title: CD4_stimulated_binding_sites

city: Philadelphia

first: Kristen

last: Lynch

state: Pennsylvania

address: 906 Stellar Chance Labs 422 Curie Blvd

department: Biochemistry and Molecular Biophysics

institute: University of Pennsylvania

description:
hnRNP L-bound RNA
Binding profile from stimulated CD4 combined CLIP-seq experiments, this sample represents 3 CD4 stimulated samples

data_processing:
Raw reads were trimmed from the 3' end for basecall quality score of 0 (PHRED score) with Perl 5.16.2
3' sequencing adaptor (RL3) was removed with cutadapt version 0.9.4
Homopolymeric ends (6+ identical bases at the 3' end of the read) were trimmed with Perl 5.16.2
Reads were aligned to the human genome (hg19) with bowtie 0.12.7, keeping only one copy of each alignment position (start and end) that aligned to no other position in the genome.
Peaks were called empirically using 100 iterations of randomization of aligned reads within each transcript at an FDR threshold of 0.001, then merged within 50nt.
Genome_build: hg19
Supplementary_files_format_and_content: BED6, score field is total number of alignments per binding site

source_name: Primary CD4+ purified from PBMC

growth_protocol: Cells were cultured in RPMI + 10% FBS at 5% CO2

extract_protocol:
Cells were UV crosslinked on ice, and lysates were immunprecipitated with anti-hnRNP L antibody (4D11) on Protein G Dynabeads, and RNAs from protein-RNA complexes were isolated and subjected to CLIP-seq library preparation.
Biological triplicate libraries were individually barcoded by two-step PCR, pooled, and sequenced on Hi-Seq 2000 (CD4 samples) or GA-Iix (JSL1 samples).
Single-end, 76 cycles (JSL1 samples) or 100 cycles (CD4 samples)

treatment_protocol: JSL1 cells were either untreated for 24 hours (resting samples) or activated with 20ng/mL PMA for 60 hours, and CD4+ cells were either untreated for 24 hours (resting samples) or activated with 10ug anti-CD3/CD28 antibodies

value: CD4+ T cells

value: primary human CD4+ purified from PBMC

tag: condition

value: anti-CD3/CD28 stimulated (60hr)


title: CD4_resting_binding_sites

status: Public on Oct 20 2013

type: SRA

country: USA

description:
hnRNP L-bound RNA
Binding profile from resting CD4 combined CLIP-seq experiments, this sample represents 3 CD4 resting samples

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

value: Resting


title: ChIP-Seq PolII IMR90

city: Cleveland

first: Fulai

last: Jin

state: OH - OHIO

address: 10900 Euclid Avenue

institute: Case Western Reserve University

library_source: genomic

data_processing:
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
For GRO-seq, the first round of mapping used the first 36 bases; the unmapped reads were then mapped in two additional iterations using first 30 or 25 bases.
For ChIP-Seq, first 36 bases of each read were used for mapping.
Genome_build: NCBI36
Supplementary_files_format_and_content: Mapped non-redundant reads for GRO-seq and ChIP-seq are in BED format. Mapped non-redundant read pairs for Hi-C are in txt format.

molecule: genomic DNA

source_name: fetal lung fibroblast

growth_protocol: IMR90 cells were grown as described in: Hawkins, R.D. et al. Distinct epigenomic landscapes of pluripotent and lineage-committed human cells. Cell Stem Cell 6, 479-91

extract_protocol:
Hi-C experiments were conducted in biological replicates using HindIII according to previous publication (Lieberman-Aiden, E. et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289-93 (2009).).  ChIP-seq protocol can be found from http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf. GRO-seq experiments were performed according to previous publication (Wang, D. et al. Reprogramming transcription by distinct classes of enhancers functionally defined by eRNA. Nature 474, 390-4 (2011).).
Libraries were prepared according to Illumina's instruction or cited literatures.

treatment_protocol: Untreated or IMR90 cells treated with TNF-α (R&D Systems, 10 ng/mL, 1 hr) or flavopiridol (Sigma, 1 μM for 1 hr for ChIP-seq experiments, and 1 μM for 2 hr for Hi-C experiments) were used.

tag: treatment

value: no treat

tag: experiment

value: ChIP-seq

tag: antibody

value: PolII (Santa Cruz sc-899)

tag: restriction enzyme

value: no


title: ChIP-Seq H3K36me3 IMR90

value: H3K36me3 (Abcam ab9050)


title: ChIP-Seq H3K36me3 IMR90+TNF-α

value: TNF-α (10ng/mL) 1hr


title: ChIP-Seq p300 IMR90+TNF-α

value: p300 (Santa Cruz sc-585)


title: ChIP-Seq H3K4me3 IMR90

value: H3K4me3 (Abcam ab8580)


title: ChIP-Seq H3K4me3 IMR90+TNF-α


title: RNA-Seq IMR90+TNF-α

data_processing:
The paired-end Hi-C reads were mapped to human genome hg18 using BOWTIE. Only first 36 bases were used for mapping when reads is longer. The two reads were mapped independently and then merged into pairs using in-house script. Duplicated read pairs from the same biological library were removed.
For GRO-seq, the first round of mapping used the first 36 bases; the unmapped reads were then mapped in two additional iterations using first 30 or 25 bases.
For ChIP-Seq, first 36 bases of each read were used for mapping.
RNA-seq data were analyzed using TOPHAT and CUFFLINK packages.
Genome_build: hg18
Supplementary_files_format_and_content: Mapped non-redundant reads for RNA-seq, GRO-seq and ChIP-seq are in BED format. Mapped non-redundant read pairs for Hi-C are in txt format.

growth_protocol: IMR90 cells were grown as described in (Hawkins, R.D. et al. Cell Stem Cell 6, 479-91). MCF7 cells (ATCC), LNCaP cells (ATCC), and Human primary HUVEC cells (Lonza) were cultured following manufacturer’s instructions.

treatment_protocol: TNF-a (R&D Systems, 10 ng/mL, 1 hr) treatment were performed in IMR90 or HUVEC cells.  Flavopiridol (Sigma, 1 μM for 1 hr) and IFN-γ (R&D, 50ng/mL for 2hrs) were performed in IMR90 cells. To find out primary TNF-α responsive genes, IMR90 cells were pre-treated with 5µg/mL of cycloheximide (sigma) for 30mins before TNF-α was added. Starvation and treatment of MCF7 cells with β-estradiol (Sigma, 100nM for 160min) were performed as described in previous literature (Hah, N. et al. Cell 145, 622-634, 2011); and LNCaP cells were starved and treated with 5α-dihydrotestosterone (DHT, 100nM, 4hr) as previously described(Wang, D. et al. Nature 474, 390-394, 2011)

value: RNA-Seq


title: ChIP-Seq p65 IMR90

value: NF-κB p65 (Santa Cruz sc-372)


title: ChIP-Seq input IMR90+TNF-α


title: Hi-C IMR90+TNF-α replicate 6

value: Hi-C

value: HindIII


title: ChIP-Seq input IMR90


title: ChIP-Seq p300 IMR90


title: ChIP-Seq p65 IMR90+TNF-α


title: JSL1_stimulated_binding_sites

description:
hnRNP L-bound RNA
Binding profile from stimulated JSL1 combined CLIP-seq experiments, this sample represents 3 JSLI stimulated samples

source_name: Jurkat-derived monoclonal

value: Jurkat-derived JSL1 (monoclonal)

value: PMA stimulated (60hr)


title: JSL1_resting_binding_sites

description:
hnRNP L-bound RNA
Binding profile from resting JSL1 combined CLIP-seq experiments, this sample represents 3 JSLI resting samples

value: CD4+ T cells


title: Hi-C H1 hESC

description: Raw data for this sample has been previously published with accession code GSM892306

source_name: embryonic stem cells


title: ChIP-Seq CTCF IMR90

value: CTCF (Millipore 07-729)


title: ChIP-Seq H3K27ac IMR90+TNF-α

value: H3K27ac (Abcam ab4729)


title: Hi-C IMR90_TNF-α replicate 2


title: ChIP-Seq H3K27ac IMR90

value: no treat


title: Hi-C IMR90_Flavopiridol

value: flavopiridol (1μM, 2hr)


title: ChIP-Seq H3K4me1 IMR90+TNF-α

value: ChIP-seq

value: H3K4me1 (Abcam ab8895)


title: ChIP-Seq H3K4me1 IMR90

value: no


title: Hi-C IMR90_TNF-α replicate 1

value: TNF-α (10ng/mL) 1hr


title: Gro-Seq IMR90

description: groseq.IMR90.fwd.wig is for forward strand reads; and groseq.IMR90.rev.wig.gz is for reverse strand reads

molecule: nuclear RNA

value: GRO-seq


title: OKF6-TERT1R RA

status: Public on Oct 19 2013

city: New York

first: Katarzyna

middle: Maria

last: Marcinkiewicz

state: NY

address: 1300 York Ave. Room E405

department: Pharmacology

institute: Weill Cornell Graduate School of Medical Sciences

data_processing:
Fastq reads were converted to Goby compact-read files (http://goby.campagnelab.org). Alignments were perfomred with GobyWeb (http://gobyweb.campagnelab.org) and the GSNAP aligner version 2011.11.17 (with support Goby file format)   Alignment parameters allowed for 2 mismatches over the length of a read and unique alignments.  GobyWeb's Plugin GSNAP_GOBY version 1.1; Goby version 1.9.8.3 (20120216154520); GobyWeb version 1.7
differential expression analysis was performed using EdgeR plugin
Compression of structured high-throughput sequencing data, Campagne F, Dorff KC,  Chambwe N,  Robinson JT, Mesirov JP, Plos One, in press [see also our pre-print of this manuscript at http://arxiv.org/abs/1211.6664]
Kevin C. Dorff, Nyasha Chambwe, Zachary Zeno, Manuele Simi, Rita Shaknovich, and Fabien Campagne. GobyWeb: simplified management and analysis of gene expression and DNA methylation sequencing data. PLOS One, 2013, 10.1371/journal.pone.0069666.
Genome_build: GRCh37

source_name: immortalized oral keratinocytes

growth_protocol: OKF6-TERT1R cells were cultured in Keratinocyte-SFM medium (# 10744019, Gibco, CA, USA), supplemented with 0.3 mM CaCl2, 0.2 ng/ml EGF, penicillin/streptomycin/L-glutamine (#10378-016, Gibco, CA, USA) and bovine pituitary extract (BPE).  SCC-9 cells were cultured in Dulbecco's Modified Eagle’s Medium: Nutrient Mixture F-12 (DMEM/F-12; Gibco, CA, USA), supplemented with 10% fetal calf serum and 400 ng/ml hydrocortisone.

extract_protocol:
For deep sequencing, total RNA was isolated from cells using an RNeasy mini kit (Quiagen Inc. Valencia, CA, USA), including an in-column DNAse treatment.
RNA sequencing was performed using Illumina TruSeqRNA technology, following the manufacturer’s protocol. Briefly, mRNA is purified using poly-T oligo-attached magnetic beads and subsequently fragmented. The cleaved RNA fragments are reverse transcribed into first strand cDNA using random primers. Next, second strand cDNA is synthesized using DNA Polymerase I and RNase H. The second strand cDNA fragments are subject to an end repair, the addition of a single ‘A’ base, and ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: For mRNA analyses, cells were plated in 10 cm2 tissue culture plates at the density of 2 × 106 cells/plate and treated with 1 μM RA or vehicle (0.1% ethanol) for 48 hours.

