Replicate 2


title: RNA_shZic2_rep4

description:
Ribosomal RNA-depleted total RNA
RNAseq after Zic2-RNAi; Replicate 4


title: RNA_shMta2_rep1

description:
Ribosomal RNA-depleted total RNA
RNAseq after Mta2-RNAi; Replicate 1


title: RNA_shMbd3_rep1

description:
Ribosomal RNA-depleted total RNA
RNAseq after Mbd3-RNAi; Replicate 1


title: RNA_shZic2_rep3

description:
Ribosomal RNA-depleted total RNA
RNAseq after Zic2-RNAi; Replicate 3


title: RNA_NonT_rep6

description:
Ribosomal RNA-depleted total RNA
RNAseq after non-targeting-RNAi; Replicate 6

value: non-targeting-RNAi


title: RNA_NonT_rep2

description:
Ribosomal RNA-depleted total RNA
RNAseq after non-targeting-RNAi; Replicate 2


title: RNA_shZic2_rep1

description:
Ribosomal RNA-depleted total RNA
RNAseq after Zic2-RNAi; Replicate 1


title: RNA_NonT_rep4

description:
Ribosomal RNA-depleted total RNA
RNAseq after non-targeting-RNAi; Replicate 4


title: RNA_NonT_rep1

description:
Ribosomal RNA-depleted total RNA
RNAseq after non-targeting-RNAi; Replicate 1


title: Input_shZic2_rep2

description: whole cell extraction following RNAi of Zic2; Replicate 2

value: RNAi of Zic2

value: no antibody


title: RNA_NonT_rep5

description:
Ribosomal RNA-depleted total RNA
RNAseq after non-targeting-RNAi; Replicate 5


title: RNA_NonT_rep3

description:
Ribosomal RNA-depleted total RNA
RNAseq after non-targeting-RNAi; Replicate 3


title: Input_NonT_rep2

description: whole cell extraction following RNAi of non-targeting; Replicate 2

value: RNAi of non-targeting


title: PolII_shZic2_rep2

description: Chromatin IP of Pol II following RNAi of Zic2; Replicate 2

value: Pol II (Santa Cruz, N20)


title: PolII_NonT_rep1

description: Chromatin IP of Pol II following RNAi of non-targeting; Replicate 1


title: H3K4me3_NonT

description: Chromatin IP of H3K4me3 following RNAi of non-targeting

value: H3K4me3 (Homemade #28)


title: H3K4me3_shZic2

description: Chromatin IP of H3K4me3 following RNAi of Zic2


title: Input_shZic2_rep3

description: whole cell extraction following RNAi of Zic2; Replicate 3


title: Input_NonT_rep3

description: whole cell extraction following RNAi of non-targeting; Replicate 3


title: H3K4me1_shZic2_rep2

description: Chromatin IP of H3K4me1 following RNAi of Zic2; Replicate 2

value: H3K4me1 (Homemade #24)


title: H3K4me1_NonT_rep1

description: Chromatin IP of H3K4me1 following RNAi of non-targeting; Replicate 1


title: H3K27ac_shZic2_rep2

description: Chromatin IP of H3K27ac following RNAi of Zic2; Replicate 2

value: H3K27ac (Abcam, ab4729)


title: H3K4me1_NonT_rep2

description: Chromatin IP of H3K4me1 following RNAi of non-targeting; Replicate 2


title: RNA_shZic2_rep2

description:
Ribosomal RNA-depleted total RNA
RNAseq after Zic2-RNAi; Replicate 2


title: H3K27ac_NonT_rep2

description: Chromatin IP of H3K27ac following RNAi of non-targeting; Replicate 2


title: H3K4me1_shZic2_rep1

description: Chromatin IP of H3K4me1 following RNAi of Zic2; Replicate 1


title: H3K27ac_shZic2_rep1

description: Chromatin IP of H3K27ac following RNAi of Zic2; Replicate 1


title: H3K27me3_shZic2_rep1

description: Chromatin IP of H3K27me3 following RNAi of Zic2; Replicate 1

value: H3K27me3 (Homemade #67)


