title: CD34_WT_TAL1

city: Morgantown

first: Gangqing

last: Hu

state: West Virginia

address: 64 Medical Center Drive

department: MicroBiology, Immunology, and Cell Biology

institute: West Virginia University

description: Chromatin IP against TAL1

data_processing: Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline (Eland). Uniquely mapped reads were kept for each lane, and for positions where multiple reads were mapped, only one read was retained (except for RNA-Seq libraries). The ChIP-enriched peaks were identified by MACS for CTCF, GATA1 and TAL1 (PMID: 18798982) and by SICER for BRG1 (PMID: 19505939). Nucleosome tag enriched regions were identified by the NPS package (PMID: 19014516).

growth_protocol: As described in (Cui et al. Cell Stem Cell. 2009 (PMID: 19128795)

extract_protocol: X-linked CD34 or CD36 cells were sonicated to about 200-500 bp of the DNA fragment to prepare the chromatin templates. Four or eight microgram of antibodies were used to incubate with chromatin templates.  The resulting ChIP-DNA was used for library construction according to the protocol (Cui et al. Cell Stem Cell. 2009 (PMID: 19128795)).  Basically, DNA was end-repaired and ligated with adapters  Ligation products wer amplified with 17 cycles and purified from agrose gel.  DNA concentration was measured before the loading to machine.

tag: condition

value: CD34 WT

tag: vendor

value: Santa cruz biotechnology

tag: batch/lot#


title: CD34_WT_RNASEQ

status: Public on Jul 01 2011

type: SRA

country: USA

description: RNA-Seq

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

extract_protocol: RNA-seq experiments for HSCs and CD36+ cells were carried out as described previously (Chepelev et al. 2009, PMID: 19528076).

treatment_protocol: As described in (Cui et al. Cell Stem Cell. 2009 (PMID: 19128795)


title: CD36_shLuc_RNASEQ

description: RNA-Seq

value: BRG1 KD shLuc control


title: CD36_shBrg1_RNASEQ

description: RNA-Seq

value: BRG1 RNAi KD


title: CD34_WT_Brg1

description: Chromatin IP against BRG1

library_source: genomic

molecule: genomic DNA

tag: antibody


title: CD34_Nucleosome

description: MNase-Seq following crosslink & Mnase


title: CD36_shbrg1_TAL1

description: Chromatin IP against TAL1


title: CD36_shBrg1_CTCF

description: Chromatin IP against CTCF

value: Anti-CTCF

value: Upstate


title: CD36_WT_input

description: Direct sequencing

value: CD36 WT


title: CD36_shLuc_input

description: Direct sequencing


title: CD36_shLuc_TAL1

description: Chromatin IP against TAL1


title: CD36_shBrg1_input

description: Direct sequencing


title: CD36_shluc_Nucleosome

description: MNase-Seq following crosslink & Mnase


title: CD34_WT_input

description: Direct sequencing


title: CD36_shbrg1_GATA1

description: Chromatin IP against GATA1

value: Abcam


title: CD36_shLuc_GATA1

description: Chromatin IP against GATA1


title: CD34_WT_CTCF

description: Chromatin IP against CTCF


title: GR_DMSO_p65KD_ChIPseq

city: Nijmegen

last: Stunnenberg

address: Geert Grooteplein 28

department: Department of Molecular Biology (274)

institute: Radboud University

description: Chromatin IP against GR in p65KD HeLaB2 cells followed by Illumina deep sequencing

data_processing:
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genomes using the Illumina Genome Analyzer Pipeline. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 200 bp to create summary windows.
Normalization: The number of tags in each track was uniformly equalized to the track containing the lower number of tags, for each condition separately
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)

source_name: HeLa B2 cells

growth_protocol: HeLa B2 cells were maintained in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% fetal calf serum (FCS) at 37°C in 5% CO2.

extract_protocol: Chromatin complexes were isolated from ~3.75x106 sonicated nuclei with relevant antibody.  Libraries were prepared according to Illumina's instructions/DNA Sample . 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 14 cycles and library fragments of ~300 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 ChIP-sequencing, chromatin from HeLa B2 cells, hormone starved for 48h and subsequently treated with either DMSO or 1µM TA for 4h with or without an additional treatment with 10ng/ml TNFα (Sigma) for the last 1h, was used for ChIP with antibodies against human GR, p65, RNAPII and p300.

tag: cell type

value: immortal cervical cancer cell

tag: cell line

value: HeLa B2

value: anti GR

tag: antibody catalog

tag: antibody manufacturer

value: Diagenode

tag: treatment

value: DMSO

tag: genotype/variation


title: RNAPII_TA_WT_ChIPseq

description: Chromatin IP against RNAPII in WT HeLaB2 cells followed by Illumina deep sequencing

value: anti RNAPII

value: TA

value: WT


title: RNAPII_TA+TNFα_WT_ChIPseq

value: TA+TNFα


title: GR_TA+TNFα_p65KD_ChIPseq


title: p65_TA+TNFα_p65KD_ChIPseq

description: Chromatin IP against p65 in p65KD HeLaB2 cells followed by Illumina deep sequencing

value: anti p65

value: Santa Cruz Biotechnologies


title: p65_DMSO_p65KD_ChIPseq


title: p65_TA+TNFα_WT_ChIPseq

description: Chromatin IP against p65 in WT HeLaB2 cells followed by Illumina deep sequencing


title: RNAPII_TNFα_WT_ChIPseq

value: TNFα


title: p65_TNFα_WT_ChIPseq


title: CD36_WT_Brg1

description: Chromatin IP against BRG1


title: CD36_shLuc_CTCF

description: Chromatin IP against CTCF

value: BRG1 KD shLuc control


title: p65_DMSO_WT_ChIPseq


title: p65_DMSO_GRKD_ChIPseq

description: Chromatin IP against p65 in GRKD HeLaB2 cells followed by Illumina deep sequencing

value: GRKD


title: p65_TA+TNFα_GRKD_ChIPseq


title: p65_TA_WT_ChIPseq


title: CD36_shbrg1_Nucleosome

description: MNase-Seq following crosslink & Mnase

value: BRG1 RNAi KD


title: GR_TA+TNFα_WT_ChIPseq

description: Chromatin IP against GR in WT HeLaB2 cells followed by Illumina deep sequencing


title: RNAPII_DMSO_WT_ChIPseq


title: GR_TNFα_WT_ChIPseq


title: GR_TA+TNFα_GRKD_ChIPseq

description: Chromatin IP against GR in GRKD HeLaB2 cells followed by Illumina deep sequencing


title: Human ES cells replicate 2 - mRNA run 3

city: St Lucia

first: Sean

last: Grimmond

state: Q

address: Services Rd

department: Institute for Molecular Bioscience

country: Australia

institute: University of Queensland

description: mRNA from human ES cells

data_processing: Raw data processed with Bioscope 1.2

molecule: total RNA

source_name: human ES cells

growth_protocol: HES2 cells were cultured as per Kolle et al., stem cells 2009

extract_protocol: Solid Whole transcriptome analysis Kit - RNA fragmented to ~100bp, RNA-DNA hybrid adaptors ligated, cDNA made, PCR amplified and gel purified

treatment_protocol: cells were treated with cycloheximide for 10 minutes prior to harvesting (Kolle et al., 2009)

tag: strain


title: Human ES cells replicate 2 - mRNA run 2

description: mRNA from human ES cells


title: Human ES cells replicate 2 - mRNA run 1

description: mRNA from human ES cells


title: Human ES cells replicate 1 - mRNA run2

description: mRNA from human ES cells


title: Human ES cells replicate 2 - mRNA run 6

description: mRNA from human ES cells


title: Human ES cells replicate 2 - mRNA run 5

description: mRNA from human ES cells


title: Human ES cells replicate 2 - mRNA run 4

description: mRNA from human ES cells


title: Human ES cells replicate 2 - mRNA run 7

description: mRNA from human ES cells


title: Human ES cells replicate 1 - cytosol polysome associated polysome fractionation - run2

description: cytosol associated RNA from human ES cells


title: Human ES cells replicate 1 - cytosol polysome associated polysome fractionation - run1


title: GR_TA_WT_ChIPseq


title: GR_DMSO_WT_ChIPseq


title: Human ES cells replicate 2 - cytosol polysome associated polysome fractionation - run1


title: Human ES cells replicate 1 - membrane polysome associated polysome fractionation - run2

description: membrane associated RNA from human ES cells


title: Human ES cells replicate 2 - cytosol polysome associated polysome fractionation - run2


title: Human ES cells replicate 2 - membrane polysome associated polysome fractionation - run2


title: Human ES cells replicate 1 - membrane polysome associated polysome fractionation - run1


title: Human ES cells replicate 2 - membrane polysome associated polysome fractionation - run1


title: GR_DMSO_GRKD_ChIPseq


title: sch9-as dot6 tod6 SDS3-TAP

city: Lausanne

first: Jacques

last: Rougemont

address: Station 15

department: School of Life Sciences

country: Switzerland

institute: EPFL

description:
1e
Chromatin IP for TAP tag. The bait proteins were tagged with Protein A (TAP tag), which binds to rabbit IgG via their constant fragment.

data_processing: Sequencing reads were mapped on the SGD1.01 (sacCer2 build) genome assembly using Bowtie 0.12.1 (Langmead et al, 2009) with parameters -n 3 --best --strata --solexa1.3-quals -a -m 20 and viewed with the USCS Genome Browser (Kent et al, 2002). Libraries sequencing and reads alignment to the yeast genome are summarized in table S7. The MACS algorithm v 1.7.3.1 (Zhang et al, 2008) was used to detect Sds3-TAP binding peaks by comparing the mapped read counts obtained from the sch9as SDS3-TAP vs. the untagged sch9as strains with parameters --mfold=2 --pvalue=1e-5.

organism: Saccharomyces cerevisiae

source_name: sch9-as dot6 tod6 SDS3-TAP nucleus

growth_protocol: Exponential growth in YPD at 30C.