tag: cell line

value: immortalized oral keratinocytes

value: 1 µM retinoic acid (RA)


title: challenged-severe pathology (SV)

city: Guangzhou

first: Xinzheng

last: Jia

state: Guangdong

address: Wushan Road

department: Animal Science

country: China

institute: South China Agricultural University

description: Sample 3

data_processing:
Illumina Casava1.7 software used for basecalling.
Low quality bases (Sanger bases quality < 20) of 3’ end were firstly trimmed using perl scripts and, second, the sequencing adapters were removed with the fastx toolkit software (http://hannonlab.cshl.edu/fastx_toolkit/). All identical sequences of sizes ranging from 16–32 nt were counted and eliminated from the initial data set
The assembled unique sequences were used to BLAST the Rfam data base 10.1 (http://rfam.sanger.ac.uk/) to remove non-miRNA sequences (rRNA, tRNA, snoRNA, etc.).
Bowtie (http://bowtie-bio.sourceforge.net /index.shtml) was used to annotate the location in the chromosomes against the chicken genome data (Ensembl Trace Archive). Through blasting the miRbase 19.0 (http://www.mirbase.org/), the perfectly matched sequences were used to count and analyze the known miRNA expression profile.
Genome_build: gallus_gallus.WASHUC2.63
Supplementary_files_format_and_content: Each library was normalized to obtain the expression of transcripts per million using total clean reads count in this study.

organism: Gallus gallus

source_name: APEC challenged_spleen

growth_protocol: 360 male non-vaccinated commercial broiler chicks were used at 1 day of age from a local hatchery. Birds were reared on wire-floored cages with adlibitum access to food and water, and a 22:2 hour light:dark cycle for the first 15 days and a 16:8 hour cycle thereafter.

extract_protocol:
Total RNA was isolated from each spleen using Trizol (Invitrogen, CA, USA) according to manufacturer’s instructions, and thereafter, three mixed RNA samples for NC, MD and SV were prepared by quantification and pooling.
Twenty ug of total RNA were purified by denaturing 15% PAGE to enrich for 16-32 nt small RNAs, and then ligated with proprietary adapters. Subsequently, cDNA was synthesized from small RNAs by reverse transcription and amplified with 15 PCR cycles to produce libraries. Amplified products were validated and quantified using an Agilent 2100 Bioanalyzer and the DNA 1000 Nano Chip Kit (Agilent, Technologies, Santa Clara, CA, USA).Deep sequencing was performed on the Genome Analyzer IIx.

treatment_protocol: Through the intra-air sac route into the left thoracic air sac, 240 non-vaccinated males at 4 weeks of age were challenged with 0.1 ml APEC O1 (10^8 colony forming units) and another 120 non-vaccinated males were non-challenged but treated with 0.1 ml PBS.

tag: age

value: 4 weeks

tag: gender

value: male

value: spleen

tag: challenged with

value: Avian pathogenic Escherichia coli (APEC)

tag: lesion score

value: 4-7; severe infection


title: challenged-mild pathology (MD)

description: Sample 2

value: 0-2; mild infection


title: SCC-9 RA

source_name: tongue squamous cell carcinoma

value: tongue squamous cell carcinoma


title: non-challenged (NC)

description: Sample 1

value: none (control)


title: OKF6-TERT1R control

value: vehicle:0.1% ethanol


title: SCC-9 control


title: Q89

status: Public on Oct 18 2013

city: Leiden

first: Lianne

last: Koens

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: The B-cells were cultured in RPMI 1640 with 10% FCS and incubated with CpG (5 μg/ml) (ODN 2006, Invivogen, San Diego, USA) and monoclonal antibodies to CD40 (0.1 μg/ml) (BD Biosciences Pharmingen, Heidelberg, Germany) for 24 hours.

data_processing:
Base calling was performed using CASAVA version 1.8.
Illumina sequence reads were aligned to the human genome using the miRDeep2.0 algorithm, which predicts precursor sequences and matches them to precursor microRNAs enlisted in the miRBase 18.0 database (http://www.mirbase.org).
Only sequences with a minimum sequence length of 17 bases were analyzed, allowing for a maximum mismatch of one base.
Genome_build: hg19
Supplementary_files_format_and_content: Raw counts per precusor microRNA and per predicted mature microRNA are represented in supplied data tables

source_name: activated B-cells 3

extract_protocol:
Total RNA was extracted from the frozen tumor samples and activated B-cells using TRIzol and according to the protocol described by the supplier (Invitrogen, Carlsbad, CA, USA).
Sequencing adaptors were ligated to total RNA on both ends of the RNA molecules and reverse-transcribed. The cDNA was pre-amplified with PCR primers containing specific sequence tags making the libraries compatible with the Illumina flow cells (Illumina, Son en Breugel, The Netherlands). Polyacrylamide gel electrophoresis size selection was performed, excising the 95-105 bp band containing the adaptor-ligated microRNA insert. Quantification and size verification was performed using a high sensitivity DNA chip (Agilent, Amstelveen, The Netherlands).

value: peripheral blood B-cells


title: Q90

source_name: activated B-cells 4


title: Q85

source_name: PCLBCL-LT case 9

value: skin tumor (lymphoma)

tag: tumor type

value: primary cutaneous diffuse large B-cell lymphoma, leg type


title: Q86

source_name: PCLBCL-LT case 10


title: Q81

source_name: PCLBCL-LT case 5


title: Q83

source_name: PCLBCL-LT case 7


title: Gro-Seq IMR90+TNF-α

description: groseq.IMR90_TNF.fwd.wig is for forward strand reads; and groseq.IMR90_TNF.rev.wig.gz is for reverse strand reads

value: no


title: Q88

source_name: activated B-cells 2


title: Q84

source_name: PCLBCL-LT case 8


title: Q82

source_name: PCLBCL-LT case 6


title: Q87

source_name: activated B-cells 1


title: Q80

source_name: PCLBCL-LT case 4


title: Q76

source_name: PCFCL case 6

value: primary cutaneous follicle center lymphoma


title: Q73

source_name: PCFCL case 3


title: Q78

source_name: PCLBCL-LT case 2


title: Q72

source_name: PCFCL case 2


title: Q74

source_name: PCFCL case 4


title: Q77

source_name: PCLBCL-LT case 1


title: E2

source_name: PCLBCL-LT case 12


title: E3

source_name: PCLBCL-LT case 13


title: E7

source_name: PCLBCL-LT case 3


title: Q71

source_name: PCFCL case 1


title: E1

source_name: PCLBCL-LT case 11


title: DHS-seq Control

city: Cambridge

first: Kinyui Alice

last: LO

state: MA

address: 77 Massachusetts Ave.

department: Biological Engineering

institute: MIT

data_processing:
Alignment: Sequence reads were obtained and mapped to NCBI37/mm9(July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS version 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), with insulin resistant samples as foreground and control sample as background
Genome Build:
DHS_seq_7-2.bed: mm9

organism: Mus musculus

source_name: 3T3-L1 differentiated untreated

growth_protocol: 3T3-L1 cells (ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% bovine serum (Invitrogen), 100 units/ml penicillin, and 100µg/ml streptomycin.  Two days after confluence (Day 0), cells were induced to differentiate with DMEM containing 10% fetal bovine serum (FBS) , 1µM dexamethasone, 10 µg/ml insulin and 0.5mM  3-isobutyl-1-methyxanthine for 2 days.  Cells were then incubated in DMEM containing 10% FBS and 10 µg/ml insulin for 2 more days.  After Day 4, Cells were maintained in DMEM containing 10% FBS, with medium change every other day.  Experiments were done on Day 8 to Day12 mature adipocytes.

extract_protocol: Intact nuclei were isolated from differentiated 3T3-L1 using a nuclei isolation kit (Sigma: NUC201).  Nuclei digestion and the DNA fraction isolation were done as described (Sabo, Kuehn et al. 2006).  In brief, at least 30 million nuclei were used for each experiment.  For each digestion, 50U/ml of DNase I (Promega RQ1 RNase-free DNase; lot number: 25308616) was used for digesting 10M cells at 37°C.  DNase I enzymatic reaction was stopped after 2 min by a SDS- and EDTA-based stop buffer.  Digested nuclei were incubated at 55°C overnight with proteinase K.  Digested DNA was then extracted using phenol chloroform, and the “2-hit” DNA fragments were isolated using a sucrose gradient.  Isolated DNA fragments were purified, subjected to the standard Illumina library preparation, and sequenced using Illumina GA II.

treatment_protocol: Before starting any insulin resistance-inducing treatment, cells were washed with PBS and changed to serum-free, low-glucose (1g/L) DMEM with 0.5% BSA.  For the TNFα treatment, cells were treated with 2.5µM of TNFα (R & D Systems) for 24h.  For hypoxia treatments, cells were incubated in a 1% oxygen chamber (Powers, Millman et al. 2010) for 24h.  Two types of hormonal stress were used to induce insulin resistance: dexamethasone treatment consisted of 24h incubation with 1µM dexamethasone (Sigma); high-insulin treatment consisted of 24h incubation of 100nM insulin (Sigma) in high glucose (4.5g/L) medium.

value: differentiated untreated

tag: passage

value: less than 10


title: ChIP-seq IgG

data_processing:
Alignment: Sequence reads were obtained and mapped to NCBI37/mm9(July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS version 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), with p65 ChIP-Sea samples as foreground and IgG sample as background
Genome Build:
ChIP_seq_IgG.bed: mm9

source_name: 3T3-L1 differentiated TNF

extract_protocol: Cells were lysed and chromatin was sonicated.The sonicated chromatin was incubated with  antibody-coupled beads overnight. The beads were then washed and the chromatin was eluted, reverse-crosslinked at 65°C overnight, treated with RNase and Proteinase K and extracted with phenol-chloroform.  The DNA was ethanol precipitated, purified and subjected to sequencing preparation using the Illumina sample preparation protocol.  Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments around 200-300bp were cut from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Sequencing was done using the Illumina Genome Analyzer II.  Antibody used: p65 (abcam 7970, lot number GR51446-1), IgG (sc-2027, lot number C0411)

treatment_protocol: For the TNFα treatment, cells were treated with 2.5µM of TNFα (R & D Systems) for 24h.

value: differentiated TNF

value: IgG

tag: vendor/catalog/lot

value: sc-2027, lot number C0411


title: DHS_seq Dex

data_processing:
Alignment: Sequence reads were obtained and mapped to NCBI37/mm9(July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS version 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), with insulin resistant samples as foreground and control sample as background
Genome Build:
DHS_seq_7-9.bed: mm9
DHS_seq_7-9_vs_7-2_1e-10_peaks.txt: mm9

source_name: 3T3-L1 differentiated Dex

value: differentiated Dex


title: DHS-seq TNF

data_processing:
Alignment: Sequence reads were obtained and mapped to NCBI37/mm9(July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS version 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), with insulin resistant samples as foreground and control sample as background
Genome Build:
DHS_seq_7-6.bed: mm9
DHS_seq_7-6_vs_7-2_1e-10_peaks.txt: mm9


title: RNA-seq Hypoxia rep3

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-15_accepted_hits.bw: mm9

molecule: polyA RNA

source_name: 3T3-L1 differentiated Hypoxia

extract_protocol: For each insulin resistance-inducing condition and the control condition, RNA-Seq experiments on biological triplicates were performed.  10ug of total RNA was used for each RNA-Seq library preparation according to the manufacturer's instructions (Illumina).  Quality of RNA was verified using bioanalyzer (Agilent); only RNA with a RIN > 9 was used for RNA-Seq.  cDNA libraries were prepared according to Illumina's instructions and sequenced by Illumina GAII.