title: Input_shZic2_rep1

description: whole cell extraction following RNAi of Zic2; Replicate 1


title: H3K27ac_NonT_rep1

description: Chromatin IP of H3K27ac following RNAi of non-targeting; Replicate 1


title: H3K27me3_shZic2_rep2

description: Chromatin IP of H3K27me3 following RNAi of Zic2; Replicate 2


title: WCE_rep2

description: whole cell extraction; Replicate 2


title: H3K27me3_NonT_rep1

description: Chromatin IP of H3K27me3 following RNAi of non-targeting; Replicate 1


title: Input_NonT_rep1

description: whole cell extraction following RNAi of non-targeting; Replicate 1


title: Chd4

description: Chromatin IP of Chd4

value: Chd4 (Abcam, ab70469)


title: Zic2_rep2

description: Chromatin IP of Zic2; Replicate 2

value: Zic2 (Abcam, ab150404)


title: WCE_rep1

description: whole cell extraction; Replicate 1


title: Zic2_rep1

description: Chromatin IP of Zic2; Replicate 1


title: Mbd3

description: Chromatin IP of Mbd3

value: Mbd3 (Bethyl, A302-528A)


title: Hi-C_Rad21HS_92_Rep1

city: Atlanta

first: Victor

middle: G

last: Corces

state: GA

address: 1510 Clifton Rd

department: Biology

institute: Emory University

description: Hi-C library made using DpnII and cells depleted of Rad21 using RNAi and subjected to heat shock at 36.5 C for 20 min

data_processing:
Library strategy: Hi-C
Hi-C reads were aligned using Bowtie 0.12.7 with default parameters and “-m 1”
PCR duplicate reads were removed
GC content, mappability, and fragment length effects were normalized as described  in Hou et al., Molecular Cell 48, 471-484 (2012).
Genome_build: dm3
Supplementary_files_format_and_content: Hi-C processed files are in a modified bed format. Each row lists the chromosome and the start and end coordinates of two interacting bins as well as the normalized interaction frequency between these two bins

growth_protocol: Kc cells were maintained in HyClone CCM3 Serum-free media.

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched with glycine and nuclear lysates were incubated with HindIII or DpnII. Fragment ends were filled with biotinylated nucleotides, ligated. After reverssion of crosslinks, DNA was purified, sonicated and used to make Illumina libraries
To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’  - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.

treatment_protocol: For triptolide and flavopiridol samples, cells were treated with 10 mM triptolide or 1 mM flavopiridol for 3 h

value: Kc167 Drosophila Embryonic Cell line


title: PolII_NonT_rep2

description: Chromatin IP of Pol II following RNAi of non-targeting; Replicate 2


title: Hi-C_CapH28_Rep1

description: Hi-C library made using DpnII and cells depleted of Cap-H2 using RNAi and grown at 25 C


title: Hi-C_CapH2_50_Rep3


title: Hi-C_Rad21NT_91_Rep1

description: Hi-C library made using DpnII and cells depleted of Rad21 using RNAi and grown at 25 C


title: Hi-C_CapH2_28_Rep2


title: Hi-C_Flavopiridol_42_Rep3

description: Hi-C library made using DpnII and cells treated with flavopiridol for 3 h and grown at 25 C


title: Hi-C_Flavopiridol7_Rep1


title: Hi-C_Flavopiridol_27_Rep2


title: H3K27me3_NonT_rep2

description: Chromatin IP of H3K27me3 following RNAi of non-targeting; Replicate 2


title: Hi-C_Triptolide6_Rep1

description: Hi-C library made using DpnII and cells treated with triptolide for 3 h and grown at 25 C


title: Hi-C_Triptolide_26_Rep2


title: Hi-C_NT_89_Rep4

description: Hi-C library made using DpnII and cells grown at 25 C


title: Hi-C_Triptolide_43_Rep3


title: Hi-C_NT_53_Rep3


title: Hi-C_HS_8_Rep2

description: Hi-C library made using HindIII and cells heat shocked at 36 C for 20 min