extract_protocol: Libraries were prepared using ChIP-Seq sample preparation kits (Illumina) according to the manufacturer's instructions. DNA fragments ends were repaired using a mix of Klenow DNA polymerase, T4 DNA polymerase and T4 polynucleotide kinase. DNA was then purified and 3' A overhangs were added using a Klenow fragment (3' to 5' exo minus). DNA was purified again and ligated to adapters. 190 ± 10bp fragments were selected using the E-Gel SizeSelect system (Invitrogen) and purified. Fragments with adapters were finally enriched with 18 cycles of PCR and purified. High-throughput sequencing of libraries was performed on a Genome Analyzer IIx machine (Illumina), each in a separate channel.

treatment_protocol: 20 min treatment with 300 nM 1NM-PP1.

tag: genotype

value: TB50alpha sch9-as::pRS304 dot6::KanMX6 tod6::BleMX6 SDS3-TAP::HIS3MX6

tag: tissue

value: nucleus

value: 300 nM 1NM-PP1 20 min


title: sch9-as stb3 dot6 tod6 SDS3-TAP

description:
1f
Chromatin IP for TAP tag. The bait proteins were tagged with Protein A (TAP tag), which binds to rabbit IgG via their constant fragment.

source_name: sch9-as stb3 dot6 tod6 SDS3-TAP nucleus

value: TB50alpha sch9-as::pRS304  stb3::NatMX4 dot6::KanMX6 tod6::BleMX6 SDS3-TAP::HIS3MX6


title: sch9-as stb3 SDS3-TAP

description:
1d
Chromatin IP for TAP tag. The bait proteins were tagged with Protein A (TAP tag), which binds to rabbit IgG via their constant fragment.

source_name: sch9-as stb3 SDS3-TAP nucleus

value: TB50alpha sch9-as::pRS304 stb3::NatMX4 SDS3-TAP::HIS3MX6


title: SCH9 STB3-TAP

description:
2b
Chromatin IP for TAP tag. The bait proteins were tagged with Protein A (TAP tag), which binds to rabbit IgG via their constant fragment.

source_name: SCH9 STB3-TAP nucleus


title: sch9-as, rep2

description:
2a
Chromatin IP for TAP tag. The bait proteins were tagged with Protein A (TAP tag), which binds to rabbit IgG via their constant fragment.

source_name: sch9-as nucleus

value: TB50alpha sch9-as::pRS304


title: SCH9 SDS3-TAP

description:
1b
Chromatin IP for TAP tag. The bait proteins were tagged with Protein A (TAP tag), which binds to rabbit IgG via their constant fragment.

source_name: SCH9 SDS3-TAP nucleus


title: sch9-as sds3 + PP1

description: mRNA (polyA+)

data_processing: Reads were mapped to unique portions of the transcriptome of S. cerevisiae. Their numbers for each mRNA was normalized to the total number of aligned reads and to the length of the unique sequence of the mRNA.

source_name: sch9-as sds3 whole cells, PP1

extract_protocol: RNA extracts were purified of genomic DNA contaminations using RNeasy kits (QIAGen). Libraries were prepared from pools of equivalent amounts of RNA from four independent experiments and sequenced using version 4 kits and single read flow cells on a Genome Analyzer IIx machine according to the manufacturerâs instructions (Illumina).

value: TB50alpha sch9-as::pRS304 sds3::HphMX4

value: whole cell

value: 300 nM 1NM-PP1 30 min


title: sch9-as, rep1

description:
1a
Chromatin IP for TAP tag. The bait proteins were tagged with Protein A (TAP tag), which binds to rabbit IgG via their constant fragment.

extract_protocol: Libraries were prepared using ChIP-Seq sample preparation kits (Illumina) according to the manufacturer's instructions. DNA fragments ends were repaired using a mix of Klenow DNA polymerase, T4 DNA polymerase and T4 polynucleotide kinase. DNA was then purified and 3' A overhangs were added using a Klenow fragment (3' to 5' exo minus). DNA was purified again and ligated to adapters. 190 ± 10 bp fragments were selected using the E-Gel SizeSelect system (Invitrogen) and purified. Fragments with adapters were finally enriched with 18 cycles of PCR and purified. High-throughput sequencing of libraries was performed on a Genome Analyzer IIx machine (Illumina), each in a separate channel.


title: Human ES cells replicate 1 - mRNA run1

description: mRNA from human ES cells


title: sch9-as sds3 + DMSO

description: mRNA (polyA+)

source_name: sch9-as sds3 whole cells, DMSO

value: DMSO 30 min


title: sch9-as STB3-TAP

description:
2c
Chromatin IP for TAP tag. The bait proteins were tagged with Protein A (TAP tag), which binds to rabbit IgG via their constant fragment.

source_name: sch9-as STB3-TAP nucleus


title: sch9-as rco1 + PP1

description: mRNA (polyA+)

source_name: sch9-as rco1 whole cells, PP1

value: TB50alpha sch9-as::pRS304 rco1::KanMX6


title: sch9-as rco1 + DMSO

description: mRNA (polyA+)

source_name: sch9-as rco1 whole cells, DMSO


title: sch9-as stb3 dot6 tod6 + PP1

description: mRNA (polyA+)

source_name: sch9-as stb3 dot6 tod6 whole cells, PP1

value: TB50alpha sch9-as::pRS304 stb3::NatMX4 dot6::KanMX6 tod6::BleMX6


title: sch9-as rpd3 + PP1

description: mRNA (polyA+)

source_name: sch9-as rpd3 whole cells, PP1

value: TB50alpha sch9-as::pRS304 rpd3::HphMX4


title: sch9-as stb3 + PP1

description: mRNA (polyA+)

source_name: sch9-as stb3 whole cells, PP1

value: TB50alpha sch9-as::pRS304 stb3::NatMX4


title: sch9-as dot6 tod6 + PP1

description: mRNA (polyA+)

source_name: sch9-as dot6 tod6 whole cells, PP1

value: TB50alpha sch9-as::pRS304 dot6::KanMX6 tod6::BleMX6


title: SCH9 + PP1

description: mRNA (polyA+)

source_name: SCH9 whole cells, PP1

value: TB50alpha SCH9::pRS304


title: sch9-as + DMSO

description: mRNA (polyA+)

source_name: sch9-as whole cells, DMSO


title: sch9-as + PP1

description: mRNA (polyA+)

source_name: sch9-as whole cells, PP1


title: sch9-as stb3 dot6 tod6 + DMSO

description: mRNA (polyA+)

source_name: sch9-as stb3 dot6 tod6 whole cells, DMSO


title: sch9-as stb3 + DMSO

description: mRNA (polyA+)

source_name: sch9-as stb3 whole cells, DMSO


title: sch9-as dot6 tod6 + DMSO

description: mRNA (polyA+)

source_name: sch9-as dot6 tod6 whole cells, DMSO


title: SCH9 + DMSO

description: mRNA (polyA+)

source_name: SCH9 whole cells, DMSO


title: HeLa ELAVL1/HuR siRNA1 5d

status: Public on Jun 30 2011

city: Berlin

first: Marvin

last: Jens

address: Robert Rössle Str. 10 (H. 87)

department: Systems Biology of Gene Regulatory Elements

country: Germany

institute: Max Delbrueck Center for Molecular Medicine

description: 120h post transfection with anti HuR siRNA1

data_processing: No adapter removal was performed. Raw reads were converted to fastq and mapped with TopHat, supplying ENSEMBL splice junctions. Resulting alignments were analyzed by cuffdiff to estimate changes in RefSeq gene model expression.

source_name: HeLa ELAVL1/HuR siRNA1 5d

extract_protocol: Illumina paired end polyA standard protocol, fragment length ~250nt, stddev ~50nt.

value: HeLa

tag: knockdown

value: ELAVL1/HuR siRNA1 (see Lebedeva et. Al 2011)

tag: time post transfection


title: HeLa ELAVL1/HuR siRNA1 2d

description: 48h post transfection with anti HuR siRNA1

source_name: HeLa ELAVL1/HuR siRNA1 2d

value: ELAVL1/HuR  siRNA1 (see Lebedeva et. Al 2011)


title: sch9-as SDS3-TAP

description:
1c
Chromatin IP for TAP tag. The bait proteins were tagged with Protein A (TAP tag), which binds to rabbit IgG via their constant fragment.

source_name: sch9-as SDS3-TAP nucleus

value: nucleus

value: 300 nM 1NM-PP1 20 min


title: bycl

city: Beijing

first: Yu-Xian

last: Zhu

address: 5# Summer Palace Road

country: China

institute: College of life sciences, Peking University

data_processing: The 35nt sequence tags from Illumina GA sequencing went through the data cleaning first, which included getting rid of the low quality tags and several kinds of contaminants from the 35nt tags. All clean tags sequence with its copy number were then summarized into a fasta format file.

organism: Gossypium hirsutum

source_name: fiber, August

extract_protocol: Briefly, after PAGE purification of small RNA molecules under 30 bases and ligation of a pair of adaptors to their 5' and 3' ends, the small RNA molecules were amplified using the adaptor primers for 17 cycles and the fragments around 90 bp (small RNA+adaptors) were isolated from agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina GA according to the manufacturer's instructions.

value: fiber

tag: developmental stage

value: 10 days post anthesis

tag: season (month)

value: August


title: eycl

source_name: fiber, February

value: February


title: HeLa mock knockdown 5d

description: reference sample collected 5 days after treatment with transfection reagents but no siRNA

source_name: HeLa mock knockdown 5d

value: mock


title: HeLa 4SU SILAC PAR-CLIP

description: pull down RNA

data_processing: Adapters were removed with FAR 1.81 (the felxible adapter remover: http://sourceforge.net/projects/theflexibleadap/) aligned to hg18 and a set of RefSeq pre-mRNA sequences with BWA 0.5.8c. Unique alignments were converted to a pileup and read clusters scored for characteristic conversions and read variability with a custom script. After stringent-false positive filtering (using antisense clusters as a decoy database) remaining clusters were output as bed files. See Lebedeva et al. 2011 for details.