value: differentiated Hypoxia


title: RNA-seq HighIns rep3

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-12_accepted_hits.bw: mm9

source_name: 3T3-L1 differentiated HighIns

value: differentiated HighIns


title: RNA-seq Hypoxia rep2

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-14_accepted_hits.bw: mm9


title: RNA-seq Dex rep2

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-8_accepted_hits.bw: mm9


title: RNA-seq Dex rep3

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-9_accepted_hits.bw: mm9


title: RNA-seq HighIns rep1

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-10_accepted_hits.bw: mm9


title: E6

source_name: PCFCL case 5


title: RNA-seq HighIns rep2

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-11_accepted_hits.bw: mm9


title: RNA-seq TNF rep1

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-4_accepted_hits.bw: mm9


title: RNA-seq Dex rep1

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-7_accepted_hits.bw: mm9


title: RNA-seq TNF rep3

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-6_accepted_hits.bw: mm9


title: RNA-seq Control rep1

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-1_accepted_hits.bw: mm9


title: RNA-seq Control rep2

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-2_accepted_hits.bw: mm9


title: RNA-seq TNF rep2

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-5_accepted_hits.bw: mm9


title: RNA-seq Control rep3

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-3_accepted_hits.bw: mm9


title: ChIP-seq TNF p65

data_processing:
Alignment: Sequence reads were obtained and mapped to NCBI37/mm9(July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS version 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), with p65 ChIP-Sea samples as foreground and IgG sample as background
Genome Build:
ChIP_seq_p65.bed: mm9
ChIP_seq_p65_vs_IgG_peaks.txt: mm9

value: abcam 7970, lot number GR51446-1


title: DHS-seq Hypoxia

data_processing:
Alignment: Sequence reads were obtained and mapped to NCBI37/mm9(July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS version 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), with insulin resistant samples as foreground and control sample as background
Genome Build:
DHS_seq_7-15.bed: mm9
DHS_seq_7-15_vs_7-2_1e-10_peaks.txt: mm9


title: SNYDER_SA1_2

city: Stanford

first: Maya

last: Kasowski

address: 300 Pasteur Drive

institute: Stanford University

data_processing:
Personal genomes were created by adding the SNPs of each individual into hg19. SNPs were obtained from the 1000 Genomes Project and from Chen et al 2012
ChIP-seq reads were aligned to personal genomes with BWA 0.6.1 (options -q 20 and the rest set to defaults)
Peaks were called using MACS2. Genome-wide signal tracks (bigWig) were generated using wiggler.
RNA-seq reads were mapped to personal transcriptomes using TOPHAT 2.0.4.
RNA-seq reads overlapping exons (Gencode v10) were obtained using HT-Seq 0.5.4
Genome_build: hg19
Supplementary_files_format_and_content: Peaks are in the narrowPeak format. bigWig files were generated using wiggler. Abundance measurements from the RNA-seq data are presented in a matrix (geneCount_mat.txt), where each row is a gene and each column is a cell line. The values in the matrix are the total counts (from HT-Seq) across both RNA-seq replicates for that cell line.
Samples represent the individual replicates. The combine data are on the Series record.

source_name: Lymphoblastoid Cell Lines

growth_protocol: Biological replicates were grown in separate batches and at separate times. Cells were grown to a density of 0.6-0.8 x 10^6/mL in 15% fetal bovine serum. RNA was obtained from lymphoblastoid cell lines (LCLs) of the same growth as used for the ChIP-seq experiments.

extract_protocol:
For ChIP-Seq, nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 x 30-s intervals). Clarified lysates corresponding to 20 million cells were treated with 1-5ug of antibody (Table S4) coupled to Protein G Dynabeads (Invitrogen #10003D, New York). The protein-DNA complexes were washed with RIPA buffer and eluted in 1% SDS TE at 65°C. An aliquot of clarified lysate was reserved as “input DNA” and handled in parallel with the immunoprecipitated samples following elution from Dynabeads. For RNA-Seq, Total RNA was extracted using Trizol (Lifetechnologies, Grand Island, NY) reagent according to the manufacturer’s instructions, then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen). RNA integrity was checked on a Bioanalyzer (Agilent, Santa Clara CA) and only RNA with an RNA integrity number (RIN) of > 9.5was used for subsequent library construction. Purified total RNA was depleted of ribosomal RNA using the Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre Biotechnologies, Madison, WI).
ChIP DNA sequencing libraries were generated according to Illumina DNA Tru-Seq DNA Sample Preparation Kit Instructions (Illumina Part # FC-121-2001, San Diego, CA). For RNA-Seq, stranded libraries were prepared following a dUTP protocol. Briefly, ~100 ng of rRNA depleted RNA were fragmented with 10 x fragmentation buffer (Lifetechnologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For second-strand synthesis dTTP was replaced with dUTP. The cDNA was endrepaired, A-tailed and Illumina TruSeq adapters were added. After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil Nglycosylase (UNG) (Lifetechnologies, N8080096) and after PCR amplification samples were sequenced on the Illumina Hi-Seq 2000.

treatment_protocol: For ChIP-Seq, cross linking was performed in 1% formaldehyde for 10 minutes at room temperature.

tag: replicate


title: SNYDER_SA1_1


title: SNYDER_RZ_2

data_processing:
Personal genomes were created by adding the SNPs of each individual into hg19. SNPs were obtained from the 1000 Genomes Project and from Chen et al 2012
ChIP-seq reads were aligned to personal genomes with BWA 0.6.1 (options -q 20 and the rest set to defaults)
Peaks were called using MACS2. Genome-wide signal tracks (bigWig) were generated using wiggler.
RNA-seq reads were mapped to personal transcriptomes using TOPHAT 2.0.4.
RNA-seq reads overlapping exons (Gencode v10) were obtained using HT-Seq 0.5.4
Genome_build: hg19
Supplementary_files_format_and_content: Peaks are in the narrowPeak format. bigWig files were generated using wiggler. Abundance measurements from the RNA-seq data are presented in a matrix (geneCount_mat.txt), where each row is a gene and each column is a cell line. The values in the matrix are the total counts (from HT-Seq) across both RNA-seq replicates for that cell line.
Samples represent the individual replicates. The combined replicate data are on the Series record.

value: RNA-seq


title: DHS_seq high insulin

data_processing:
Alignment: Sequence reads were obtained and mapped to NCBI37/mm9(July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS version 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), with insulin resistant samples as foreground and control sample as background
Genome Build:
DHS_seq_52-7.bed: mm9
DHS_seq_52-7_vs_52-1_1e-10_peaks.txt: mm9


title: SNYDER_RZ_1


title: SNYDER_H3K4me3_2


title: SNYDER_Input_1

value: Input


title: RNA-seq Hypoxia rep1

data_processing:
Pair-end, 36-bp reads from each sample were aligned to the mouse genome (mm9 build) using TopHat (version 1.1.0).
Differential expression:  Differential expression of each insulin resistance model versus the control model was quantified using Cuffdiff (Trapnell, Williams et al. 2010) (version 1.0.3). Differentially expressed genes are those that have a log2 fold change of > 0.58 or < -0.58 and a q-value < 0.05 when compared to the control condition.  We also required that the differentially expressed genes used for downstream analysis have a FPKM greater than 0.1 in the control condition.
Genome Build:
95-13_accepted_hits.bw: mm9