title: Hi-C_NT_25_Rep2


title: Hi-C_HS_7_Rep1


title: Hi-C_NT5_Rep1


title: Z4_NT_Rep1

description: chromatin IP against Z4

data_processing:
Alignment: Mates from a paired end sequence were combined into a single fastq file and mapped to the D.melanogaster (dm3) genome using Bowtie 1.0.1 software using the default setting.
wig files: wig files were obtained using the Model-based Analysis of ChIP-Seq (MACS1.4.2) algorithm using standard settings and -m 1
Genome_build: dm3
Supplementary_files_format_and_content: wig files were generated using MACS1.4.2

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature.  Crosslinking was quenched with glycine and nuclear lysates were sonicated to generate 200–1000 bp DNA fragments.  Chromatin was pre-cleared overnight at 4oC with protein A sepharose beads and then incubated overnight with antibody at 4oC.  Chromatin was then precipitated with Protein A Sepharose beads for 2 hours at 4oC.  After washing and eluting from beads the crosslinking was reversed and DNA was isolated.
To generate sequencing libraries, ChIP DNA was prepared for adaptor ligation by end repair (‘End-It DNA End Repair Kit’  - Epicentre Cat# ER0720) and addition of ‘A’ base to 3’ ends (Klenow 3’-5’ exo- NEB Cat# M0212S). Illumina adaptors (Illumina Cat# PE-102-1001) were titrated according to prepared DNA ChIP sample concentration, and ligated with T4 ligase (NEB Cat# M0202S). Ligated ChIP samples were PCR amplified using Illumina primers  and Phusion DNA polymerase (NEB Cat# F-530L) and size selected for 200-300bp by gel extraction.


title: TFIIIC_HS_Rep2

description: chromatin IP against TFIIIC

value: TFIIIC


title: Z4_HS_Rep1

description: chromatin IP against Z4


title: TFIIIC_NT_Rep1

description: chromatin IP against TFIIIC


title: Wild-type MBD-seq

city: Kyotanabe

first: Keizo

last: Nishikawa

state: Kyoto

address: 1-3, Tatara Miyakodani

department: Medical Life Systems

country: Japan

institute: Graduate School of Life and Medical Sciences

data_processing:
MBD-seq reads passing the quality controls were mapped onto the mouse genome assembly mm9 using bowtie version 0.12.7.
Peaks were detected using MACS version 1.4.2 with default parameter and without control samples.
Genome_build: mm9
Supplementary_files_format_and_content: wig files

extract_protocol:
Cells were lysed with genome buffer (50mM Tris-HCl pH8.0, 100 mM NaCl, 20 mM EDTA, 1% SDS, 140 μg/mL protenase K) and treated with RNase. Subsequently genomic DNA was purified with Phenol-Chloroform DNA extraction.
Genomic DNA was sonicated to 200-500 bp fragment with Covaris (Covaris). Methylated DNA was enriched with EpiXplore Methylated DNA Enrichment Kit (Takara) according to manufacturer’s protocol. Multiplexed MBD-seq libraries were prepared from 10 ng of methylated DNA fragment using TruSeq ChIP Sample Prep Kit (Illumina). For sequencing using Hiseq2000, cluster generation was performed using TruSeq PE Cluster Kit v3 (Illumina). Sequencing was performed by a single-read run mode with total 200 cycles.

treatment_protocol: Nonadherent bone marrow cells derived from mice were seeded and cultured in alpha-MEM with 10%FBS containing M-CSF. After 2 days, adherent cells were used as bone marrow-derived monocyte/macrophage precursor cells (BMMs). The BMMs were further cultured in the presence of RANKL and M-CSF to generate osteoclasts.