source_name: HeLa 4U SILAC PAR-CLIP

extract_protocol: PARCLIP + small RNA Sequencing

value: Santa Cruz

tag: antibody catalog #

tag: culture medium

value: SILAC


title: HeLa 4SU DMEM PAR-CLIP

description: pull down RNA

source_name: HeLa 4SU DMEM PAR-CLIP

value: DMEM


title: HeLa 6SG SILAC PAR-CLIP

description: pull down RNA

source_name: HeLa 6SG SILAC PAR-CLIP


title: sch9-as rpd3 + DMSO

description: mRNA (polyA+)

source_name: sch9-as rpd3 whole cells, DMSO

value: TB50alpha sch9-as::pRS304 rpd3::HphMX4

value: whole cell

value: DMSO 30 min


title: SST_2

status: Public on Jun 29 2011

city: cold spring harbor

first: Miao

last: He

state: new york

address: 1 bungtown road

department: Neuroscience

institute: Cold Spring Harbor Laboratory

data_processing: Raw Illumina sequencing reads were trimmed from 3' linker, filtered for low-quality reads, and collapsed to unique sequences retaining their individual read count information. Unique sequences 18nt or longer in length were mapped to the University of California at Santa Cruz mm9 assembly of the mouse genome using bowtie allowing no mismatch. miRNA annotations were made according to miRbase version 16.[miRNA_annotation.txt is provided as supplementary file on Series records]

organism: Mus musculus

source_name: SST

extract_protocol: Neocortex and cerebellum of  P56 mouse brain were dissected on ice and flash frozen in liquid nitrogen, ground to a fine powder, and resuspend in 10 volume of  ice-cold lysis buffer (10mM HEPES pH7.4, 100mM KCl, 5mM MaCl2, 0.5%NP-40, 1mM DTT, 100U/ml RNasin) containing Roche  Complete proteinase inhibitors, EDTA-free. Tissue suspension was homogenized using glass douncer. Homogenates were centrifuged for 30min at 13,000g, 4C to pellet cell debris and unsolubilized material. Mouse-anti-c-Myc(sc-40, Santa Cruz Biotechnology), mouse-anti-Ago2(2E12-1C9, Abnova) or mouse IgG1(Molipore) conjugated protein G Dynabeads(Invitrogen) were added into supernatant, and the mixture was incubated in  4C with end-over-end rotation for 4 hours. Beads were washed twice with low salt NT2 buffer(50mM Tris.Hcl pH 7.5, 150mM NaCl, 1mM MgCl2, 0.5%NP-40, 1mM DTT, 100U/ml RNasin) and twice with high salt NT2 buffer(50mM Tris.Hcl pH 7.5, 600mM NaCl, 1mM MgCl2, 0.5%NP-40, 1mM DTT, 100U/ml RNasin) and treated with 0.6mg/ml proteinase K for 20min at 55C. RNA was extracted by acid phenochloroform(Ambion), followed by chloroform, and  precipitated  with sodium acetate and  glycoblue(Ambion) in ethanol overnight -80C. RNA pellet was washed once in 75% ethanol and resuspend in water for further application.RNA was successively ligated to 3â and 5â adaptors, gel purified after each ligation, reverse transcribed and PCR amplified using Solexa sequencing primers. PCR product was gel purified, quantified , and sequenced for 36 cycles on  Illumina Genome Analyzer II. Radiolabeled 19nt and 21nt RNA oligos were used to trace RNA for gel purification, and were depleted by PmelI digestion after PCR amplification.

tag: background strain

tag: mouse age

value: Neocortex

tag: number of pooled tissues

tag: ip antibody

value: anti-myc (sc-40, Santa Cruz Biotechnology)


title: NeuroD1_ChIPSeq

city: Vancouver

first: Patrick

last: Plettner

state: BC

address: 100-570 West 7th Avenue

country: Canada

institute: BC Cancer Agency GSC

description: Chromatin IP against NeuroD1

data_processing: Alignment: Sequence reads were mapped to mm9 (NCBI 37) using BWA (v 0.5.7) and default parameters.

source_name: Pancreatic islets_NeuroD1

growth_protocol: Islets were purified by collagenase digestion, filtration through a 70um filter with subsequent hand picking, livers were perfused and homogenized.

extract_protocol: Cells were fixed in 1% formaldehyde and incubated at room temperature (RT) for 10min, prior to the addition of glycine to 0.125M followed by incubation at RT for 5min. Cells were pelleted, washed and resuspended in 500ul ChIP cell lysis buffer (10mM Tris-Cl, pH 8.0, 10mM NaCl, 3mM MgCl2, 0.5% NP-40) containing 1x protease inhibitor cocktail (Thermo Scientific, Waltham, MA, USA). Cells were then rehomogenized, incubated on ice for 5min and repelleted. The pellet was resuspended in 400ul ChIP nuclear lysis buffer (1% SDS, 5mM EDTA, 50mM Tris-Cl, pH 8.1) supplemented with protease inhibitor cocktail tablets (Thermo Scientific). Cells were sonicated in ice-water bath (Sonicator 3000, Misonix, Farmingdale, NY, USA) for 24 cycles of 30s on, 30s off. Samples were pelleted to remove cellular debris and transferred to fresh tubes.

tag: age

value: 8-10 week old

tag: tissue/cell type

value: hand-picked pancreatic islets

tag: chip antibody

value: NeuroD1 (Santa Cruz sc-1084 X lot H1709)


title: MafA_ChIPSeq

description: Chromatin IP against MafA

source_name: Pancreatic islets_MafA

value: MafA (Abcam ab17976 lot 950583)


title: SST_1


title: Neocortex_3

source_name: Neocortex

value: C57BL/6 & BALB/c

value: anti-Ago2 (2E12-1C9, Abnova)


title: H3K9me3_Liver_ChIPSeq

description: Chromatin IP against H3K9me3

value: whole liver

value: H3K9me3 (Abcam ab8898 lot AP248039)


title: PV_2

source_name: PV


title: H3K27me3_Liver_ChIPSeq

description: Chromatin IP against H3K27me3


title: PV_1


title: Neocortex_1


title: H3K9me3_ChIPSeq

description: Chromatin IP against H3K9me3

source_name: Pancreatic islets_H3K9me3


title: Neocortex_2


title: Gad2_3


title: Gad2_2


title: Camk2a_3


title: Camk2a_1


title: Purkinje_3

source_name: Purkinje

value: C57BL/6 & black swiss

value: Cerebellum


title: Purkinje_2


title: Purkinje_1


title: Cerebellum_3

source_name: Cerebellum


title: H3K27me3_ChIPSeq

description: Chromatin IP against H3K27me3

source_name: Pancreatic islets

value: H3K27me3 (Millipore 07-449 lot DAM1641103)


title: Cerebellum_1


title: Cerebellum_2


title: Stam_HRE_Input_1

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

data_processing: For data processing details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwTfbs

source_name: HRE

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRE_Stam_protocol.pdf

extract_protocol: For extraction protocol details see: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=wgEncodeUwTfbs

tag: cell

value: HRE

tag: cell organism

value: Human

tag: cell description

value: Human Renal Epithelial cells (normal)

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

tag: cell sex

value: U

tag: antibody

value: Input

tag: replicate


title: Stam_HL-60_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HL-60_Stam_protocol.pdf

value: Human promyelocytic leukemia cells. (PMID:276884)

value: cancer

value: F


title: Stam_SAEC_CTCF_2

source_name: SAEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:SAEC_Stam_protocol.pdf

value: SAEC

value: Small Airway Epithelial Cells

value: CTCF

tag: antibody description

value: rabbit polyclonal

tag: antibody target description

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendor name

value: Millipore


title: Gad2_1

tag: background strain

tag: mouse age

tag: tissue

value: Neocortex

value: anti-myc (sc-40, Santa Cruz Biotechnology)


title: Camk2a_2

value: C57BL/6 & BALB/c

tag: number of pooled tissues

tag: ip antibody


title: Stam_HCT-116_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:HCT-116_protocol.pdf UW_Stam:HCT116_Stam_protocol.pdf

value: Human

value: colorectal carcinoma (PMID:7214343)

value: endoderm

value: M


title: Stam_AoAF_Input_1

source_name: AoAF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AoAF_Stam_protocol.pdf

value: AoAF

value: aortic adventitial fibroblast cells

value: normal

value: mesoderm

value: Input


title: Stam_HMF_Input_1

source_name: HMF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMF_Stam_protocol.pdf

value: HMF

value: human mammary fibroblasts

value: F


title: Stam_GM12872_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12872_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown


title: Stam_WERI-Rb-1_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:WERI-Rb-1_Stam_protocol.pdf

value: retinoblastoma (PMID:844036)


title: Stam_GM12875_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12875_Stam_protocol.pdf

value: CTCF

value: rabbit polyclonal

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore


title: Stam_BJ_Input_1

source_name: BJ

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:BJ-tert_Stam_protocol.pdf

value: BJ

value: Human

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC.  (PMID:9916803)

value: ectoderm


title: Stam_AG04450_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG04450_Stam_protocol.pdf

value: fetal lung fibroblast

value: normal

value: M


title: Stam_WERI-Rb-1_CTCF_1


title: Stam_HEK293_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

value: embryonic kidney. (PMID:11967234)

value: cancer

value: endoderm

value: U

value: Input


title: Stam_HCFaa_Input_1

source_name: HCFaa

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCFaa_Stam_protocol.pdf

value: HCFaa

value: Human Cardiac Fibroblasts-Adult Atrial

value: F


title: Stam_GM12864_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12864_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown

value: mesoderm

value: CTCF

value: rabbit polyclonal

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.


title: Stam_HPF_Input_1

source_name: HPF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPF_Stam_protocol.pdf

value: HPF

value: Human

value: Human Pulmonary Fibroblasts isolated from lung tissue


title: Stam_MCF-7_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Duke/UNC/UTA/EBI_Open_Chromatin:MCF-7_Crawford_protocol.pdf Yale_TFBS(Farnham):MCF-7_Farnham_protocol.pdf UW_Stam:Stam_15_protocols.pdf

value: mammary gland, adenocarcinoma. (PMID:4357757)


title: Stam_HepG2_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HepG2_protocol.pdf

value: liver carcinoma

value: cancer

value: M


title: Stam_HMEC_Input_1

source_name: HMEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Broad_Histone:HMEC_Bernstein_protocol.pdf Duke/UNC/UTA/EBI_Open_Chromatin:HMEC_Crawford_protocol.pdf UW_Stam:HMEC_Stam_protocol.pdf

value: HMEC

value: Human Mammary Epithelial Cells

value: U

value: Input


title: Stam_GM12865_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12865_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: F


title: Stam_GM12864_Input_1

value: unknown

value: mesoderm


title: Stam_GM12874_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12874_Stam_protocol.pdf

value: CTCF

value: rabbit polyclonal

value: Millipore


title: Stam_HMEC_CTCF_1

value: Human

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.