title: SNYDER_H3K4me1_1


title: SNYDER_H3K4me1_2


title: SNYDER_H3K4me3_1


title: SNYDER_H3K36me3_2.2


title: SNYDER_H3K36me3_1


title: SNYDER_H3K36me3_2


title: SNYDER_H3K27me3_2


title: SNYDER_H3K27Ac_1


title: SNYDER_H3K27Ac_1.2


title: SNYDER_H3K27Ac_2


title: SNYDER_H3K27Ac_1.3


title: SNYDER_CTCF_2.2

value: CTCF


title: SNYDER_CTCF_2.2.2


title: SNYDER_CTCF_2


title: GM2630_RZ_2


title: GM2630_SA1_1


title: GM2630_Input_1


title: GM2630_RZ_1


title: GM2630_SA1_2


title: GM2630_H3K36me3_2


title: GM2630_H3K4me1_1


title: GM2630_H3K4me3_1


title: GM2630_H3K36me3_1


title: GM2630_H3K27Ac_2


title: GM2630_H3K27me3_1


title: GM2630_CTCF_2


title: GM2630_H3K27Ac_1


title: GM2630_CTCF_2.2


title: GM2630_CTCF_1


title: SNYDER_H3K27me3_1


title: GM2630_H3K4me3_2


title: SNYDER_H3K27Ac_1.1


title: SNYDER_CTCF_1


title: GM2610_SA1_1


title: GM2610_H3K4me3_2


title: GM2610_RZ_2

value: RZ


title: GM2610_H3K4me3_1


title: GM2610_Input_1


title: GM2610_H3K36me3_2


title: GM2610_H3K4me1_1


title: GM2610_H3K27me3_2


title: GM2630_H3K27me3_2


title: GM2630_H3K4me1_2


title: GM2610_H3K27me3_1


title: GM2610_H3K27Ac_2


title: GM2610_H3K36me3_1


title: GM2610_H3K27Ac_1


title: GM2610_H3K4me1_2


title: GM2610_CTCF_2


title: GM2610_RZ_1


title: GM2610_CTCF_2.2


title: GM2610_SA1_2


title: GM2588_RZ_1


title: GM2588_SA1_1


title: GM2588_Input_1


title: GM2588_RZ_2


title: GM2610_CTCF_1


title: GM2588_H3K4me3_2


title: GM2588_H3K4me1_2


title: GM2588_H3K4me3_1


title: GM2588_H3K4me1_1


title: GM2588_H3K36me3_2


title: GM2588_H3K27me3_2


title: GM2588_H3K27me3_1


title: GM2588_H3K27Ac_1


title: GM2255_SA1_2


title: GM2588_H3K27Ac_2


title: GM2588_H3K36me3_1


title: GM2588_CTCF_2


title: GM2255_SA1_1


title: GM2255_RZ_1


title: GM2588_CTCF_1


title: GM2255_H3K4me3_1


title: GM2255_H3K4me1_1


title: GM2255_Input_1


title: GM2255_H3K4me1_2


title: GM2255_H3K36me3_1


title: GM2255_H3K4me3_2


title: GM2255_H3K27me3_2


title: GM2255_RZ_2


title: GM2255_H3K36me3_2


title: GM2255_H3K27Ac_1


title: GM2255_CTCF_2.2


title: GM2588_SA1_2


title: GM2255_H3K27Ac_2


title: GM2255_CTCF_1


title: GM19240_SA1_2


title: GM19240_RZ_1


title: GM19240_RZ_2


title: GM2588_CTCF_2.2


title: GM19240_Input_1


title: GM19240_H3K4me3_4.2


title: GM19240_SA1_1


title: GM19240_H3K4me1_3


title: GM19240_H3K4me3_1


title: GM19240_H3K4me1_2


title: GM19240_H3K4me3_3


title: GM19240_H3K36me3_2


title: GM2255_CTCF_2


title: GM19240_H3K4me3_2


title: GM19240_H3K4me1_1


title: GM19240_H3K36me3_1


title: GM19240_H3K27me3_2


title: GM19240_H3K27me3_1


title: GM19240_H3K27me3_1.2


title: GM19240_CTCF_2


title: GM19240_H3K27Ac_1


title: GM19240_H3K27Ac_2


title: GM19239_SA1_1


title: GM19240_CTCF_1


title: GM19239_SA1_2


title: GM19239_RZ_2


title: GM19239_Input_1


title: GM19239_RZ_1


title: GM19239_H3K4me3_1.1


title: GM19239_H3K4me3_3


title: GM19239_H3K4me1_3


title: GM19239_H3K4me1_2


title: GM19239_H3K4me3_2


title: GM19239_H3K27me3_2


title: GM19240_H3K27me3_2.2


title: GM19239_H3K36me3_1


title: GM19239_H3K27me3_2.2


title: GM19239_H3K27Ac_3


title: GM19239_H3K27Ac_2


title: GM19239_H3K27Ac_1.1


title: GM19239_H3K27me3_1.3


title: GM19239_H3K36me3_2


title: GM19240_H3K27Ac_3


title: GM19239_CTCF_1


title: GM19239_H3K27me3_1.1


title: GM19238_RZ_1


title: GM19238_RZ_2


title: GM19239_CTCF_2


title: GM19238_SA1_2


title: GM19238_Input_1


title: GM19238_H3K4me3_3


title: GM19238_H3K4me3_2


title: GM19238_H3K4me3_1


title: GM19238_H3K4me1_3


title: GM19238_H3K4me1_2


title: GM19238_H3K4me1_1


title: GM19238_H3K36me3_1


title: GM19238_H3K36me3_2


title: GM19238_H3K27me3_2


title: GM19238_H3K27me3_1


title: GM19238_CTCF_2


title: GM19238_CTCF_1


title: GM19238_H3K27me3_1.2


title: GM19238_H3K27Ac_1


title: GM19193_SA1_1


title: GM19238_H3K27Ac_3


title: GM19193_H3K4me3_2


title: GM19193_H3K4me1_1


title: GM19193_RZ_1


title: GM19238_SA1_1


title: GM19193_H3K36me3_2


title: GM19193_Input_1


title: GM19193_H3K27me3_1


title: GM19193_H3K4me1_2


title: GM19193_SA1_2


title: GM19193_H3K36me3_1


title: GM19193_RZ_2


title: GM19193_H3K27Ac_1


title: GM19193_CTCF_2


title: GM19239_H3K4me1_1.1


title: GM19193_CTCF_1


title: GM19099_SA1_1


title: GM19099_RZ_2


title: GM19099_RZ_1


title: GM19238_H3K27Ac_2


title: GM19099_Input_1


title: GM19099_H3K4me3_1


title: GM19099_H3K4me3_2


title: GM19193_H3K4me3_1


title: GM19099_H3K4me1_2


title: GM19193_H3K27me3_2


title: GM19099_H3K4me1_1


title: GM19099_H3K36me3_1


title: GM19099_H3K36me3_2


title: GM19099_CTCF_2


title: GM19099_H3K27Ac_2


title: GM19099_H3K27me3_1


title: GM19193_H3K27Ac_2


title: GM18951_RZ_2


title: GM18951_SA1_2


title: GM18951_SA1_1


title: GM18951_Input_1


title: GM19099_H3K27me3_2


title: GM19099_H3K27Ac_1


title: GM18951_RZ_1


title: GM18951_H3K4me1_2


title: GM18951_H3K4me3_1


title: GM19099_SA1_2


title: GM18951_H3K4me1_1


title: GM18951_H3K36me3_2


title: GM18951_H3K36me3_1


title: GM2255_H3K27me3_1


title: GM18951_H3K27me3_2


title: GM18951_H3K27me3_1


title: GM19099_CTCF_1


title: GM18951_H3K27Ac_2


title: GM18951_H3K4me3_2


title: DHS_seq Control2

data_processing:
Alignment: Sequence reads were obtained and mapped to NCBI37/mm9(July, 2007) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS version 1.4) algorithm (http://liulab.dfci.harvard.edu/MACS/), with insulin resistant samples as foreground and control sample as background
Genome Build:
DHS_seq_52-1.bed: mm9

source_name: 3T3-L1 differentiated Control2

value: differentiated Control2


title: Damaged_p53_ChIPSeq

city: Houston

first: Kadir

middle: Caner

last: Akdemir

state: TX

address: 1515 Holcombe Blvd

institute: MD Anderson Cancer Center

data_processing:
Sequence reads were obtained and mapped to the February 2006 human reference sequence (hg18) using the Illumina Genome Analyzer Pipeline using Illumina’s ELAND software.
Enriched regions for each condition were normalized to input DNA and detected with MACS (Zhang et al., 2008) with a cut-off P < 10-8 for Damage and Differentiation P< 10-10 for Untreated.
Genome_build: hg18
Supplementary_files_format_and_content: peak and aligned bed files

source_name: H9 hESC

growth_protocol: Human Embryonic Stem (WA09) Cells were obtained from National Stem Cell Bank (Madison, WI) and cultured according to the protocol from WiCell Research Insitute. Briefly, WA09 cells were maintained in hESC culture medium on γ-irradiated Mouse Embryonic Fibroblasts (MEFs) prepared using WiCell instructions. hESCs ranging from passage number 32-38 were used for all of our experiments. hESC complete culture medium is composed of DMEM/F12 supplemented with 20% knockout serum replacement, 1 mM L-glutamine, 1% nonessential amino acids, 4 ng/ml human FGF2 (all from Invitrogen), and 0.1 mM 2-mercaptoethanol (Sigma). The medium was changed daily, and cells were passaged every 4–6 days with 1 mg/ml Collagen IV (Invitrogen). For differentiation studies hESCs were cultured in differentiation media (hESC media without FGF) containing 1 μM Retinoic Acid (RA) with fresh medium change daily. hESCs were also maintained as feeder-free cultures on hESC qualified Matrigel (BD Biosciences) in mTeSR1 media (Stem Cell Technologies) and CM (MEF conditioned media). Passage 32 hESCs were grown on mTeSR1 media for 5 passages.  hESCs were cultured on Matrigel (BD Biosciences) following manufacturer’s instructions, received fresh mTeSR1 media everyday and cells were passaged every 4-6 days with 1 mg/ml Dispase (Stem Cell Technologies).

extract_protocol: Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.  Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

treatment_protocol: For differentiating hESCs cultured on mTeSR1, 1 μM Retinoic Acid (RA) was added to homemade MEF-CM (Conditioned Media, without additional FGF). CM media was prepared in our facility by culturing γ-irradiated MEFs in complete hESC culture media for 24 hours, and collected every day, filtered and freezed at -20 degrees. FGF was added to CM media before use to a final concentration of 10 ng/ml to culture the cells grown on Matrigel under pluripotent conditions.

value: DOX-damaged induced hESC

tag: chip antibody

tag: antibody vendor

value: Santa Cruz Biotechnology


title: Untreated_p53_ChIPSeq

value: Pluripotent hESC


title: GM18526_RZ_2


title: GM18526_RZ_1


title: GM18951_CTCF_2


title: GM18526_SA1_2


title: GM18526_SA1_1


title: GM18526_Input_1


title: GM18526_H3K4me1_1


title: GM18526_H3K4me1_2


title: GM18951_CTCF_1


title: GM18526_H3K4me3_1


title: GM18526_H3K4me3_2


title: GM18526_H3K27me3_2


title: GM18526_H3K36me3_1


title: GM18526_H3K27me3_1


title: GM18526_H3K27Ac_2


title: Differentiating_p53_ChIPSeq

value: RA-mediated differentiating hESC


title: input DNA


title: GM18526_CTCF_1


title: GM18526_CTCF_2


title: GM18505_SA1_2


title: GM18505_SA1_1


title: GM18505_RZ_2


title: GM18951_H3K27Ac_1


title: GM18505_Input_1


title: GM18505_RZ_1


title: GM18505_H3K4me3_2


title: GM18505_H3K4me3_1


title: GM18505_H3K4me1_2


title: GM18526_H3K36me3_2


title: GM18505_H3K4me1_1


title: GM18505_H3K36me3_2


title: GM18505_H3K27me3_1


title: GM18505_CTCF_2


title: GM18505_H3K27Ac_1


title: GM18505_H3K27me3_2


title: GM18505_CTCF_1


title: GM18526_H3K27Ac_1


title: GM18486_Input_1


title: GM18505_H3K27Ac_2


title: GM18505_H3K36me3_1


title: GM18486_H3K4me3_2


title: GM18486_H3K4me1_1


title: GM18486_H3K36me3_2


title: GM18486_H3K4me3_1


title: GM18486_SA1_2


title: GM18486_H3K27me3_2


title: GM18486_H3K36me3_1


title: GM18486_H3K27me3_1


title: GM18486_H3K27Ac_2


title: GM18486_H3K27Ac_1


title: GM18486_CTCF_1


title: GM18486_CTCF_1.2


title: GM12892_SA1_1


title: GM12892_RZ_2


title: GM18486_CTCF_2


title: GM12892_RZ_1


title: GM12892_Input_1


title: GM12892_SA1_2


title: GM12892_H3K4me3_3


title: GM18486_H3K4me1_2


title: GM18486_SA1_1


title: GM12892_H3K4me1_2


title: GM12892_H3K4me3_2


title: GM12892_H3K36me3_2


title: GM12892_H3K4me1_3


title: GM12892_H3K27me3_2


title: GM12892_H3K27me3_1.2


title: GM12892_H3K4me1_1


title: GM12892_H3K4me3_1


title: GM12892_H3K27me3_1


title: GM12892_CTCF_2


title: GM12892_H3K36me3_1


title: GM12892_H3K27Ac_3


title: GM12891_SA1_2


title: GM12892_H3K27Ac_1


title: GM12892_CTCF_1


title: GM12892_H3K27me3_2.2


title: GM12891_RZ_2


title: GM12892_H3K27Ac_2


title: GM12891_SA1_1


title: GM12891_Input_1


title: GM12891_RZ_1


title: GM12891_H3K4me3_2


title: GM12891_H3K4me3_1


title: GM12891_H3K4me1_2


title: GM12891_H3K4me3_3


title: GM12891_H3K4me1_3


title: GM12891_H3K36me3_1


title: GM12891_H3K27me3_2


title: GM12891_H3K27me3_1


title: GM12891_H3K27me3_2.2


title: GM12891_H3K36me3_2


title: GM12891_H3K27me3_1.2


title: GM12891_H3K27Ac_3


title: GM12891_H3K27Ac_1


title: GM12890_RZ_2


title: GM12890_SA1_2


title: GM12890_SA1_1


title: GM12890_H3K4me3_2


title: GM12890_RZ_1


title: GM12890_H3K4me1_2


title: GM12890_H3K4me1_1


title: GM12890_H3K4me3_1


title: GM12890_Input_1


title: GM12891_H3K4me1_1


title: GM12890_H3K36me3_1


title: GM12890_H3K36me3_2


title: GM12890_H3K27Ac_2


title: GM12890_H3K27me3_1


title: GM12890_H3K36me3_1.2


title: GM12890_CTCF_2.2


title: GM12890_CTCF_2


title: GM12890_H3K27Ac_1


title: GM12890_H3K27me3_2


title: GM12891_H3K27Ac_2


title: GM12878_SA1_1


title: GM12878_SA1_2


title: GM12878_RZ_2


title: GM12878_RZ_1


title: GM12890_CTCF_1


title: GM12878_SA1_1.2


title: GM12878_Input_1


title: GM12891_CTCF_1


title: H3K4me3 ChIP-seq 256-cell

city: Shanghai

first: Yong

last: Zhang

address: 1239 Siping Road

institute: Tongji University

data_processing:
All sequenced reads were aligned using bowtie version 4.1.2.
Uniquely mapped reads with a maximum of two mismatches were kept.
For nucleosome and histone modification ChIP-seq samples, all mapped reads were extended to 147 bp in their 3’ direction, and the middle 73 bp were piled up to generate wig files.
For Pol II ChIP-seq samples, MACS version 1.4.2 was used to generate wig files.
Genome_build: zv9
Supplementary_files_format_and_content: wig format

organism: Danio rerio

source_name: embryos

growth_protocol: Zebrafish were maintained and raised under standard conditions. Wild-type embryos were collected at the 1-cell stage, synchronized and allowed to develop to the desired stage at 28°C.