tag: gender

value: Female

tag: genotype/variation

value: Wild-type

value: Bone marrow-derived osteoclasts


title: Dnmt3a knockout MBD-seq

source_name: Dnmt3a knockout_osteoclasts

value: Dnmt3a knockout


title: TFIIIC_NT_Rep2

description: chromatin IP against TFIIIC


title: SuHw_HS_Rep1

description: chromatin IP against SuHw

value: SuHw


title: RNAPII_HS_Rep1

description: chromatin IP against RNAPII

value: RNAPII


title: Rad21_NT_Rep3

description: chromatin IP against Rad21


title: RNAPII_flavopiridol_Rep1

description: chromatin IP against RNAPII


title: PolII_shZic2_rep1

description: Chromatin IP of Pol II following RNAi of Zic2; Replicate 1

value: embryonic stem cell

value: RNAi of Zic2


title: Rad21_NT_Rep2

description: chromatin IP against Rad21


title: Rad21_NT_Rep1

description: chromatin IP against Rad21


title: RNAPII_NT_Rep1

description: chromatin IP against RNAPII


title: Pc_RJ_HS_Rep1

description: chromatin IP against Pc_RJ


title: Modmdg4_HS_Rep2

description: chromatin IP against Modmdg4


title: Pc_VP_NT_Rep1

description: chromatin IP against Pc_VP


title: Pc_RJ_NT_Rep1

description: chromatin IP against Pc_RJ


title: Modmdg4_HS_Rep1

description: chromatin IP against Modmdg4


title: L3mbt_NT_Rep1

description: chromatin IP against L3mbt


title: L3mbt_HS_Rep1

description: chromatin IP against L3mbt


title: IgG_input_NT_Rep1

description: chromatin IP against IgG

value: IgG


title: IgG_input_HS_Rep1

description: chromatin IP against IgG


title: TFIIIC_HS_Rep1

description: chromatin IP against TFIIIC


title: H3K27ac_HS_Rep1

description: chromatin IP against H3K27ac


title: H3K9me2_HS_Rep1

description: chromatin IP against H3K9me2


title: IgG_input_NT_Rep2

description: chromatin IP against IgG


title: H3K9me2_NT_Rep1

description: chromatin IP against H3K9me2


title: H3K4me3_NT_Rep2

description: chromatin IP against H3K4me3


title: RNAPII_triptolide_Rep1

description: chromatin IP against RNAPII


title: H3K4me3_HS_Rep2

description: chromatin IP against H3K4me3


title: H3K4me1_NT_Rep2

description: chromatin IP against H3K4me1


title: Fs1h-L_NT_Rep2

description: chromatin IP against Fs1h-L


title: H3K4me1_HS_Rep1

description: chromatin IP against H3K4me1


title: H3K4me1_HS_Rep2

description: chromatin IP against H3K4me1


title: Fs1h-L_HS_Rep1

description: chromatin IP against Fs1h-L


title: CTCF_HS_Rep2

description: chromatin IP against CTCF

value: CTCF


title: Fs1h-L_NT_Rep1

description: chromatin IP against Fs1h-L


title: DREF_HS_Rep1

description: chromatin IP against DREF

value: DREF


title: Rad21_HS_Rep1

description: chromatin IP against Rad21


title: CTCF_NT_Rep2

description: chromatin IP against CTCF


title: DREF_NT_Rep2

description: chromatin IP against DREF


title: CTCF_HS_Rep1

description: chromatin IP against CTCF


title: CP190_HS_Rep3

description: chromatin IP against CP190


title: CP190_HS_Rep2

description: chromatin IP against CP190


title: CP190_NT_Rep2

description: chromatin IP against CP190


title: CP190_HS_Rep1

description: chromatin IP against CP190


title: Chromator_NT_Rep2

description: chromatin IP against Chromator

value: Chromator


title: Chromator_NT_Rep1

description: chromatin IP against Chromator


title: H3K4me3_HS_Rep1

description: chromatin IP against H3K4me3


title: Chromator_HS_Rep2