title: Stam_BJ_CTCF_2

value: BJ

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC.  (PMID:9916803)

value: normal

value: ectoderm


title: Stam_HCPEpiC_Input_1

source_name: HCPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCPEpiC_Stam_protocol.pdf

value: HCPEpiC

value: Human Choroid Plexus Epithelial Cells


title: Stam_HRPEpiC_Input_1

source_name: HRPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRPEpiC_Stam_protocol.pdf

value: HRPEpiC

value: Human Retinal Pigment Epithelial Cells

value: U


title: Stam_HUVEC_Input_1

source_name: HUVEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HUVEC_protocol.pdf

value: HUVEC

value: umbilical vein endothelial cells

value: Input


title: Stam_AG10803_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG10803_Stam_protocol.pdf

value: abdominal skin fibroblasts from apparently heathly 22 year old

value: "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell

value: mesoderm

value: M

value: CTCF


title: Stam_HPAF_CTCF_2

source_name: HPAF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPAF_Stam_protocol.pdf

value: HPAF

value: Human

value: Human Pulmonary Artery Fibroblasts

value: rabbit polyclonal

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore


title: Stam_NHEK_CTCF_2

source_name: NHEK

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Keratinocyte_protocol.pdf

value: NHEK

value: epidermal keratinocytes

value: normal

value: ectoderm

value: F


title: Stam_AG09309_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09309_Stam_protocol.pdf

value: adult toe fibroblast from apparently healthy 21 year old

value: "7% of the cells examined showing random chromosome loss/gain" -Coriell


title: Stam_HUVEC_CTCF_2

value: HUVEC

value: umbilical vein endothelial cells

value: U


title: Stam_Caco-2_CTCF_1

value: cancer

value: endoderm

value: M

value: CTCF


title: Stam_HBMEC_Input_1

source_name: HBMEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HBMEC_Myers_protocol.pdf

value: HBMEC

value: Human

value: Human Brain Microvascular Endothelial Cells

value: Input


title: Stam_HCPEpiC_CTCF_2

value: HCPEpiC

value: Human Choroid Plexus Epithelial Cells

value: rabbit polyclonal

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore


title: Stam_NHEK_Input_1

value: NHEK

value: epidermal keratinocytes

value: normal

value: ectoderm

value: F


title: Stam_GM12874_CTCF_2

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown

value: mesoderm


title: Stam_GM12874_Input_1

value: M


title: Stam_HCM_Input_1

source_name: HCM

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCM_Stam_protocol.pdf

value: HCM

value: Human

value: Human Cardiac Myocytes

value: U


title: Stam_HeLa-S3_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HeLa-S3:HeLa-S3_protocol.pdf HeLa-S3_IFN_Crawford:HeLa-S3_IFN_Crawford_protocol.pdf

value: cervical carcinoma

value: cancer

value: CTCF


title: Stam_AoAF_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AoAF_Stam_protocol.pdf

value: AoAF

value: aortic adventitial fibroblast cells

value: rabbit polyclonal

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore


title: Stam_HRE_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRE_Stam_protocol.pdf

value: HRE

value: Human Renal Epithelial cells (normal)

value: normal


title: Stam_AG10803_Input_1

value: abdominal skin fibroblasts from apparently heathly 22 year old

value: "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell

value: mesoderm

value: Input


title: Stam_K562_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/K562_protocol.pdf

value: Human

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: F


title: Stam_GM06990_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

value: Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment:Epstein-Barr Virus transformed


title: Stam_GM12873_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12873_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown

value: CTCF


title: Stam_AG09319_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09319_Stam_protocol.pdf

value: gum tissue fibroblasts from apparently heathly 24 year old

value: rabbit polyclonal


title: Stam_HeLa-S3_CTCF_1

value: cervical carcinoma

value: cancer

value: ectoderm

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore


title: Stam_GM12875_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12875_Stam_protocol.pdf


title: Stam_HEEpiC_CTCF_2

source_name: HEEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HEEpiC_Stam_protocol.pdf

value: HEEpiC

value: Human Esophageal Epithelial Cells

value: endoderm

value: U


title: Stam_HCFaa_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCFaa_Stam_protocol.pdf

value: HCFaa

value: Human

value: Human Cardiac Fibroblasts-Adult Atrial


title: Stam_AG09319_CTCF_2

value: normal

value: mesoderm

value: F


title: Stam_GM12865_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12865_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown

value: CTCF


title: Stam_HRE_CTCF_1

value: HRE

value: Human Renal Epithelial cells (normal)

value: rabbit polyclonal


title: Stam_HeLa-S3_Input_1

value: cervical carcinoma

value: cancer

value: ectoderm

value: Input


title: Stam_NHDF-neo_Input_1

source_name: NHDF-neo

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:NHDF-neo_Stam_protocol.pdf

value: NHDF-neo

value: Neonatal Human Dermal Fibroblasts

value: U


title: Stam_GM12865_CTCF_1

value: Human

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore


title: Stam_HPF_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPF_Stam_protocol.pdf

value: HPF

value: Human Pulmonary Fibroblasts isolated from lung tissue


title: Stam_K562_Input_1

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: mesoderm

value: F


title: Stam_HepG2_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HepG2_protocol.pdf

value: liver carcinoma

value: endoderm

value: M

value: CTCF


title: Stam_HBMEC_CTCF_1

value: HBMEC

value: Human Brain Microvascular Endothelial Cells

value: rabbit polyclonal


title: Stam_AG09309_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09309_Stam_protocol.pdf

value: adult toe fibroblast from apparently healthy 21 year old

value: "7% of the cells examined showing random chromosome loss/gain" -Coriell

value: Input


title: Stam_NB4_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Yale_TFBS:NB4_protocol.pdf UW_Stam:NB4_Stam_protocol.pdf

value: Human

value: acute promyelocytic leukemia cell line. (PMID:1995093)

value: cancer

value: U


title: Stam_AG10803_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG10803_Stam_protocol.pdf

value: abdominal skin fibroblasts from apparently heathly 22 year old

value: "8% of the cells examined showing random chromosome loss, 2% showing random chromosome gain, and 2% showing 69,XYY" -Coriell

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore


title: Stam_HA-sp_Input_1

source_name: HA-sp

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HA-sp_Stam_protocol.pdf

value: HA-sp

value: Human astrocytes spinal cord

value: normal

value: Astrocytic


title: Stam_HCF_Input_1

source_name: HCF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCF_Stam_protocol.pdf

value: HCF

value: Human Cardiac Fibroblasts

value: mesoderm


title: Stam_HCPEpiC_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HCPEpiC_Stam_protocol.pdf

value: HCPEpiC

value: Human Choroid Plexus Epithelial Cells

value: CTCF

value: rabbit polyclonal


title: Stam_HEEpiC_CTCF_1

value: HEEpiC

value: Human

value: Human Esophageal Epithelial Cells

value: endoderm


title: Stam_HBMEC_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HBMEC_Myers_protocol.pdf

value: HBMEC

value: Human Brain Microvascular Endothelial Cells

value: U

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.


title: Stam_HPAF_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPAF_Stam_protocol.pdf

value: HPAF

value: Human Pulmonary Artery Fibroblasts

value: Input


title: Stam_GM06990_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

value: Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment:Epstein-Barr Virus transformed

value: normal

value: F

value: Millipore


title: Stam_NHEK_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/Keratinocyte_protocol.pdf

value: NHEK

value: epidermal keratinocytes

value: ectoderm

value: CTCF


title: Stam_GM12878_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/GM12878_protocol.pdf

value: Human

value: lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: mesoderm

value: rabbit polyclonal


title: Stam_GM06990_CTCF_2


title: Stam_HVMF_Input_1

source_name: HVMF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HVMF_Stam_protocol.pdf

value: HVMF

value: Human Villous Mesenchymal Fibroblast Cells

value: U


title: Stam_AG04449_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG04449_Stam_protocol.pdf

value: fetal buttock/thigh fibroblast

value: M


title: Stam_GM12878_CTCF_1

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.


title: Stam_GM12801_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12801_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment:Epstein-Barr Virus transformed

value: unknown

value: Input


title: NHEK_PolII_REP1

city: Chapel Hill

first: Terry

last: Furey

state: NC

address: 5022 Genetic Medicine Building, CB#7264

department: Genetics

institute: UNC-Chapel Hill

description: Chromatin IP against Pol2

data_processing: Sequences from each experiment were aligned to the genome (hg18) using Maq (Li et al., 2008) and those that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes). The resulting digital signal was converted to a continuous wiggle track using F-Seq (http://www.genome.duke.edu/labs/furey/software/fseq/) that employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Discrete sites (peaks) were identified from DNase-seq using by setting a F-Seq score cutoff based on fitting these data to a gamma distribution and determining the threshold at a p-value of 0.05.

growth_protocol: Cells were grown according to the approved ENCODE cell culture protocols.Specific protocol descriptions can be found at http://genome.ucsc.edu/ENCODE/cellTypes.html.

extract_protocol:
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 3â 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.
ChIP was performed by cross-linking proteins to DNA using 1% formaldehyde solution (Bhinge et al. 2007; Birney et al. 2007). Immunoprecipitated DNA were sequenced using Illumina sequencers, (ChIP-seq). Input sequencing data were generated for GM12878, K562, HeLa-S3, HepG2, and HUVEC by cross-linking chromatin, shearing and reversing cross-links without immunoprecipitating.