extract_protocol:
For nucleosome and histone modification ChIP-seq samples, between 250 and 650 embryos were carefully staged, dechorionated and fixed in 1% formaldehyde for 3 minutes at room temperature. Formaldehyde was quenched by adding glycine to a final concentration of 0.125M. Embryos were rinsed 3 times in ice-cold PBS, immediately resuspended in cell lysis buffer (10mM Tris-HCl pH7.5/10mM NaCl/0.5%NP40) and lysed for 3 to 4 min on ice. Nuclei were collected by centrifugation, washed with ice-cold PBS, collected by centrifugation again and resuspended in digestion buffer (50mM Tris-HCl pH7.5/1mM CaCl2/0.2%Triton X-100). Samples were divided into 200μl aliquots, prewarmed to 25°C and incubated with MNase (stored in MNase storage buffer (10mM Hepes pH7.5/100mM NaCl/1mM CaCl2/50% glycerol) and diluted in MNase dilution buffer (50mM Tris-HCl pH8/10mM NaCl/126mM CaCl2/5% glycerol)). Concentration of MNase and time of incubation were optimized to obtain 80% mononucleosomes as determined by BioAnalyzer analysis.
Libraries were prepared using the Illumina sequencing library preparation protocol.

tag: tissue

value: embryos

tag: developmental stage

value: 2.5 hpf (256-cell stage)

tag: chip antibody lot number

value: H3K4me3 (millipore 07-473)


title: GM12891_CTCF_2


title: GM12878_H3K4me3_3


title: H3K36me3 ChIP-seq dome

value: 4.5 hpf (dome/30% epiboly stage)

value: H3K36me3 (abcam ab9050)


title: GM12878_H3K4me3_1


title: GM12878_H3K4me1_2


title: Pol II ChIP-seq dome 4H8

extract_protocol:
For Pol II ChIP-seq samples, between 400 and 800 embryos were carefully staged, dechorionated and fixed in 1.85% formaldehyde and 12.5% DMSO for 15 minutes at room temperature. Formaldehyde was quenched by adding glycine to a final concentration of 0.125M. Embryos were rinsed 3 times in ice-cold PBS, immediately resuspended in cell lysis buffer (10mM Tris-HCl pH7.5/10mM NaCl/0.5%NP40) and lysed for 15 min on ice. Nuclei were collected by centrifugation, resuspended in nuclei lysis buffer (50mM Tris-HCl pH7.5/10mM EDTA/1%SDS) and lysed for 10 min on ice. Samples were diluted 3 times in IP dilution buffer (16.7mM Tris-HCl pH7.5/167mM NaCl/1.2mM EDTA/0.01%SDS) and sonicated to obtain fragments of ~400 bp. Triton X-100 was added to a final concentration of 0.75% and the lysate was incubated overnight while rotating at 4°C with 25μl of protein G magnetic Dynabeads (Invitrogen) that had been pre-bound to an excess amount of antibody. Bound complexes were extensively washed with RIPA (50mM HEPES pH7.6/1mM EDTA/0.7%DOC/1%Igepal/0.5MLiCl) and TBS and then eluted from the beads with elution buffer (50mM NaHCO3/1%SDS). Cross-links were reversed o/n at 65°C, and DNA purified by QIAquick PCR purification kit (QIAGEN). For MNase/ChIP between 300 and 700 embryos were used per condition and after dialysis, chromatin was added to the bead/antibody complex as described above.
Libraries were prepared using the Illumina sequencing library preparation protocol.

value: Pol II (ab5408)


title: GM12878_H3K4me1_3


title: H3K27me3 ChIP-seq dome

value: H3K27me3 (Millipore 07-449)


title: H3K4me3 ChIP-seq dome


title: H3K4me3 ChIP-seq oblong

value: 3.5 hpf (oblong stage)


title: GM12878_H3K36me3_2


title: nucleosome dome rep 2

value: H3 (abcam ab1791)


title: nucleosome dome rep 1


title: GM12878_H3K27me3_2


title: nucleosome 256-cell rep 2


title: GM12878_H3K27me3_2.2


title: GM12878_H3K27me3_1


title: GM12878_H3K27Ac_4.4


title: nucleosome 256-cell rep 1


title: GM12878_H3K27me3_1.2


title: GM12878_H3K27Ac_4.1


title: GM12878_H3K27Ac_4.3


title: GM12878_H3K4me3_2


title: GM12878_H3K27Ac_2


title: Input_total_male_germ_cells

city: La Tronche

first: Sophie

last: Rousseaux

address: Bd de la Chantourne

department: IAB

country: France

institute: INSERM-UGA

data_processing:
Sequence reads of 75+35 bp reads were produced with a SOLiD hq5500xl sequencer, according to standard Life Technologies protocols. The sequence reads were analyzed with the LifeScope™ software suite (cms_4448431.pdf).
After sequence read mapping to version 9 build 37 of the mouse genome allowing up to 4 mismatches, only reads mapping once to the genome were retained for subsequent analyses, to prevent spurious calls in repetitive regions.
two BAM files were generated by the LifeScope pipeline, corresponding to the two biological conditions ChIP-seq  antiTH2B and its input
BAM files were transformed into SAM format (Li et al, 2009; PMID: 19505943).
Genome_build: mm9
Supplementary_files_format_and_content: Bed and wig files were generated using SICER with following parameters : W200, G600, FDR 0.01 (for WIG) and 0.01 (for BED)

source_name: Male germ cells

extract_protocol: Standard Applied Biosystems Life Technologies protocols were followed for the creation of short-insert bar-coded, paired-end libraries (insert length ~150 bp) according to the ChIP-seq Kit Guide from the manufacturer (cms_079323.pdf) and library preparation guide (cms_081748.pdf).

treatment_protocol: Total spermatogenic cell suspensions were prepared from wt mice and used for ChIP with an anti-TH2B antibody exactly as previously reported in (Tan et al, 2011; PMID: 21925322).

tag: cell type

value: Total male germ cells from adult mice

value: anti TH2B

tag: genotype

value: wild type


title: Pol II ChIP-seq dome 8WG16

value: Pol II (8WG16/Covance MMS-126R)


title: ChipSeq_antiTH2B_total_male_germ_cells


title: GM12878_H3K4me1_1

tag: antibody


title: GM12878_H3K27Ac_3

tag: cell line


title: GM12878_CTCF_2

value: CTCF


title: GM12878_H3K27Ac_1


title: GM10847_SA1_1


title: GM10847_SA1_2


title: GM12878_CTCF_1


title: GM12878_H3K36me3_1


title: GM10847_RZ_2

value: RNA-seq


title: GM10847_Input_1

value: Input


title: GM10847_RZ_1


title: GM10847_H3K4me3_2


title: GM10847_H3K4me3_1


title: GM10847_H3K4me1_2


title: GM10847_H3K4me1_1


title: GM10847_H3K36me3_2


title: GM10847_H3K36me3_1


title: GM12878_H3K27Ac_4.2


title: GM10847_H3K27Ac_2


title: GM10847_H3K27me3_2


title: Differentiating_H3K27me3_ChIPSeq

value: RA-mediated differentiating hESC

value: Milipore


title: Differentiating_H3K4me3_ChIPSeq


title: Untreated_H3K4me3_ChIPSeq

value: Pluripotent hESC


title: ArcA IP ChIP-seq Anaerobic Biological replicate 1

status: Public on Oct 17 2013

city: Madison

first: Dan

last: Park

state: WI

address: 440 Henry Mall

institute: UW Madison

data_processing:
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads.
genome build: U00096.2
Genome Build:
ArcA_anaerobic_ChIP-seq_IP_A.wig: U00096.2

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

source_name: Anaerobic Cultures

growth_protocol: Cells were grown anaerobically (95% N2 and 5% CO2) until mid-log phase (OD600 of 0.3) and treated with 1% final volumen formaldehyde for ten minutes. Sodium phosphate (1/100 vol. of 1M, pH 7.6; 10 mM final) was added to the mid-log cultures followed by formaldehyde to 1% final, and anaerobic sparging was continued for 10 min. Cold 2.5 M glycine was added to 100mM and the mixture was incubated at 4 °C with anaerobic sparging for 30 minutes to stop the crosslinking. Cells were spun at 5000 x g, and washed repeatedly with phosphate buffered saline before being frozen at -80 °C.

extract_protocol: 10 ng of DNA were submitted to the University of Wisconsin-Madison DNA Sequencing Facility for ChIP-seq library preparation.  Samples were sheared to 200-500 nt during the IP process to facilitate library preparation.  All libraries were generated using reagents from the Illumina Paired End Sample Preparation Kit (Illumina) and the Illumina protocol “Preparing Samples for ChIP Sequencing of DNA” (Illumina part # 11257047 RevA) as per the manufacturer’s instructions, except products of the ligation reaction were purified by gel electrophoresis using 2% SizeSelect agarose gels (Invitrogen) targeting 400 bp fragments.  After library construction and amplification, quality and quantity were assessed using an Agilent DNA 1000 series chip assay (Agilent) and QuantIT PicoGreen dsDNA Kit (Invitrogen), respectively, and libraries were standardized to 10μM.  Cluster generation was performed using a cBot Single Read Cluster Generation Kit (v4) and placed on the Illumina cBot.  Single read, 75 bp (rep A) or 36 bp (rep B) runs were performed, using standard SBS kits (v4) and SCS 2.6 on an Illumina Genome Analyzer IIx.   Basecalling was performed using the standard Illumina Pipeline version 1.6.