description: chromatin IP against Chromator


title: CBP_NT_Rep2

description: chromatin IP against CBP

value: CBP


title: CBP_NT_Rep1

description: chromatin IP against CBP


title: CBP_NT_Rep3

description: chromatin IP against CBP


title: CapH2_NT_Rep1

description: chromatin IP against CapH2


title: CBP_HS_Rep2

description: chromatin IP against CBP


title: BEAF_NT_Rep2

description: chromatin IP against BEAF

value: BEAF


title: CapH2_NT_Rep2

description: chromatin IP against CapH2


title: Chromator_HS_Rep1

description: chromatin IP against Chromator


title: CapH2_HS_Rep2

description: chromatin IP against CapH2


title: CapH2_HS_Rep1

description: chromatin IP against CapH2


title: BEAF_HS_Rep1

description: chromatin IP against BEAF


title: BRD3 +GATA1

description: #62 BRD3 +GATA1

source_name: G1E_BRD3 +GATA1

value: GATA1 null erythroblasts (G1E)

value: 100nM estradiol for 24 hours

value: BRD3 sera

tag: chip antibody info.


title: HA BRD3 +GATA1

description: Cell express HA tagged BRD3

value: GATA1 null erythroblasts

value: HA (homemade)


title: BRD3 G1E

description: #63 BRD3 G1E

source_name: G1E_BRD3 G1E


title: TRF2_ChIPseq_HeLa1.2.11

city: MONTPELLIER CEDEX 5

first: Jérôme

last: Déjardin

address: 141, rue de la Cardonille

country: France

institute: Institute of Human Genetics

description: Telomerase-positive HeLa cervical carcinoma cell line

data_processing:
Base-calling performed by Fasteris SA (CASAVA pipeline v.1.8.2)
50 nt-long sequenced reads were mapped onto the genome sequence of Homo sapiens (hg18 assembly) according to sequencing quality using Bowtie.
For genome-wide enrichment analysis, only reads perfectly matching the human genome were retrieved (one mismatch was nevertheless allowed on low-quality nucleotides using –e 20 option). Redundant reads as well as reads mapping to multiple genomic locations were also discarded.
Enrichment peaks were called using SISSRs v 1.4 (Jothi et al., 2008) with default parameters using input DNA as background. Peaks corresponding to repetitive regions were discarded using BEDTools (Quinlan & Hall, 2010) (satellites 2/3, alpha/beta satellites and ribosomal DNAs genomic positions were retrieved from the UCSC repeatmasker track (http://genome.ucsc.edu/)).
Annotation of the identified peaks as well as peak overlap and motif discovery were performed using HOMER tool suite (Heinz et al., 2010)
Genome_build: NCBI36
Supplementary_files_format_and_content: BigWig files were generated using HOMER tool suite (Heinz et al., 2010) and represent normalized fragment density profile (based on genome-unique unredundant perfectly mapping reads). BED files contain coordinates (chromosome, start and end) of called peaks.

source_name: HeLa 1.2.11 ALT (-) cells, TRF2 ChIP

growth_protocol: Cells were cultured in DMEM glutamax with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared by Fasteris SA (Switzerland) and were sequenced on HiSeq 2000.

tag: cell line

value: HeLa

tag: alt status

value: anti-TRF2 / Rabbit polyclonal IgG (Santa Cruz sc-9143)


title: NR2C2_ChIPseq_HeLa1.2.11

source_name: HeLa 1.2.11 ALT (-) cells, NR2C2 ChIP

value: anti-NR2C2 / Mouse monoclonal IgG (PPMX PP-H0107B-00)


title: HMBOX1_ChIPseq_HeLa1.2.11

source_name: HeLa 1.2.11 ALT (-) cells, HMBOX1 ChIP

value: anti-HMBOX1 / Rabbit polyclonal IgG (Abcam ab97643)