tag: cell line

value: NHEK

tag: cell type

value: normal epidermal keratinocytes

value: Covance


title: NHEK_cMYC_REP1

description: Chromatin IP against c-Myc

value: Santa Cruz


title: K562_PolII_REP2

description: Chromatin IP against Pol2

value: chronic myeloid leukemia


title: K562_PolII_REP1

description: Chromatin IP against Pol2


title: K562_INPUT

description: Chromatin Input


title: K562_cMYC_REP3

description: Chromatin IP against c-Myc


title: Stam_SK-N-SH_RA_Input_1

tag: cell

tag: cell organism

value: Human

value: neuroblastoma cell line, treatment:differentiated with retinoic acid. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: cancer

value: ectoderm

value: F


title: HUVEC_INPUT

description: Chromatin Input

value: HUVEC

value: umbilical vein endothelial cells


title: HUVEC_PolII_REP2

description: Chromatin IP against Pol2


title: K562_cMYC_REP1

description: Chromatin IP against c-Myc


title: Stam_HEEpiC_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HEEpiC_Stam_protocol.pdf

value: HEEpiC

tag: cell description

value: Human Esophageal Epithelial Cells

value: endoderm

value: U


title: HUVEC_cMYC_REP1

description: Chromatin IP against c-Myc


title: Stam_HPF_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPF_Stam_protocol.pdf

value: HPF

value: Human Pulmonary Fibroblasts isolated from lung tissue

value: CTCF

value: rabbit polyclonal

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore


title: K562_cMYC_REP2

description: Chromatin IP against c-Myc

value: chronic myeloid leukemia

value: Santa Cruz


title: Stam_AG04450_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG04450_Stam_protocol.pdf

value: Human

value: fetal lung fibroblast

tag: cell karyotype

value: normal

tag: cell lineage

value: mesoderm

value: M

value: Input


title: HUVEC_PolII_REP1

description: Chromatin IP against Pol2

value: HUVEC

value: umbilical vein endothelial cells

value: Covance


title: Stam_GM12801_CTCF_1

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah, Treatment:Epstein-Barr Virus transformed

value: unknown

tag: cell sex

tag: antibody


title: HepG2_PolII_REP1

description: Chromatin IP against Pol2

value: liver carcinoma cells


title: Stam_AG04449_CTCF_1

value: fetal buttock/thigh fibroblast

value: CTCF

tag: antibody description

value: rabbit polyclonal

tag: replicate


title: HepG2_INPUT

description: Chromatin Input


title: Stam_GM12872_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12872_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

tag: antibody target description

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

tag: antibody vendor name

value: Millipore


title: HepG2_cMYC_REP1

description: Chromatin IP against c-Myc

value: Santa Cruz


title: HepG2_PolII_REP3

description: Chromatin IP against Pol2


title: HepG2_cMYC_REP2

description: Chromatin IP against c-Myc


title: HepG2_cMYC_REP3

description: Chromatin IP against c-Myc


title: HepG2_CTCF_REP2

description: Chromatin IP against CTCF


title: Stam_SK-N-SH_RA_CTCF_1

value: Human

value: neuroblastoma cell line, treatment:differentiated with retinoic acid. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: cancer

value: ectoderm

value: F


title: HepG2_CTCF_REP1

description: Chromatin IP against CTCF


title: Stam_GM12872_CTCF_2

value: mesoderm

value: M


title: HelaS3_PolII_REP2

description: Chromatin IP against Pol2

value: cervical carcinoma

value: Covance


title: HelaS3_PolII_REP1

description: Chromatin IP against Pol2


title: Stam_Caco-2_Input_1

value: endoderm

value: Input


title: Stam_K562_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/K562_protocol.pdf

value: leukemia, "The continuous cell line K-562 was established by Lozzio and Lozzio from the pleural effusion of a 53-year-old female with chronic myelogenous leukemia in terminal blast crises." - ATCC

value: CTCF


title: HelaS3_cMYC_REP1

description: Chromatin IP against c-Myc


title: HelaS3_cMYC_REP2

description: Chromatin IP against c-Myc


title: H1_ES_cMYC_REP1

description: Chromatin IP against c-Myc

value: embryonic stem cells


title: H1_ES_PolII_REP1

description: Chromatin IP against Pol2


title: GM12878_INPUT

description: Chromatin Input

value: lymphoblastoid cells


title: GM12878_PolII_REP2

description: Chromatin IP against Pol2


title: Stam_HA-sp_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HA-sp_Stam_protocol.pdf

value: HA-sp

value: Human astrocytes spinal cord

value: normal

value: Astrocytic

value: U

value: rabbit polyclonal

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore


title: Stam_HL-60_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HL-60_Stam_protocol.pdf

value: Human

value: Human promyelocytic leukemia cells. (PMID:276884)

value: cancer

value: F


title: GM12878_cMYC_REP2

description: Chromatin IP against c-Myc

value: Santa Cruz


title: NHEK_FAIRE_REP2

description: FAIRE-seq

data_processing: Sequences from each experiment were aligned to the genome using Maq (Li et al., 2008) and those that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes). The resulting digital signal was converted to a continuous wiggle track using F-Seq (http://www.genome.duke.edu/labs/furey/software/fseq/) that employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Discrete sites (peaks) were identified from DNase-seq using by setting a F-Seq score cutoff based on fitting these data to a gamma distribution and determining the threshold at a p-value of 0.1.

source_name: normal human epidermal keratinocytes

extract_protocol:
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 3â 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.
FAIRE was performed as described (Giresi et al. 2007; Giresi and Lieb 2009) DNA fragments are prepped for sequencing using the recommended protocol except that samples are amplified prior to gel extraction. Amplified DNA between 150 and 300 bp are excised from the gel, recovered using Qiagen Gel Extraction kit, and sequenced.

value: NHEK

value: normal human epidermal keratinocytes


title: Stam_GM12873_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12873_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown

value: mesoderm

value: CTCF


title: HepG2_PolII_REP2

description: Chromatin IP against Pol2

value: liver carcinoma cells

value: Covance


title: Stam_HEK293_CTCF_2

value: embryonic kidney. (PMID:11967234)

value: endoderm

value: U


title: HelaS3_INPUT

description: Chromatin Input

value: cervical carcinoma


title: NHEK_FAIRE_REP1

description: FAIRE-seq


title: HUVEC_FAIRE_REP2

description: FAIRE-seq

source_name: umbilical vein endothelial cells

value: HUVEC

value: umbilical vein endothelial cells


title: Stam_SAEC_CTCF_1

source_name: SAEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:SAEC_Stam_protocol.pdf

value: SAEC

value: Human

value: Small Airway Epithelial Cells

value: normal

value: rabbit polyclonal

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.

value: Millipore


title: HepG2_FAIRE_REP3

description: FAIRE-seq

source_name: liver carcinoma cells


title: K562_FAIRE_REP2

description: FAIRE-seq

source_name: chronic myeloid leukemia

value: chronic myeloid leukemia


title: HUVEC_FAIRE_REP1

description: FAIRE-seq


title: Stam_Caco-2_CTCF_2

value: cancer

value: M

value: CTCF


title: Stam_HepG2_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HepG2_protocol.pdf

value: liver carcinoma


title: Stam_SAEC_Input_1

value: Input


title: GM12878_PolII_REP1

description: Chromatin IP against Pol2

value: lymphoblastoid cells

value: Covance


title: HelaS3_FAIRE_REP2

description: FAIRE-seq

source_name: cervical carcinoma

value: cervical carcinoma


title: HepG2_FAIRE_REP1

description: FAIRE-seq

value: liver carcinoma cells


title: Stam_HPAF_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HPAF_Stam_protocol.pdf

value: HPAF

value: Human Pulmonary Artery Fibroblasts

value: U


title: HelaS3_FAIRE_REP1

description: FAIRE-seq


title: GM12878_cMYC_REP1

description: Chromatin IP against c-Myc

value: Santa Cruz


title: H1_ES_FAIRE_REP2

description: FAIRE-seq

source_name: human embryonic stem cells

value: human embryonic stem cells


title: Stam_AG09309_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09309_Stam_protocol.pdf

value: Human

value: adult toe fibroblast from apparently healthy 21 year old

value: "7% of the cells examined showing random chromosome loss/gain" -Coriell

value: mesoderm

value: F

value: rabbit polyclonal

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.


title: H1_ES_FAIRE_REP1

description: FAIRE-seq


title: Stam_GM12873_Input_1

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown

value: Input


title: Stam_WERI-Rb-1_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:WERI-Rb-1_Stam_protocol.pdf

value: retinoblastoma (PMID:844036)

value: CTCF

value: Millipore


title: Stam_AG04449_CTCF_2

value: fetal buttock/thigh fibroblast

value: normal

value: M


title: GM12878_FAIRE_REP1

description: FAIRE-seq

source_name: lymphoblastoid cells

value: lymphoblastoid cells


title: GM12878_FAIRE_REP2

description: FAIRE-seq


title: GM12878_FAIRE_REP3

description: FAIRE-seq


title: Stam_BJ_CTCF_1

source_name: BJ

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:BJ-tert_Stam_protocol.pdf

value: BJ

value: Human

value: skin fibroblast, "The line was established from skin taken from normal foreskin." - ATCC.  (PMID:9916803)

value: ectoderm


title: K562_FAIRE_REP1

description: FAIRE-seq

value: chronic myeloid leukemia


title: Stam_HMF_CTCF_2

source_name: HMF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HMF_Stam_protocol.pdf

value: HMF

value: human mammary fibroblasts

value: F

value: rabbit polyclonal


title: Stam_GM12864_CTCF_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12864_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown

value: mesoderm

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.


title: HepG2_DNASE_REP3

description: Dnase-seq

growth_protocol: Cells were grown according to the approved ENCODE cell culture protocols.Specific protocol descriptions can be found at http://genome.ucsc.edu/ENCODE/cellTypes.html.

extract_protocol:
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 3â 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.
DNase-seq was performed as described (Song and Crawford 2010) with the only modification of oligo 1b synthesized with a 5â phosphate to increase the efficiency of ligation.