treatment_protocol: Cell pellets (from initial 50 ml of culture) were thawed and resuspended in 250ul of IP buffer (100 mM Tris pH 8, 300 mM NaCl, 2% TritonX-100) and sonicated using a microtip sonicator set at 10% output for 20 second intervals with periods of cooling in between. Cells were then treated for one hour at 4 °C with RNase A (2 ng/ml) micrococcal nuclease (50 units), 20 μM CaCl2,1.2 mM KCl, 0.3 mM NaCl, 6 mM sucrose, and 10 μM DTT. After treatment, a distribution of DNA fragments ranging from 200-600 bp was detected by agarose-gel electrophoretic separation of a small sample that was de-crosslinked by incubation at 65 °C for >4 hr. EDTA was added to 10 mM to stop the micrococcal nuclease and the samples were spun down to remove cell debris. The lysate was then incubated with a 50/50 slurry of Sepharose protein A beads and protein G beads in IP buffer for 2-3 hours at 4 °C. The beads were removed by centrifugation and antibody was added to the pre-cleared lysate for an overnight incubation. The next day, 30 μl of a 50/50 slurry of Sepharose protein A and G beads in IP buffer was added to the lysate to capture antibody-protein-DNA complex for one hour at 4 °C. Beads were then washed once with 1 ml of 250 mM LiCl wash buffer (100 mM Tris pH 8, 250 mM LiCl, 2% TritonX-100), twice with 600 mM NaCl wash buffer (100 mM Tris pH 8, 600 mM NaCl, 2%SDS), twice with 300 mM NaCl wash buffer (100 mM Tris pH 8, 300 mM NaCl, 2%SDS), and twice with TE. Elution buffer (50 mM Tris pH 8, 10 mM EDTA, 1% SDS) was added after the final wash step, and beads were incubated at 65 °C for 30 minutes toremove the crosslinked protein-DNA complexes from the beads. After centrifugation to remove the beads, the samples were incubated overnight at 65 °C to reverse the protein-DNA formaldehyde crosslinks. DNA was purified using Qiagen’s PCR Purification kit and eluted to a final volume of 50ul with EB.

value: polyclonal antiserum was raised against His6-ArcA then Affinity Purified using purified ArcA to yield the polyclonal antibodies used for ChIP

tag: strain

value: Wild Type K-12

tag: culture condition

value: Anaerobic Cultures


title: GM10847_CTCF_1


title: Cybrid_tRNA_Trp_5556GA_RP_rep2

city: Amsterdam

first: Koos

last: Rooijers

address: Plesmanlaan 121

department: Gene Regulation

institute: Netherlands Cancer Institute

description: Cybrid cells: 143B rho(0) cells fused with enucleating cells derived from patient material

data_processing:
(Ribosome profiling data only) Adapter sequences were trimmed from raw data using cutadapt 1.1 with parameters (--quality-base=33 -O 12 -m 20)
rRNA was filtered from data by alignment to transcript database compiled from Ensembl 37.65 (gene categories “rRNA”, “rRNA_pseudogene” and “Mt_rRNA”) using bowtie (v2.0.2) with parameters (–seed 42 --end-to-end -N 1 -L 20 -i C,1 -D 5 -R 5) and retention of the unmapped reads.
Analogous to rRNA filtering, tRNA was filtered by alignment to a tRNA database compiled from the GrRNAdb (Chan and Lowe, NAR, 2009).
Reads not mapped in previous steps were used in final alignment using tophat (v2.0.6) with parameters (--seed 42 -n 2 -m 1 --no-novel-juncs --no-novel-indels --no-coverage-search --segment-length 20) to hg19 and a transcriptome index compiled from Ensembl 37.65, RefSeq (obtained from UCSC 7AUG2012) and the Broad Linc catalog (obtained from http://www.broadinstitute.org/genome_bio/human_lincrnas/)
Genome_build: hg19
Supplementary_files_format_and_content: WIG files were generated from alignment files output by tophat in the final alignment step, only using primary alignments and alignments with mapping quality >= 10. Scores indicate read coverage, normalized to reads per 10 million reads.

source_name: Osteosarcoma

growth_protocol: Cells were cultured in DMEM supplemented with 10% heat-inactivated fetal calf serum (FCS) in 5% CO2 at 37 deg. Celcius.

extract_protocol:
Approximately 30e6 cells were treated with chloramphenicol (100μg/ml) for 15 minutes and cycloheximide (100μg/ml) for 5 minutes. Cells were lysed in buffer B (20 mM Tris-HCl, pH 7.8, 100mM KCl, 10mM MgCl2, 1% Triton X-100, 2mM DTT, 100 μg/ml chloramphenicol, 100 μg/ml cycloheximide, 1x Complete protease inhibitor). Lysates were centrifuged at 5000 rpm and the supernatant was treated with 2U/μl of RNase I (Ambion) for 40 minutes at room temperature. Lysates were fractionated on a linear sucrose gradient (7% - 47%) using the SW- 41Ti rotor at 36,000 rpm for 2hrs. Fractions enriched in mito-monosomes and cytosolic monosomes were identified by western blotting, pooled and treated with proteinase K (Roche) in 1% SDS. Released RPFs were purified using Trizol reagent (Invitrogen) following the manufacturer’s instructions.
RNA was gel-purified on a denaturing 10% polyacrylamide urea (7 M) gel. A section corresponding to 25-36 nucleotides was excised, eluted and ethanol precipitated. The resulting fragments were 3′-dephosphorylated using T4 polynucleotide kinase (New England Biolabs Inc. Beverly, MA, USA) for 6 h at 37°C in 2-(N-morpholino)ethanesulfonic acid (MES) buffer (100 mM MES-NaOH, pH 5.5, 10 mM MgCl2, 10 mM β-mercaptoethanol, 300 mM NaCl). 3′ adaptor was added with T4 RNA ligase 1 (New England Biolabs Inc. Beverly, MA, USA) for 2.5 h at 37°C. Ligation products were 5′-phosphorylated with T4 polynucleotide kinase for 30 min at 37°C. 5′ adaptor was added with T4 RNA ligase 1 for 18 h at 22°C.

value: Cybrid

tag: mtdna genotype

tag: sample type

value: other


title: GM10847_CTCF_2


title: Cybrid_control_RP_rep2

value: control


title: GM10847_H3K27Ac_1


title: Untreated_H3K27me3_ChIPSeq


title: GM10847_CTCF_2.2


title: ArcA IP ChIP-seq Anaerobic Biological replicate 2

data_processing:
Sequence reads were aligned to the published E. coli K-12 MG1655 genome (U00096.2) using the software packages SOAP (Li et al, 2009) and ELAND (within the Illumina Genome Analyzer Pipeline Software), allowing at most two mismatches.  Sequence reads with sequences that did not align to the genome, aligned to multiple locations on the genome, or contained more than two mismatches were discarded from further analysis (<10% of reads) (Supplemental Files).  For visualization the raw tag density at each position was calculated using QuEST (Valouev et al, 2008) and normalized as tag density per million uniquely mapped reads.
genome build: U00096.2
Genome Build:
ArcA_anaerobic_ChIP-seq_IP_B.wig: U00096.2


title: NIH3T3 pBabe-puro-3

city: Copenhagen

first: Mikkel

last: Rohde

address: Strandboulevarden 49

country: Denmark

institute: Danish Cancer Society

data_processing:
Basecalling was performed using CASAVA
Fastq data files were imported the the CLC Genomic Workbench software package and mapped to the mouse genomic reference sequence. Only reads were a minimum og 50% of the sequence would align with al least 90% match were included.
All expression levels were calculated as RPKM by the CLC Genomic Workbench software package. Based on this the fold change in expression levels for all genes was calculated between the 3 untransformed and the 3 transformed samples.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file with RPKM values for each sample and fold change between mean RPKM of the 3 untransformed samples vs mean RPKM of the 3 transformed samples.

growth_protocol: Cells were grown in RPMI supplemented with 10% FCS and NEAA

extract_protocol:
Total RNA was extracted using the Nucleospin RNA II kit from Macherey Nagel
Libraries were constructed using the Illumina mRNA-Seq 8-Sample Prep Kit

value: NIH3T3 MEFs

tag: transduction

value: pBabe-Puro


title: NIH3T3 pBabe-puro-1


title: DBD, immunoprecipitation

city: Sydney

first: Jon

last: Burdach

state: NSW

address: UNSW

department: BABS

country: Australia

institute: University of New South Wales

description: rep1 and 2

data_processing:
Libraries (6 inputs and 6 IP samples) were multiplexed into four lanes using sample specific adapters such that there were 3 samples per lane.   Samples were sequenced using 50 bp chemistry on the HiSeq 2000 (Illumina, San Diego, CA). Quality control on the sequence data was performed using FastQC v0.10.1 available from http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Base-calling and demultiplexing was performed using the standard Illumina software packaged with the HiSeq2000. Quality control on the sequence data was performed using FastQC v0.10.1 available from http://www.bioinformatics.babraham.ac.uk/projects/fastqc/.
Reads were aligned to the mm9/NCBI37 Mus musculus genome using Bowtie2 v2.0.0-beta7 (Langmead and Salzberg 2012). In the first round, Bowtie2 was set to --very-sensitive and –D 40. Non-aligned reads were subjected to a second round of alignment where the read could be soft clipped by running Bowtie2 with the switch --very-sensitive-local. Resulting alignments were sorted, merged and indexed using Samtools v0.1.18 (Li et al. 2009).
Peak calling and downstream analysis was primarily performed using the HOMER software package v4.1 (available from http://biowhat.ucsd.edu/homer/ngs/index.html) (Heinz et al. 2010). The script findPeaks.pl was used to for peak discovery using the paired input sample as a control with the settings -style factor, -F 5 and -L 5, requiring 5x fold enrichment over input and 5x fold enrichment over background (surrounding 10 kb) to call a peak. Peaks were subjected to an FDR cut-off of 0.001. Peaks were merged using mergePeaks using the switch -d given meaning that peaks had to literally overlap in genomic space to be considered overlapping. Peak lists were annotated using annotatePeaks.pl using the HOMER annotation set for mm9/NCBI37.
HOMER was used to quantify ChIP tag density at peak locations across the genome. Tags were counted within 400 bp around the peak centre (as peak widths could vary across the three different samples). All tag counts were normalised to 100M reads and were thus expressed as reads/100M reads to allow comparison across samples.  HOMER was also used to create bedgraph files using the makeUCSCfile program.
Genome_build: mm9/NCBI37
Supplementary_files_format_and_content: Processed data files include 1) a normalised ChIP tag density track (.bedgraph).  This tag density track reflects the normalised tag density across the merged replicates. 2) Peak lists for each individual replicate (tab-delimited-txt). 3) Peak lists that reflect the overlap between replicates and include log2 normalised tag counts for each peak (tab-delimited-txt). 4) A matrix table that includes peaks across all three conditions and  log2 normalised tag counts for each peak  (tab-delimited-txt).

source_name: Klf3-/- murine embryonic fibroblasts, rescued with DBD-V5

growth_protocol: Cells were grown in DMEM supplemented with 10% FCS and with 1X PSG

extract_protocol:
ChIP was conducted in duplicate on Klf3-/- MEFs expressing recombinant Klf3, ΔDL or DBD. Aproximately 5x107 cells were used for each experiment and ChIP was conducted as previously described (Schmidt et al. 2009) using an anti-V5 antibody (Cat# R960-CUS, Life Technologies, Carlsbad, CA).
Library preparation was performed using the TruSeq DNA Sample Preparation Kit (Cat# FC-121-2001, Illumina, San Diego, CA) according to manufacturer’s instructions with minor modifications. Adapter sequences were diluted 1/40 before use and following adapter ligation, the library size extracted from the gel was 100-280 bp (excluding adapters) in line with the size of sonicated fragments.

value: MEFs

tag: genotype/variation

value: Klf3-/- rescued with DBD-V5


title: MEF

city: Kyoto

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

country: Japan

institute: Kyoto University

data_processing:
Potential sequencing errors were corrected using the SOLiD Accuracy Enhancement Tool.
RNA-seq reads were aligned to the mm9 genome assembly using BioScopev1.3 with default setting in Whole Transcriptome Mapping
Genome_build: mm9
Supplementary_files_format_and_content: The .wig file was generated using  the sam2wig run (BioScopev1.3) with the default values for visualization on the UCSC Genome Browser.