title: B-ALL, ETV6/RUNX1

first: Seung-Tae

last: Lee

address: 1450 3rd Street

description: WGBS data of B-cell acute lymphoblastic leukemia cells

data_processing:
From the human genome (GRCh37) and NCBI viral genome (v35), two reference sequences including reference C2T (all Cs were replaced by T) and reference G2A (all Gs were replaced by A) were generated, and to these, each paired-end read was aligned using the GEM software.
Up to four mismatches were allowed, and read pairs with unique compatible mappings (to the same chromosome and in the expected orientation) were selected.
After mapping, most likely genotype and methylation % in each C were estimated, using the software developed at the Centro Nacional de Análisis Genómico, which takes into account the observed bases, base quality scores and the strand origin of each read pair.
The confidence in the genotype call was estimated by the Phred-scaled likelihood. CpG sites were selected where both bases were called as homozygous CC followed by GG with a Phred score of ≥20.
Sites with >500× coverage depth were excluded to avoid highly repetitive regions
Genome_build: GRCh37, hg19
Supplementary_files_format_and_content: tab-delimited text file include methylation % estimation for each CpG

source_name: B-cell acute lymphoblastic leukemia with ETV6/RUNX1 translocation

extract_protocol:
AllPrep DNA/RNA Mini Kit (Qiagen) according to manufacturer's instructions
We sheared the DNA by sonication to 50–500 bp with a Covaris E220, followed by selecting 150- to 300-bp fragments using AMPure XP beads (Agencourt Bioscience).
Genomic DNA libraries were constructed using the TruSeq Sample Preparation kit (Illumina).
Two rounds of sodium bisulfite-conversion of DNA using the EpiTexy Bisulfite kit (Qiagen) was performed to get a conversion efficiency of >99%.

value: bone marrow / peripheral blood

tag: subjects

value: children with B-ALL (California Childhood Cancer Study)

tag: age

value: M

tag: cytogenetics


title: HMBOX1_ChIPseq_VA13

description: WI-38 VA-13_2RA is a SV40-transformed variant of the WI38 cell line (female embryonic lung fibrobasts).

source_name: WI-38 VA13 ALT (+) cells, HMBOX1 ChIP


title: VA13_inputDNA

source_name: WI-38 VA13 ALT (+) cells, VA13 input DNA


title: TRF2_ChIPseq_VA13

source_name: WI-38 VA13 ALT (+) cells, TRF2 ChIP


title: NR2C2_ChIPseq_VA13

source_name: WI-38 VA13 ALT (+) cells, NR2C2 ChIP


title: CBP_HS_Rep1

description: chromatin IP against CBP

tag: cell type

value: Kc167 Drosophila Embryonic Cell line


title: HeLa1.2.11_inputDNA

source_name: HeLa 1.2.11 ALT (-) cells, HeLa input DNA


title: Ins1-ACREBvirus-Con

city: La Jolla

first: Sam

last: Van de Velde

address: 10010 North Torrey Pines Road

department: Peptide Biology Laboratories

institute: Salk Institute

description: processed data file: CONACREB_cuffdiff_2xinduced.xlsx

data_processing:
Libraries were quantitated by Qubit (Invitrogen), and run on a MiSeq instrument with paired-end 75bp reads using v3 chemistry (Illumina).
Reads were aligned against the rat rn5 genome build using Tophat2
Gene expression levels were analyzed with Cuffdiff
FSK induced genes (2 fold cutoff) in low glucose conditions were selected for cluster analysis
Genome_build: rn5; GCF_000001895.4

growth_protocol: INS-1 insulinoma cells were cultured in RPMI (corning cellgro) containing 10% fetal bovine serum (Gemini Bio Products), 100 μg/mL penicillin-streptomycin (corning cellgro)  and 1 mM sodium pyruvate (corning cellgro).

extract_protocol:
Total RNA was extracted with Trizol reagent and cleaned up over an Rneasy column (Qiagen)
RNA-Seq libraries were prepared using the mRNA isolation protocol and the NEBNext-Ultra kits from New England Biolabs following the manufacturers protocols.