tag: tissue origin

value: liver

value: carcinoma cells


title: HepG2_FAIRE_REP2

description: FAIRE-seq

value: liver carcinoma cells


title: HepG2_DNASE_REP2

description: Dnase-seq


title: Stam_HUVEC_CTCF_1

source_name: HUVEC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HUVEC_protocol.pdf

value: HUVEC

value: umbilical vein endothelial cells

value: normal

value: U

value: CTCF

value: Millipore


title: Stam_HRPEpiC_CTCF_1

source_name: HRPEpiC

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:HRPEpiC_Stam_protocol.pdf

value: HRPEpiC

value: Human

value: Human Retinal Pigment Epithelial Cells

value: ectoderm


title: HepG2_DNASE_REP1

description: Dnase-seq


title: Stam_Jurkat_Input_1

source_name: Jurkat

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/HudsonAlpha:Jurkat_protocol.pdf UW_Stam:Jurkat_Stam_protocol.pdf

value: Jurkat

value: T lymphoblastoid derived from an acute T cell leukemia, "The Jurkat cell line was established from the peripheral blood of a 14 year old boy by Schneider et al., and was originally designated JM." - ATCC. (PMID:68013)

value: cancer

value: M

value: Input


title: Stam_GM12875_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:GM12875_Stam_protocol.pdf

value: B-Lymphocyte, Lymphoblastoid, International HapMap Project, CEPH/Utah pedigree 1459, Treatment:Epstein-Barr Virus transformed

value: unknown

value: mesoderm

value: F

value: rabbit polyclonal

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.


title: Stam_GM12878_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/GM12878_protocol.pdf

value: lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

value: normal


title: Stam_AG09319_Input_1

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AG09319_Stam_protocol.pdf

value: gum tissue fibroblasts from apparently heathly 24 year old


title: Stam_SK-N-SH_RA_CTCF_2

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:Stam_15_protocols.pdf

value: Human

value: neuroblastoma cell line, treatment:differentiated with retinoic acid. (Biedler, et al. Morphology and Growth, Tumorigenicity, and Cytogenetics of Human Neuroblastoma Cells in Continuous Culture. Cancer Research 33, 2643-2652, November 1973.)

value: CTCF

value: Millipore


title: Stam_HMF_CTCF_1

value: HMF

value: human mammary fibroblasts


title: Stam_AoAF_CTCF_1

source_name: AoAF

growth_protocol: Cells were grown according to ENCODE cell culture protocols: http://genome.ucsc.edu/ENCODE/protocols/cells/human/UW_Stam:AoAF_Stam_protocol.pdf

value: AoAF

value: aortic adventitial fibroblast cells


title: GM12878_DNAse_REP1

city: Austin

first: Vishy

last: Iyer

state: TX

address: 2500 Speedway Dr. MBB 3.212

department: Molecular Biosciences

institute: University of Texas at Austin

description: DNase-Seq

data_processing:
Sequences from each experiment were aligned to the genome using Maq (Li et al., 2008) and those that aligned to 4 or fewer locations were retained. Other sequences were also filtered based on their alignment to problematic regions (such as satellites and rRNA genes). The resulting digital signal was converted to a continuous wiggle track using F-Seq that employs Parzen kernel density estimation to create base pair scores (Boyle et al., 2008b). Discrete DNase HS, FAIRE, and ChIP sites (peaks) were identified from DNase/ChIP-seq using F-Seq by setting a Parzen cutoff based on ROC curve analysis using peaks and non-peaks identified from DNase/ChIP-chip using NimbleGen Human ENCODE tiling arrays (1% of the genome).
Regions of enriched signal in either DNaseI HS,  or ChIP experiments. Peaks were called based on signals created using F-Seq, a software program developed at Duke (Boyle et al., 2008b). Significant regions were determined by performing ROC analysis of sequence data using data from the 1% ENCODE arrays, and determining a cut-off value at approximately the 95% sensitivity level. The solid vertical line in the peak represents the point with highest signal. ENCODE Peaks tables contain a p-value for statistical significance. For these data, this was determined by fitting the data to a gamma distribution

growth_protocol: Cells were grown according to the approved ENCODE cell culture protocols.

extract_protocol:
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.
DNaseI hypersensitive sites were isolated using methods called DNase-seq or DNase-chip (Boyle et al., 2008a, Crawford et al., 2006). Briefly, cells were lysed with NP40, and intact nuclei were digested with optimal levels of DNaseI enzyme. DNaseI digested ends were captured from three different DNase concentrations, and material was sequenced using Illumina (Solexa) sequencing. DNase-seq data were verified using material that was hybridized to NimbleGen Human ENCODE tiling arrays (1% of the genome). Multiple independent growths (replicates) were compared to verify the reproducibility of the data.

tag: individual


title: GM12878_DNAse_REP2

description: DNase-Seq


title: GM12891_DNAse_REP1

description: DNase-Seq


title: rhesus_kidney

status: Public on Jun 25 2011

city: Dedham

first: Adnan

last: Derti

state: MA

address: 100 Alden Street

department: Bioinformatics

institute: personal

data_processing:
Alignments. Using Soap2, reads were aligned to the respective genome (human: hg19 if so indicated in the file name, hg18 otherwise; rhesus: rheMac2; mouse: mm9; rat: rn4; dog: canFam2) and to splice junctions from all available known (Refseq, UCSC Known Genes, Ensembl, ESTs) and predicted transcripts (Genscan, N-Scan), and to junctions formed from one- and two-exon-skipping events predicted in these transcripts. Only reads aligning to unique loci were retained.
Filtering. A modified PolyA-Seq assay was performed on a UHR sample, using a T(10) primer ("noVN") instead of T(10)VN. Genomic alignments was performed with Blat. Reads with perfectly aligned 3' ends (except those matching ends of mRNAs or ESTs, or known polyA sites) were considered to locate internal priming sites, while reads with unalignable 3' As were deemed to identify true polyA sites. A frequency matrix for the 10 bases downstream of all alignments was created for each of these two sets of sites. These matrices were used to score the 10-mer downstream of every read alignment from previous samples. Alignments were retained if the log of the odds (true polyA site / internal priming site) was 3 or greater.
Peak/site detection. Following filtering, ends of reads within 25 bp of each other on the same strand were clustered.

organism: Macaca mulatta

source_name: kidney

extract_protocol: 2 µL 0.1 uM tailed dT primer T(10)VN was combined with 150 ng polyA+ RNA in a final volume of 11 µL; for the human noVN experiment, the primer consisted only of T(10). The primer-template mix was heated at 65 °C for 5 min and chilled on ice before adding 9 µL reverse transcription master mix (4 µL 5x buffer, 2 µL 10 mM dNTPs, 1 µL 100 mM DTT, 1 µL RNaseOUT and 1 µL SuperScript III enzyme). The 20 µL reverse transcription reaction was incubated at 40 °C for 90 min, 70 °C for 15 min and cooled to 4 °C. RNA template was degraded by adding 1 µL RNase H (Invitrogen Corp.) and incubating at 37 °C for 20 min, 75 °C for 15 min and cooling to 4 °C. DNA was subsequently purified using the QIAquick PCR Purification kit and eluted with 65 µL elution buffer (Qiagen, Inc.). For second-strand synthesis, 60 µL purified cDNA was added to 40 µL Klenow master mix (12 µL water, 10 µL 10x NEBuffer 2, 5 µL 10 mM dNTPs, 3 µL 5 units/ul exo- Klenow fragment; M0212L,New England Biolabs, Inc.) and 10 µL 10 uM tailed random hexamer primer. The 100 µL reaction was incubated at 37 °C for 30 min and cooled to 4 °C. DNA was purified from the second-strand reaction by incubating with 1.8 volumes of Agencourt AMPure XP beads (Beckman Coulter) for 5 minutes, washing twice with 70% EtOH and eluting with 50 µL of elution buffer. This step greatly reduced the number of clones with inserts less than 40 nucleotides. For PCR amplification, 33 µL of purified second-strand synthesis reaction was combined with 17 µL of PCR master mix (10 µL 5x Buffer 2, 1 µL 25 mM MgCl2, 1 µL 10 mM dNTPs, 2 µL 10 uM forward primer, 2 µL 10 uM reverse primer, 1 µL ExpandPLUS enzyme; Roche Diagnostics Corp.). Samples were denatured for 2 min at 94 °C followed by 2 cycles of 94 °C for 10 s, 40 °C for 2 min, 72 °C for 1 min; 8 cycles of 94 °C for 10 s, 60 °C for 30 s, 72 °C for 1 min; 15 cycles of 94 °C for 15 s, 60 °C for 30 s, 72 °C for 1 min; and 72 °C for 5 min to polish ends before cooling to 4 °C. Double-stranded DNA was purified using AMPure XP beads as described above.

treatment_protocol: PolyA+ RNA was isolated using the Dynabead mRNA Purification Kit according to the manufacturer's instructions (Invitrogen, cat # 610.06)

tag: tissue

value: kidney


title: GM12878_DNAse_REP3

description: DNase-Seq


title: rhesus_liver

source_name: liver

value: liver


title: rhesus_brain

source_name: brain

value: brain


title: rhesus_ileum

source_name: ileum

value: ileum


title: rhesus_testis

source_name: testis

value: testis


title: human_noVN

source_name: UHR (MAQC)

tag: sample type

value: universal human reference (MAQC)


title: human_UHR


title: human_muscle

source_name: muscle

value: muscle


title: mouse_testis


title: human_maqc-UHR2


title: human_testis


title: human_maqc-UHR1


title: mouse_liver


title: mouse_muscle


title: mouse_kidney


title: human_maqc-brain2

source_name: brain (MAQC)

value: brain (MAQC)


title: human_maqc-brain1


title: Stam_HEK293_CTCF_1

value: embryonic kidney. (PMID:11967234)

value: cancer

value: endoderm

value: U

value: rabbit polyclonal

value: CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.