source_name: Mouse embryonic fibrobrasts

growth_protocol: Mouse embryonic fibroblasts were grown in DMEM, 10% FBS, 50 units/ml penicillin and 50 mg/ml streptomycin. Pluripotent stem cells were grown in ES cell medium (DMEM containing 15% FBS,1X non-essential amino acids (NEAA), 5.5 mM 2-mercaptoethanol (2-ME), 50 units/ml penicillin and 50 mg/ml streptomycin) on feeder layers of mitomycin-C-treated SNL cells stably expressing the puromycin-resistance gene.

extract_protocol:
cytoplasmic total RNA was isolated with RNeasy mini kit (QIAGEN), and then mRNA was isolated with FastTrack MAG Maxi mRNA Isolation Kit (Invitrogen).
RNA libraries were prepared for sequencing using SOLiD  Whole Transcriptome Analysis Kit.   Note that libraries with adaptor A were sequenced from 5 ′ end of the sense strand of the RNA, and libraries with adaptor B were sequenced from the opposite strand (reverse complement of the RNA).

value: Mouse embryonic fibroblast

value: mixed genetic background (DBA/2, C57BL/6, 129S4)

tag: passages


title: NIH3T3 c-srcY527F-1

source_name: Immortalized embryonic fibroblasts_pBabe-Puro containing c-srcY527F

value: pBabe-Puro containing c-srcY527F


title: iPS_178B5

source_name: Induced prulipotent stem cells


title: ΔDL, input

description: rep1 and 2

source_name: Klf3-/- murine embryonic fibroblasts, rescued with ΔDL-V5

value: Klf3-/- rescued with delta-DL-V5


title: DBD, input

description: rep1 and 2


title: ΔDL, immunoprecipitation

description: rep1 and 2

value: anti-V5 antibody (Cat# R960-CUS, Life Technologies, Carlsbad, CA)


title: GM10847_H3K27me3_1

tag: replicate


title: iPS_492B4


title: NIH3T3 c-srcY527F-2


title: KLF3, immunoprecipitation

description: rep1 and 2

source_name: Klf3-/- murine embryonic fibroblasts, rescued with Klf3-V5

value: Klf3-/- rescued with Klf3-V5


title: NIH3T3 c-srcY527F-3


title: KLF3, input

description: rep1 and 2


title: ES

source_name: Embryonic stem cells


title: MEF_AdapterB


title: iPS_AdapterA


title: iPS_AdapterB


title: NIH3T3 pBabe-puro-2


title: MEF_AdaptorA


title: GM19204

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

data_processing:
Reads were aligned to the genome using BWA v0.5.9.
Reads not mapping to the genome, mapping ambiguously, or mapping with a quality score less than 10 were filtered out with SAMtools v0.1.18.
The number of reads overlapping a single exon from a defined set of orthologous exons (available at http://gilad.uchicago.edu/orthoExon) were counted.
The read counts were used to calculate the reads per kilobase per million mapped reads (RPKM).
To facilitate comparisons with mass spec. data, the RPKM measures for an internal reference cell line (GM19238) were used to calculate a log2-ratio of expression measurements.
Genome_build: hg19, panTro3 and rheMac2
Supplementary_files_format_and_content: .txt files: Each line represents a gene. Column 1 contains the Ensembl gene ID. Column 2 contains the RPKM measure for that gene in that individual.

growth_protocol: Cells were cultured in RPMI-1640 media supplemented with 15% FBS, 2mM L-glutamine, 100 IU/mL penicillin and 100ug/mL streptomycin. Cells were incubated at 37°C with 5% CO2 . Cells were split every 2-3 days.

extract_protocol: RNA was extracted using the Qiagen RNeasy Mini kit. Libraries were constucted with the Illumina TruSeq kit.  Libraries were subsequently sequenced on a Hi-Seq 2000 by standard protocol.

value: lymphoblastoid cell line

tag: gender

value: Female


title: GM18516

value: Male


title: GM19238


title: GM19193


title: Cybrid_control_RNAseq_rep1

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: polyA RNA


title: Cybrid_control_RP_rep1

value: Cybrid


title: Cybrid_tRNA_Trp_5556GA_RP_rep1

value: other


title: GM18505


title: Cybrid_tRNA_Trp_5556GA_RNAseq_rep1


title: BJ_RP_rep1

source_name: Foreskin fibroblast

value: Foreskin fibroblast

value: BJ


title: BJ_RP_rep2


title: 12h_MM1S_20nM_bortezomib_ribosome_footprint

city: San Francisco

first: Arun

middle: P.

last: Wiita

state: CA

address: 185 Berry St., Suite 290

department: Laboratory Medicine

institute: University of California, San Francisco

data_processing:
Base-calling: CASAVA v. 1.7
Demultiplexing: Sample barcodes and linker-1 sequence were removed from reads using in-house Python script (raw data files provided after this step)
Alignment: bowtie v.0.7 with up to two mismatches allowed. Reads were first aligned versus human rRNA sequences and tRNA sequences with only unaligned sequenced carried through for analysis. Reads were then aligned versus canonical transcripts from build hg19 (UCSC) and unaligned reads were aligned against the full hg19 build.
Read assignment to transcripts: in-house C++ script. Only reads uniquely mapping to a single location in a canonical hg19 transcript were included for analysis.
Read normalization: RPKM based on total number of uniquely assigned reads from in-house C++ script and hg19 canonical transcript length (processed file provided after this step)
Genome_build: hg19
Supplementary_files_format_and_content: raw reads and RPKM values in attached Excel files indicate read assignments to each UCSC transcript identifier

source_name: MM1.S myeloma cell line

extract_protocol:
Ribosome footprints were isolated from 80S ribosomes by ultracentrifugation followed by gel-based size selection, as previously described (Ingolia et al, Cell 2011). Poly(A) mRNA was isolated using poly-d(T) coated magnetic beads, then size-selected by PAGE after alkaline fragmentation.
Libraries were constructed as previously described (Ingolia et al, 2011). Briefly, size-selected ribosome footprint and poly(A) mRNA fragments were ligated to Linker-1 oligonucleotide (IDT) by T4 RNA ligase following PNK dephosphorylation. Ligated RNA was purified after gel-based separation.  Reverse transcription to cDNA was carried out using SuperScript III enzyme. cDNA fragments were purified after gel-based separation. Ribosomal RNA subtraction was performed on ribosome footprint samples using biotinylated oligonucleotides (listed in Stern-Ginossar et al, Science 2012) and streptavidin-coated magnetic beads.  Samples were circularized using Circ Ligase (Epicentre) and PCR amplified using primers containing Illumina barcodes for final libraries. Up to four samples were multiplexed in a single lane for sequencing.

treatment_protocol: 0h samples untreated, all others 20 nM bortezomib treated. Ribosome footprint samples treated with 0.1 mg/mL cycloheximide for 1 min immediately prior to harvesting.

tag: cycloheximide

value: 0.1 mg/mL cycloheximide

tag: time point

value: ribosome footprint


title: 9h_MM1S_20nM_bortezomib_ribosome_footprint


title: 12h_MM1S_20nM_bortezomib_polyA_mRNA

value: poly(A) mRNA


title: BJ_RNAseq_rep1


title: 6h_MM1S_20nM_bortezomib_polyA_mRNA


title: 3h_MM1S_20nM_bortezomib_ribosome_footprint


title: 6h_MM1S_20nM_bortezomib_ribosome_footprint


title: 9h_MM1S_20nM_bortezomib_polyA_mRNA


title: AG18358

organism: Pan troglodytes


title: 3h_MM1S_20nM_bortezomib_polyA_mRNA


title: 1.5h_MM1S_20nM_bortezomib_ribosome_footprint


title: 1.5h_MM1S_20nM_bortezomib_polyA_mRNA


title: AG18359


title: 0h_MM1S_untreated_ribosome_footprint

value: 0h (untreated)


title: S003659


title: GM18507


title: 0h_MM1S_untreated_polyA_mRNA


title: PT91


title: S004973


title: BJ_RNAseq_rep2


title: R290-96

organism: Macaca mulatta


title: Sox2 ChIP-seq, Sox2KO Day2

city: Wako

first: Itoshi

last: NIKAIDO

state: Saitama

address: 2-1 Hirosawa

department: Center for Biosystems Dynamics Research

institute: RIKEN

description: Chromatin IP against Sox2, negative control

data_processing:
Basecalls performed using CASAVA version 1.8.2. Sequence reads were aligned to the mouse reference genome (mm9) using Bowtie2 with default parameters. Sequence reads overlapping with repetitive sequences were removed using BedTools and repeat region data from UCSC Genome Browse. Peak Calling was performed using MACS2 with input DNA as a control and with a q-value cutoff of 0.05.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using MACS2. The signals were normalized by sequencing depth of million mapped reads with the --SPMR option.

source_name: 2TS22C ES cells, +Tet, Day 2

growth_protocol: ES cells were maintained in GMEM supplemented with 10% FBS and 1,000 U/ml LIF on gelatin-coated dishes.

extract_protocol: Chromatin was enzymatically sheared into fragments with an average size of 300-500 bp using the ChIP-IT Express Enzymatic Kit (Active Motif). Sequencing libraries were prepared from ChIP DNA according to the manufacturer's protocols. Briefly, ChP DNA was end-repaired, A-tailed, ligated to the adapters, size selected to 200-400 bp and amplified by 18 cycles of PCR.

treatment_protocol: TS cells were induced in GMEM/10% FBS supplemented with 1 ug/ml Tet, 50 ng/ml human FGF4, 2 ug/ml heparin, 10 ng/ml human Activin A and 2 mM L-glutamine on MEF feeders.