treatment_protocol: Cells were treated with 2.8 or 20 mM glucose for 3 days, and with 10 uM forskolin or DMSO vehicle for 2 hours. Cells were exposed to adenovirus for 2 days

value: insulinoma cells

value: 11 mM glucose + DMSO for 2hrs

tag: exposed to

value: adeno ACREB


title: Ins1-ACREBvirus-FSK

value: 11 mM glucose + 10uM FSK for 2hrs


title: cocinj_7d4h_S2

data_processing:
Tophat 2.0.6--frag-bias-correct --multi-readcorrect
Cufflinks 2.0.2--frag-bias-correct --multi-readcorrect
Genome_build: NCBIM37 Ensembl 62
Supplementary_files_format_and_content: TAB delimited text file of differential gene list

source_name: mouse NAc repeated saline control 4hr withdraw RNAseq

extract_protocol:
following regulation qiagen kit protocol for RNA isolation
following illumina kit protocol for library prep

treatment_protocol: chornic daily cocaine ip injection at 20mg/kg bodyweight

tag: tissue

value: nucleus accumbens

value: RNA-seq

tag: treatment

value: Saline

tag: strain


title: cocinj_7d4h_S3

tag: strategy


title: Ins1-novirus-Con-Tx

tag: treated with


title: Ins1-highGlucose-FSK-Tx

description: processed data file: glcFSK_cuffdiff_2xinduced.xlsx

value: 20 mM glucose for 3 days +10uM FSK for 2hrs


title: cocinj_7d4h_S1


title: cocinj_7d4h_C3

source_name: mouse NAc repeated cocaine 4hr withdraw RNAseq

value: Cocaine


title: B-ALL, hyperdiploid

source_name: B-cell acute lymphoblastic leukemia with hyperdiploid chromosomes

value: F

value: hyperdiploid


title: cocinj_7d4h_C2


title: Ins1-highGlucose-Con-Tx

value: 20 mM glucose for 3 days  + DMSO for 2hrs


title: Ins1-lowGlucose-FSK-Tx

value: 2.8 mM glucose for 3 days +10uM FSK for 2hrs


title: Ins1-novirus-FSK-Tx


title: NR2F2_ChIPseq_HeLa1.2.11

source_name: HeLa 1.2.11 ALT (-) cells, NR2F2 ChIP

value: HeLa

value: anti-NR2F2 / Rabbit polyclonal IgG (Abcam ab50487)


title: SC9_RRBS

status: Public on Feb 21 2015

city: Augusta

first: Huidong

last: Shi

department: Georgia Cancer Center

institute: Augusta University

description: DNA methylation analysis using bisulfite sequencing

data_processing:
To map the sequencing reads from RRBS, we extracted sequenceable regions from the human genome (hg18) that were within 100bp from the MspI sites at both ends. Each sequenceable region was indexed by converting all C’s and G’s to T’s and A’s, respectively, i.e., two different reference databases. Bowtie was used to map the cleaned reads to each of the two reference databases after converting all C’s to T’s.
For each read, an in-house script computed the best of all alignments for the different loci using two different reference databases based on the number of mismatches after realigning the original read and reference sequences. The script also determined the methylation status of each cytosine residue by comparing the bisulfite-converted sequence to the reference sequence.
Another in-house script piled reads for each cytosine in the reference genome and counted the numbers of reads that contained methylated and unmethylated cytosines, respectively. Finally the methylation of each CpG site was defined as the fraction of methylated reads to that of methylated and unmethylated reads combined. CpGs with < 5 reads were filtered out for further analyses.
Genome_build: hg18
Supplementary_files_format_and_content: BED format, Methylation level at each CpG sites ( a value between 0 and 1)

source_name: Normal CD19+ B-cells

growth_protocol: Primary B-cells were isolated from CLL using Dynal B-cell Isolation Kit (Invitrogen, Carlsbad, CA, USA); Normal B-cell samples were purchased from ALLCells.