title: mouse_brain


title: dog_testis

organism: Canis lupus familiaris


title: human_liver


title: rat_brain

organism: Rattus norvegicus


title: human_kidney


title: human_brain


title: Jurkat_Wildtype_1

city: La Jo

first: Traver

last: Hart

address: 10550 North Torrey Pines Road, MEM241B

department: Molecular & Experimental Medicine

institute: The Scripps Research Institute

description: Bisulfite Treated

data_processing: SAM analysis

source_name: Jurkat DNA

extract_protocol: Wildtype and hypermethylated Jurkat genomic DNA (New England Biolabs) was bisulfite treated using the Epitect Bisulfite kit (QIAGEN) according to the manufacturer's instructions.  Bisulfite treated genomic DNA was amplified by microdroplet PCR amplification on an RDT 1000 (RainDance Technologies) with a custom primer library according to the manufacturer's instructions.  Briefly, micrdroplets containing genomic DNA were merged with microdroplets from the custom primer droplet library.  The custom primer droplet library consists of a collection of individual primer droplets, where each primer droplet contains matched pairs of forward and reverse primer (for each amplicon defined within the primer library.  For primers covering a CpG, a degenerate base (C/T or G/A, depending on the strand) was used at that location. The RDT1000 generated each PCR droplet by pairing a single genomic DNA template droplet with a single primer droplet.  Paired droplets flow past an electrode embedded in the chip and are instantly merged together. All resulting PCR droplets were automatically dispensed as an emulsion into a single PCR tube and transferred to a standard thermal cycler for PCR amplification.  Each sample generated more than 1 million singleplex PCR droplets. Samples were amplified for 55 cycles, the droplet emulsion was broken, and the PCR product was purified over a MinElute column (QIAGEN) following the manufacturerâs recommended protocol. RainDance PCR products were fragmented to 200 bp using a Covaris S2. Fragmented PCR product 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 and dATP to yield a protruding 3- 'A' base for ligation of adapters which have a single 'T' base overhang at the 3' end. After adapter ligation DNA was PCR amplified for 15 cycles and library fragments of ~350 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.

tag: disease state

value: Acute T Cell Leukemia

value: wildtype


title: Jurkate_Hypermethylated_1

description: Bisulfite Treated

source_name: CpG Methylase (M.SssI) treated Jurkat DNA

value: hypermethylated


title: dog_brain


title: dog_kidney

value: kidney


title: Sox3_condXi_NPC 129Xi-CastXa (#177)

status: Public on Jun 24 2011

city: Utrecht

first: Erik

last: Splinter

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: 4C PCR product

data_processing: The initial step in the 4C-seq analysis is the alignment of the sequencing reads to a reduced genome of sequences that flank HindIII sites (fragment ends), using custom perl scripts. Due to their ambiguous nature in reporting contacts, repetitive fragment ends were excluded from subsequent analysis. The reduced genome was based on mouse mm9.

source_name: Neural progenitor cells

growth_protocol: NPCs were generated according to Conti and collogues (Conti et al. 2005) with slight modifications. In brief ES cells (129SVJ/CAST) were differentiated in N2B27 (StemCell Recourses) for 7 days, followed by the formation of neural spheres in N2B27 supplemented with EGF and FGF (10ng/ml). 3 day old spheres were allowed to attach to the culture dish to expand NPCs. After 2 passages cells were seeded in low density and colonies were picked and analyzed for NPC identity using IF (Oct4-Nestin-Gfap-Tubulin) and proper XCI (Xist cloud with RNA FISH; mono allelic gene expression; promoter CpG methylation) (also see Splinter et al., 2011, Genes & Development).

extract_protocol: The initial steps of the 4C procedure, as published before (Simonis et al., 2006, Nature Genetics), remain unchanged. Cells are cross linked using 2% formaldehyde for 10min at room temperature in PBS 10%FCS, nuclei are isolated, after which chromatin is digested with HindIII and subsequently ligated under diluted conditions. After reversal of the cross links the DNA is purified and treated with the second restriction enzyme treatment (indicated in the sample description). After a second re-ligation step the sample is purified and a 4C PCR is applied. In order to design an allele-specific 4C procedure the viewpoint fragment is chosen such that a RFLP is located in between the primers used in the PCR amplification. As a consequence only the allele which is not digested by the second restriction enzyme can contribute to the 4C PCR product and is analyzed either by dedicated micro-array or high throughput sequencing. Note that the R23a viewpoint is located on mouse chromosome 8 and does interrogate both alleles.

treatment_protocol: cells are cross linked using 2% formaldehyde for 10minutes at room temperature in 10%FCS/PBS

tag: strain

tag: cell type

value: ES-derived neural progenitor cells

tag: template number

tag: template preparation

value: 1st digestion HindIII; 2nd digestion Csp6I; digestion post PCR Tsp509I


title: Slitrk4_KOXi_NPC 129Xi-CastXa (#180)

description: 4C PCR product

value: 129SvJ-knock out Xist/CAST

value: 1st digestion HindIII; 2nd digestion Csp6I; Cre mediated Xist knock out was achieved by first differentiating 129SVJ-Xist2lox/CAST ES cells  (Csankovszki et al. 1999) to NPCs. NPCs showing proper XCI were transfected with pCMV-Cre-puro using AmaxaÂ® according to manufacturers protocol, followed by transient puromycin selection for 2 days. XistKO NPCs were cultured an additional 12 days with cell numbers increasing >10 fold before analysis to dilute out stable Xi markers.


title: R23a_KOXi_NPC 129Xi-CastXa (#182)

description: 4C PCR product

value: 1st digestion HindIII; 2nd digestion DpnII/PvuII; Cre mediated Xist knock out was achieved by first differentiating 129SVJ-Xist2lox/CAST ES cells  (Csankovszki et al. 1999) to NPCs. NPCs showing proper XCI were transfected with pCMV-Cre-puro using AmaxaÂ® according to manufacturers protocol, followed by transient puromycin selection for 2 days. XistKO NPCs were cultured an additional 12 days with cell numbers increasing >10 fold before analysis to dilute out stable Xi markers.


title: Pcdh11X_KOXi_NPC 129Xi-CastXa (#181)

description: 4C PCR product

value: 1st digestion HindIII; 2nd digestion DpnII; Cre mediated Xist knock out was achieved by first differentiating 129SVJ-Xist2lox/CAST ES cells  (Csankovszki et al. 1999) to NPCs. NPCs showing proper XCI were transfected with pCMV-Cre-puro using AmaxaÂ® according to manufacturers protocol, followed by transient puromycin selection for 2 days. XistKO NPCs were cultured an additional 12 days with cell numbers increasing >10 fold before analysis to dilute out stable Xi markers.


title: Pctk1_KOXi_NPC 129Xi-CastXa (#182)

description: 4C PCR product


title: Sox3_KOXi_NPC 129Xi-CastXa (#180)

description: 4C PCR product

value: 1st digestion HindIII; 2nd digestion Csp6I; digestion post PCR Tsp509I; Cre mediated Xist knock out was achieved by first differentiating 129SVJ-Xist2lox/CAST ES cells  (Csankovszki et al. 1999) to NPCs. NPCs showing proper XCI were transfected with pCMV-Cre-puro using AmaxaÂ® according to manufacturers protocol, followed by transient puromycin selection for 2 days. XistKO NPCs were cultured an additional 12 days with cell numbers increasing >10 fold before analysis to dilute out stable Xi markers.


title: Jarid1C_condXi_NPC 129Xi-CastXa (#178)

description: 4C PCR product

value: 1st digestion HindIII; 2nd digestion DpnII


title: Mecp2_KOXi_NPC 129Xi-CastXa (#180)

description: 4C PCR product


title: Slitrk4_condXi_NPC 129Xi-CastXa (#177)

description: 4C PCR product

value: 1st digestion HindIII; 2nd digestion Csp6I


title: Xist_condXi_NPC 129Xi-CastXa (#177)

description: 4C PCR product

value: 1st digestion HindIII; 2nd digestion Csp6I; digestion post PCR BamHI


title: Mecp2_condXi_NPC 129Xi-CastXa (#177)

description: 4C PCR product


title: rat_testis

value: testis


title: Pcdh11X_condXi_NPC 129Xi-CastXa (#178)

description: 4C PCR product


title: Pctk1_condXi_NPC 129Xi-CastXa (#179)

description: 4C PCR product

value: 1st digestion HindIII; 2nd digestion DpnII/PvuII


title: Jarid1C_Xi_NPC 129Xi-CASTXa (#137)

description: 4C PCR product

value: 1st digestion HindIII; 2nd digestion NlaIII;linearization NcoI


title: Xist_Xi_NPC 129Xi-CASTXa (#170)

description: 4C PCR product


title: R23a_NPC 129Xi-CastXa (#179)

description: 4C PCR product


title: Pcdh11x_Xi_NPC 129Xa-CASTXi (#169)

description: 4C PCR product

value: 1st digestion HindIII; 2nd digestion Csp6I;digestion post PCR SnaBI


title: Slitrk4 _Xi_NPC 129Xi-CASTXa (#170)

description: 4C PCR product


title: MeCP2_Xi_NPC 129Xi-CASTXa (#170)

description: 4C PCR product


title: Jarid1C_KOXi_NPC 129Xi-CastXa (#181)

description: 4C PCR product


title: Pctk1_Xi_NPC 129Xi-CASTXa (#137)

description: 4C PCR product


title: Jarid1C_Xa_NPC 129Xa-CASTXi (#132)

description: 4C PCR product


title: Slitrk4_Xa_NPC 129Xa-CASTXi (#169)

description: 4C PCR product


title: MeCP2_Xa_NPC 129Xa-CASTXi (#169)

description: 4C PCR product


title: Pctk1_Xa_NPC 129Xa-CASTXi (#132)

description: 4C PCR product


title: R23a_NPC 129Xa-CASTXi (#132)

description: 4C PCR product


title: Lamin B ChIP-Seq

status: Public on Jun 23 2011

city: Singapore

first: Lusy

last: Handoko

address: 60 Biopolis street 02-01

country: Singapore

institute: Genome Institute of Singapore

description:
Chromatin IP against Lamin B
ChIP-Seq

data_processing:
Sequence reads were aligned to the mm8 genome assembly using the Illumina Genome Analyzer Pipeline. Uniquely aligned reads with two or fewer mismatches were kept.
Peaks were called using CCAT software (http://cmb.gis.a-star.edu.sg/ChIPSeq/tools.htm). ChIA-PET data was processed with ChIA-PET Tool software (Li G, Fullwood MJ, Xu H, Mulawadi FH, Velkov S, Vega V, Ariyaratne PN, Mohamed YB, Ooi HS, Tennakoon C, Wei CL, Ruan Y, Sung WK. 2010. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing. Genome Biol 11:R22).