tag: treatment

value: Tet

tag: time

value: 2 days

tag: chip antibody

value: Sox2 produced in-house

tag: condition

value: On MEF feeders


title: Sox2 ChIP-seq, Oct3/4KO Day2

description: Chromatin IP against Sox2

source_name: ZHBTc4 ES cells, +Tet, Day 2

value: On MEF feeders, with FGF4/heparin/Activin A


title: 150-99

tag: cell type

value: lymphoblastoid cell line


title: R249-97


title: Sox2 ChIP-seq, Oct3/4KO Day4

description: Chromatin IP against Sox2

source_name: ZHBTc4 ES cells, +Tet, Day 4

tag: cell line

value: 4 days


title: Sox2 ChIP-seq, Oct3/4KO Day3

description: Chromatin IP against Sox2

source_name: ZHBTc4 ES cells, +Tet, Day 3

tag: strain

value: 3 days


title: 265-95

value: Male


title: rCGG_Cb_5hmC_3

city: Atlanta

first: Bing

last: Yao

state: GA

address: 615 Michael St. Rm 323

department: Human Genetics

institute: Emory University

data_processing:
FASTQ sequence files from biological replicates were separately aligned to mouse NCBI37v1/ mm9 references using Bowtie 0.12.9.
Each unique mapped read (.bed files) with no more than 2 mismatches in the first 25 bp were generated by in house script
Unique mapped reads were sorted by in house script
We used Model-based Analysis of ChIP-Seq (MACS) software to identify DhMRs between wild-type and rCGG mice by directly comparing one to the other, rather than comparing to the input. The effective genome size = 1.87 × 109, tag size = 38, bandwidth = 200, P value cutoff = 1.00 × 10−5.
Identified wild-type- and rCGG-specific DhMRs were annotated to various genomic regions and associated genes by HOMER (Hypergeometric Optimization of Motif EnRichment) software
Genome_build: mm9
Supplementary_files_format_and_content: MACS_peaks

source_name: Cerebellum

extract_protocol:
Cerebella samples were homogenized on ice by 2 ml Dounce tissue grinder in lysis buffer (100 mM Tris-HCl (pH 8.5), 5 mM EDTA, 0.2% SDS (vol/vol), 200 mM NaCl). Proteinase K was freshly added to the buffer, and samples were kept at 55°C overnight. An equal volume of phenol:chloroform:isoamyl alcohol (25:24:1, saturated with 10 mM Tris (pH 8.0) and 1 mM EDTA; P-3803, Sigma) was added at the second day, mixed completely, and centrifuged at top speed on desktop centrifugation for 10 min. Supernatant was then mixed with an equal volume of isopropanol to precipitate DNA. DNA pellets were washed with 70% ethanol and eluted with 10 mM Tris-HCl (pH 8.0). Chemical labeling-based 5hmC enrichment was applied. Briefly, DNA was sonicated to 100-500 bp, and then mixed with 100-μl solution containing 50 mM HEPES buffer (pH 7.9), 25 mM MgCl2, 250 μM UDP-6-N3-Glu, and 2.25 μM wild-type β-glucosyltransferase. Reactions were incubated for 1 h at 37°C. DNA substrates were purified via Qiagen DNA purification kit. 150 μM dibenzocyclooctyne modified biotin was then added to the purified DNA, and the labeling reaction was performed for 2 h at 37°C. The biotin-labelled DNA was enriched by Streptavidin-coupled Dynabeads (Dynabeads® MyOne™ Streptavidin T1, Life Technologies) and purified by Qiagen DNA purification kit.
5hmC-captured libraries were generated by the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina according to the manufacturer's protocol. In short, 25 ng of input genomic DNA or 5hmC-captured DNA were used. DNA fragments between 150 and 300 bp were gel-purified after the adapter ligation step. An Agilent 2100 BioAnalyzer was used to quantify the amplified DNA. 20-pM diluted libraries were eventually used for sequencing. We performed 38-cycle single-end sequencing using Version 4 Cluster Generation and Sequencing Kits (Part #15002739 and #15005236 respectively) and Version 7.0 recipes. Image processing and sequence extraction were done using the standard Illumina Pipeline.

tag: age

value: 16 weeks

value: FXTAS


title: rCGG_Cb_5hmC_1


title: rCGG_Cb_5hmC_2


title: wildtype_littermate_Cb_5hmC_3

value: wildtype


title: Sox2 ChIP-seq, Oct3/4KO Day0

description: Chromatin IP against Sox2

source_name: ZHBTc4 ES cells, untreated

value: control

value: 0 day


title: wildtype_littermate_Cb_5hmC_1


title: HTS345 H3K9ac_ChIPSeq

status: Public on Oct 16 2013

city: Corvallis

first: Kristina

middle: M

last: Smith

state: OR

department: Biochemisty and Biophysics

institute: Oregon State University

data_processing:
Basecalls were made with RTA1.8_CASAVA1.7
ChIPSeq reads were trimmed of adapter sequence and mapped to v2 of the Fusarium fujikuroi genome with BWA software using default options
samtools were used to convert BWA output to sorted bam files, and BEDTools bamToBed was used to convert alignment files to bed format
EpiChIP_V0.9.7-e3.jar was used to calculate normalized locus chromatin state (NLCS) values for each gene. Window size was each gene without upstream or downstream sequence.
Genome_build: Fusarium fujikuroi v2
Supplementary_files_format_and_content: Files are tab delimited .txt files with columns Gene name, chromosome, bases (length of gene) and NLCS value.

organism: Fusarium fujikuroi

source_name: mycelium

growth_protocol: Cells were pre-cultivated for 72 hours in Darken medium, then 500 µl of the pre-culture was inoculated into 100 ml ICI medium with either 6 mM or 60 mM glutamine for additional 72 hours.

extract_protocol:
Lysates were clarified from sonicated mycelial tissue and histone-DNA complexes were isolated with antibody.
DNA obtained by ChIP was end-repaired and ligated to adapters as described in Pomraning KR, Smith KM, Bredeweg EL, Connolly LR, Phatale PA, et al. (2012) Library preparation and data analysis packages for rapid genome sequencing. Methods Mol Biol 944: 1-22.

tag: glutamine

value: 60 mM

tag: antibody


title: wildtype_littermate_Cb_5hmC_2


title: HTS333 H3K9ac_ChIPSeq

value: 6 mM


title: HTS326 H3K9me3_ChIPSeq


title: HTS363 H3K4me2_ChIPSeq


title: untreated 3

city: Vancouver

first: Christopher

last: Fjell

state: BC

address: Room 166 - 1081 Burrard Street

department: Medicine

country: Canada

institute: University of British Columbia

description:
count_6
untreated

data_processing:
convert to sequence CASAVA 1.7 (Illumina)
map sequence to genpme with tophat 1.0, bowtie 0.12.7
mapped to genes using R package GenomicRanges 2.12.1
Genome_build: Genome Reference Consortium release GRCh37.rel59
Supplementary_files_format_and_content: Format is three columns tab-delimited, for Ensembl gene ID, gene transcript counts, and normalized counts as rpmkm. First line is a header is ID, count, rpmkm.

source_name: monocytes from healthy volunteers

extract_protocol: RNA was isolated from cell lysates using the Qiagen RNA Isolation Kit (Qiagen, Valencia, CA), as per the manufacturerâ??s instructions, treated with RNase free DNase (Qiagen, Valencia, CA), and eluted in RNase-free water (Ambion, Austin, TX). The RNA concentration was assessed using a NanoDrop spectrophotometer, while RNA integrity and purity was determined by Agilent 2100 Bioanalyzer using RNA Nano kits (Agilent technologies). 500 ng of totalÂ RNAÂ was processed according to the Illumina TruSeqÂ RNAÂ sample preparation guide (Illumina catalogue number FC-122-1002). Briefly, mRNA was purified using poly-dT beads, followed by synthesis of the first and second cDNA strands, end repair addition of an poly-A overhang, and ligation of adapters and unique barcodes, as per the manufacturerâ€™s instructions. DNA enrichment was carried out via a 15-cycle PCR. Following quantification, 8 pM of dsDNA was used for cluster generation on a CBOT instrument (Illumina, San Diego, CA).Â

treatment_protocol: isolated from 3 healthy donors, and left unstimulated  or stimulated for 4 hours with 20 μg/ml IDR-1018.

value: monocytes

value: untreated

tag: disease status

value: healthy volunteers


title: 4 hours with 20 μg/ml IDR-1018 3

description:
count_7
4 hours with 20 μg/ml IDR-1018


title: untreated 2

description:
count_4
untreated


title: 4 hours with 20 μg/ml IDR-1018 2

description:
count_5
4 hours with 20 μg/ml IDR-1018


title: 4 hours with 20 μg/ml IDR-1018 1

description:
count_3
4 hours with 20 μg/ml IDR-1018


title: Input_Spermatocytes_2

status: Public on Oct 15 2013

data_processing:
Sequence reads of 50+35 bp reads were produced with a SOLiDTM 4 sequencer, according to standard Life Technologies protocols. The sequence reads were analyzed with the BioScope™ software suite (cms_4448431.pdf).
After sequence read mapping to version 9 build 37 of the mouse genome allowing up to 4 mismatches, only reads mapping once to the genome were retained for subsequent analyses, to prevent spurious calls in repetitive regions.
Four BAM files were generated by the Bioscope pipeline, corresponding to the two biological conditions (P, anti-ha ChIP-seq from premeiotic spermatocytes and R, anti-ha ChIP-seq from postmeiotic, round spermatids), and their respective sonicated DNA inputs.
BAM files were transformed into SAM format (Li et al, 2009; PMID: 19505943).
Genome_build: mm9
Supplementary_files_format_and_content: Bed and wig files were generated using SICER with following parameters : W200, G600, FDR 0.000001 (for WIG) and 0.001 (for BED)

source_name: Male germ cells

treatment_protocol: Spermatogenic cell suspensions from th2b+/tag mice were fractionated using a BSA gradient and pooled fraction of spermatocytes and round spermatids were used for ChIP with an anti-ha antibody exactly as previously reported in (Tan et al, 2011; PMID: 21925322).

value: Spermatocytes (meiotic)

tag: genotype

value: Th2b+/tag mice


title: Th2b_ChipSeq_Spermatocytes

value: anti-HA (Abcam, ab9110)


title: Sox2 ChIP-seq, Oct3/4KO Day1

description: Chromatin IP against Sox2

source_name: ZHBTc4 ES cells, +Tet, Day 1

value: Tet

value: 1 day

value: Sox2 produced in-house

value: On MEF feeders, with FGF4/heparin/Activin A


title: Th2b_ChipSeq_Round spermatids

value: Round spermatids (post-meiotic)


title: untreated 1

description:
count_2
untreated


title: R181-96

value: lymphoblastoid cell line

value: Male


title: Sample_N3

city: Philadelphia

first: Junhyong

last: Kim

state: PA

address: 433 S University Avenue

department: Biology

institute: University of Pennsylvania

description:
The transgenic mice express the fluorescent ubiquitination-based cell cycle indicator,  Fucci  probe mAG-hGem (1/110) driven by the ubiquitously expressed cytomegalovirus (CMV) promoter (Sakaue-Sawano et al. Cell 2008).The fluorescent probe, mAG-hGem (1/110), consisting of a green fluorescent protein, mAG (monomeric Azami Green) fused to ubiquitination domains (110 amino acid residues at the N-terminus) of human DNA replication factor, Geminin (hGem). Male hemizygous (Tg/-) transgenic adult mice were backcrossed with female wildtype C57/BL6  to generate about 50% F1 transgenic and wildtype control littermates.
processed data file: CIRTs_cardio.txt

data_processing:
For dendrite and soma samples Illumina Casave 1.3 software for base-calling
For BAT and cardiomyocyte samples Illumina Casave 1.8.1 software for base-calling
Sequenced reads were trimmed for adaptor sequence, then mapped to mm9 whole genome (for mouse samples) and rn4 whole genome for rat samples using RUM 2.0.3_04 pipeline for the dendritic ans soma sample, RUM 1.09 for BAT samples and RUM 1.11 for cardiomyocytes with default parameters
Reads mapping the intronic regions of genes by paired-end alignment were counted
Genome_build: mm9 for mouse and rn4 for rat
Supplementary_files_format_and_content: tab-delimited text file containing the processed putative cytoplasmically retained intronic contig coordinates along with the #reads mapping to each

extract_protocol:
single cells and dendrites were harvested by mechanical isolation, RNA was extracted using the freeze/thaw method, and aRNA amplified
RNA libraries were prepared for sequencing using standard Illumina protocols

value: transgenic C57BL/6

value: Embryonic 14.5D

tag: tissue

value: Cardiomyocyte

tag: amplification

value: 3x aRNA


title: Sample_N25


title: Sample_N7


title: Sample_N5


title: Sample_N28


title: Sample_N24


title: Input_ChipSeq_Round spermatids_2


title: Sample_N23