extract_protocol:
Genomic DNA was extracted using Qiagen kit
RRBS was performed according to a previously published protocol (Gu et al. 2010; Meissner et al. 2008) with minor modifications. For each sample, 1  g genomic DNA was first digested overnight using 20 units of MspI (New England Biolabs, NEB). The digested DNA was end-repaired and adenylated in a 20  l reaction consisting of 10U of Klenow fragments (exo-, Enzymatics, MA, USA), and 2  l premixed nucleotide triphosphates (1 mM dGTP, 10 mM dATP, 1 mM methylated dCTP). The reaction was incubated at 30 C for 30 min followed by 37 C for an additional 30 min. The methylated Illumina adapters were ligated with adenylated DNA fragments in a 20  l reaction containing 1  l concentrated T4 ligase (Enzymatics) at room temperature for 15 minutes. The ligation products were gel-selected for fragments with insertion sizes of 40 to 120 bp and 120 to 220 base pairs as previously suggested (Gu et al. 2010; Meissner et al. 2008).  Bisulfite treatment of the sequencing library was conducted using the EZ DNA methylation kit (Zymo Research, Irvine, CA) according to manufacturer's protocol. The final libraries were generated by PCR amplification of 5 ?m of bisulfite-converted template using PfuTurbo Cx Hotstart polymerase and Illumina pair-end PCR primers (PE1.0 and PE2.0).

treatment_protocol: No treatment invovled.

tag: tissues

value: Blood

value: CD19+ B-cells

value: Normal


title: SC7_RRBS


title: SC4N_RRBS

source_name: Normal Naïve B-cells

value: CD19+/ IgD+ naïve


title: SC5_RRBS


title: NR2F2_ChIPseq_VA13

source_name: WI-38 VA13 ALT (+) cells, NR2F2 ChIP

tag: chip antibody


title: SC4M_RRBS

source_name: Normal Memory B-cells

value: CD19+/CD27+ memory B-cells


title: SC3_RRBS


title: SC2_RRBS


title: CLL9281_RRBS

source_name: CLL primary B-cells

value: Tumor


title: SC1_RRBS


title: CLL9216_RRBS


title: CLL9193_RRBS


title: CLL9194_RRBS


title: cocinj_7d4h_C1

value: nucleus accumbens


title: Ins1-lowGlucose-Con-Tx

value: insulinoma cells

value: 2.8 mM glucose for 3 days + DMSO for 2hrs


title: CLL9128_RRBS


title: CLL8919_RRBS


title: CLL8545_RRBS


title: CLL0849_RRBS


title: CLL1104_RRBS


title: CLL0934_RRBS


title: CLL0949_RRBS


title: CLL0996_RRBS


title: CLL1124_RRBS


title: CLL1193_RRBS


title: SC4_RRBS


title: SC2N_RRBS


title: CLL0775_RRBS


title: CLL0745_RRBS


title: CLL0659_RRBS


title: CLL0700_RRBS


title: CLL0680_RRBS


title: CLL0625_RRBS


title: CLL0683_RRBS


title: CLL0515_RRBS


title: CLL0463_RRBS


title: CLL0430_RRBS


title: CLL9130_RRBS


title: CLL6536_RRBS


title: CLL6159_RRBS


title: CLL0335_RRBS


title: CLL0377_RRBS


title: CLL0275_RRBS


title: CLL0321_RRBS


title: SC3_RNA-seq

description: Transcriptome analysis by RNA-seq

data_processing:
TopHat 2.0.8b [1] was used for mapping sequence reads to the human genome (hg19) with the parameter for Illumina stranded sequencing (--library-type fr-firststrand).
BedTools 2.16.2 [2] and bedGraphToBigWig generated stranded binary wiggle files after in-house scripts split reads mapped to each strand.
FeatureCounts 1.4.6 was used to compute the number of reads mapped to each gene and transcript. DESeq 1.10.1 [4] for differential expression analysis.
DESeq 1.10.1 was used for differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Excel spreadsheet contains FPKM values for each transcript in all samples.

extract_protocol:
RNA was extracted using Qiagen AllPrep DNA/RNA/miRNA Universal Kit
RNA-seq libarary was prepared using Illumina TrueSeq mRNA library preparation kit.

value: normal


title: SC1_RNA-seq

description: Transcriptome analysis by RNA-seq