source_name: embryonic stem cells

growth_protocol: E14 ES cells were grown as described in Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-17 (2008)

extract_protocol: ChIP-Seq (p300, CTCF, Lamin B, RNA Pol II): ChIP was performed from sonicated cross-linked mouse E14 cell extracts as described in Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 133, 1106-17 (2008).ChIP DNA was de-cross-linked. 7-12 ng of ChIP DNA was subjected to sample preparation followed by the manufacturer's instruction. Briefly, DNA was end-polished with T4 DNA polymerase and kinase. After column purification, Solexa adaptors were ligated to the ChIP DNA fragments and subjected to 15 cycles of PCR amplification. 200-300 bp DNA were selectively excised and purified from the gel using Qiagen gel extraction kit. The DNA fragments were then sequenced on Illumina GAIIx platform. 36 bp sequences were generated and mapped to mm8 genome by ELAND_extended program. Minimal 10 million uniquely mapped locations were generated from each ChIP-seq experiment.

treatment_protocol: no treatment

tag: antibody (chip)

value: Lamin B (Santa Cruz sc-6216, Lot #L1008)


title: Integrating 5 Hydroxymethylcytosine into the Epigenetic Landscape of Human Embryonic Stem Cells Input

city: Atlanta

first: Keith

middle: E

last: Szulwach

state: GA

address: 615 Michael Street, Whitehead Suite 301

department: Human Genetics

institute: Emory University

description: 5hmC Capture and Sequencing

data_processing: Processed data not provided. It will be included in the publication.

source_name: H1 human ES cell

growth_protocol: H1 human ES cells were maintained on mitomycin C-treated STO cells in ES medium consisting of DMEM/F12 medium (Invitrogen) supplemented with 20% serum replacement (SR; Invitrogen), 1 mM L-glutamine (Invitrogen), 100 Î¼M nonessential amino acids (Invitrogen), 0.1 mM Ã-mercaptoethanol (Sigma), 1X Antibiotics-Antimycotic (Invitrogen), and 4 ng/mL bFGF (Invitrogen).

extract_protocol: Genomic DNA was purified from tissue using Wizard genomic DNA purification kit (Promega) with additional Proteinase K treatment and rehydrated in 10 mM Tris (pH 7.9). Genomic DNA samples were sonicated to 100-500 bp by Misonix sonicator 3000 (using microtip, 3 pulses of 30 seconds each with 2 min of rest and a power output level of two). 5-hmC labelling reactions were performed in a 100-ÂµL solution containing 50 mM HEPES buffer (pH 7.9), 25 mM MgCl2, 300 ng/Î¼L sonicated genomic DNA (100-500 bp), 250 Î¼M UDP-6-N3-Glu or UDP-Glu, and 2.25 Î¼M wild-type BGT. The reactions were incubated for 1 hr at 37 Â°C. After the reaction, the DNA substrates were purified by Qiagen DNA purification kit or by phenol-chloroform precipitation and reconstituted in H2O. Biotin addition by click chemistry was performed by adding 150 Î¼M dibenzocyclooctyne modified biotin into the DNA solution, and the reaction mixture was incubated for 2 hr at 37 Â°C. The DNA samples were then purified by Qiagen DNA purification kit. Biotin Labeled 5-hmC DNAs were purified/enriched by Pierce Monomeric Avidin Kit (Thermo) following manufacturerâs recommendations. After elution, the biotin-5-N3-gmC containing DNA was concentrated by 10 K Amicon Ultra-0.5 mL Centrifugal Filters (Millipore) and purified by Qiagen DNA purification kit. 25 ng genomic DNA, 5-hmC-captured DNA, or control captured DNA (in the absence of biotin) were used to initiate library preparation following the Illumina protocol for âPreparing Samples for ChIP Sequencing of DNAâ (Part# 111257047 Rev. A). DNA fragments ~150-300 bp were gel purified after the adapter ligation step and amplified by 18 cycles PCR.

tag: treatment

value: Non-enriched input genomic DNA

tag: cell line


title: CTCF ChIP-Seq

description:
Chromatin IP against CTCF
ChIP-Seq


title: p300 ChIP-Seq

description:
Chromatin IP against p300
ChIP-Seq

value: p300 (Santa Cruz sc-585, Lot #G0308)


title: Integrating 5 Hydroxymethylcytosine into the Epigenetic Landscape of Human Embryonic Stem Cells 5hmC

description: 5hmC Capture and Sequencing

value: 5-hmC enriched genomic DNA


title: CTCF ChIA-PET IME051

description:
Chromatin IP against CTCF followed by close proximity ligation (ChIA-PET), biological replicate 2, technical replicate 2
ChIA-PET (Pair end Sequencing)

extract_protocol: ChIA-PET (CTCF): ChIP was performed from sonicated cross-linked mouse E14 cell extracts as described in Chen, X. et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells.Cell 133, 1106-17 (2008). CTCF ChIA-PET libraries were constructed accordingly to Fullwood, M.J. et al. An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462, 58-64 (2009), with a few modifications.ChIP Chromatin on the beads was divided into two aliquots and each aliquot was ligated with two different barcoded biotinylated half-linkers (linker A or linker B) that contain a flanking MmeI site using T4 DNA ligase. These chromatins ligated with different linkers were pooled and molecular circularization/ligation was carried out in extremely dilute condition. After ligation, DNA was purified and digested with Mme I. The biotinylated PETs purified on Streptavidin Dynabeads were ligated with a sequencing adapter by T4 DNA ligase (RT for 16h with rotation). The nick on one strand of the DNA at the ligation site was subsequently repaired by incubation with E. coli DNA polymerase I at RT for 2h, followed by 18-20 rounds of PCR. The PCR product of~223 bp, was purified from the gel and used as the template for Illumina GAIIx 2x36 bp pair end sequencing.


title: CTCF ChIA-PET IME041_42

description:
Chromatin IP against CTCF followed by close proximity ligation (ChIA-PET), biological replicate 1
ChIA-PET (Pair end Sequencing)


title: RNA Pol II ChIP-Seq

description:
Chromatin IP against RNAP II
ChIP-Seq

value: RNA Pol II (8WG16 clone, MMS-126R, Covance, Lot #14944802)


title: Pcdh11x_Xa_NPC 129Xi-CASTXa (#170)

description: 4C PCR product

value: ES-derived neural progenitor cells


title: CTCF ChIA-PET IME043

description:
Chromatin IP against CTCF followed by close proximity ligation (ChIA-PET), biological replicate 2, technical replicate 1
ChIA-PET (Pair end Sequencing)


title: MEL_PU.1_B2

city: Bronx

first: Sandeep

middle: Nagaraj

last: Wontakal

state: NY

address: 1300 Morris Park Ave Chanin 402

department: Cell Biology

institute: Albert Einstein College of Medicine

description: Chromatin immunoprecipitation was performed using an antibody against PU.1

data_processing: Peak detection to mm9 was done using cisGenome and spp software.

source_name: Murine erythroleukemia (MEL) cells stably transfected with Gata-1 fused to ER

growth_protocol: MEL cells were grown in DMEM supplemented with 10% FBS (Gemini), 2mM L-glutamine, and 5mg/ml puromycin. ES-EPs were cultured in StemPro34 media (Invitrogen) supplmented with 2u/ml Epogen (Amgen), 40ng/ml hIGF-1 (Sigma), 10-6M dexamethosone (Sigma), 100ng/ml murine SCF (R&D Systems/Invitrogen), and 0.1% -mercaptoethanol (Gibco). ES-EP were maintained between 1-6x106 cells/ml by adding fresh media daily.

extract_protocol: Libraries were prepared as recommended by Illumina.

tag: clone #

tag: chip antibody

tag: antibody vendor

value: Santa Cruz

tag: antibody catalog #

tag: antibody lot #


title: MEL_PU.1_A1


title: ES-EP_PU.1_A2

source_name: ES-cell derived erythroid progenitors


title: ES-EP_PU.1_B2


title: MEL_PU.1_B1


title: ES-EP_Input2

description: Input DNA that was used for chromatin immunoprecipitation


title: ES-EP_Input1


title: R23a_NPC 129Xi-CASTXa (#137)

description: 4C PCR product


title: ES-EP_PU.1_A1


title: MEL_PU.1_A2


title: MBD_st12.5_500mM

city: Darlinghurst

first: Ozren

last: Bogdanovic

state: NSW

address: 384 Victoria Street

department: Genomics and Epigenetics

institute: Garvan Institute of Medical Research

description: methylated DNA affinity capture

data_processing: Reads were mapped to the X.tropicalis genome (version JGI4.1) with ELAND, reads in identical positions were removed and peaks were called using MACS with p-value 1e-5

organism: Xenopus tropicalis

source_name: whole embryo

growth_protocol: Xenopus tropicalis embryos were obtained from a natural mating procedure after human chorion gonadotropin injection, dejellied in 3% cysteine and collected at Nieuwkoop-Faber stage 9 and 12.5

extract_protocol: Genomic DNA was sheared by sonication to ~ 500 bp fragments.  Methylated DNA was affinity purified using H6-GST-MBD fusion protein (Diagenode) following the manufacturers’ protocol with one modification. The DNA was eluted in several steps with increasing NaCl concentrations: 2 x 200mM, 1 x 300mM (washing steps 1-3), 500mM and 700mM (elutions 1 and 2)

value: whole embryo

tag: fraction

value: 500mM elution

tag: developmental stage

tag: bait

value: H6-GST-MBD fusion protein (Diagenode)


title: MBD_st9_700mM

description: methylated DNA affinity capture

tag: tissue

value: 700mM elution


title: MBD_st12.5_700mM

description: methylated DNA affinity capture


title: MBD_st9_500mM

description: methylated DNA affinity capture


title: DNA Input

description: total sonicated chromatin


title: ES-EP_PU.1_B1