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| Status |
Public on Mar 15, 2010 |
| Title |
GM12878_CTCF_REP2 |
| Sample type |
SRA |
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| Source name |
lymphoblastoid cells
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| Organism |
Homo sapiens |
| Characteristics |
individual: NA12878
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| Biomaterial provider |
Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA12878
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| Growth protocol |
Cells were grown according to the approved ENCODE cell culture protocols.
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| Extracted molecule |
genomic DNA |
| Extraction 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.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
Chromatin IP against CTCF
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| 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
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| Submission date |
Dec 23, 2009 |
| Last update date |
May 15, 2019 |
| Contact name |
Vishy Iyer |
| E-mail(s) |
[email protected]
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| Phone |
5122327833
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| Organization name |
University of Texas at Austin
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| Department |
Molecular Biosciences
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| Street address |
2500 Speedway Dr. MBB 3.212
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| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
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| Platform ID |
GPL9052 |
| Series (3) |
| GSE19622 |
Individual-specific and allele-specific chromatin signatures in diverse human populations |
| GSE30227 |
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity |
| GSE32883 |
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells |
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| Relations |
| SRA |
SRX017022 |
| BioSample |
SAMN00009069 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM489291_wgEncodeUtaChIPseqAlignmentsRep2Gm12878CtcfV2.tagAlign_20.txt.gz |
187.3 Mb |
(ftp)(http) |
TXT |
| GSM489291_wgEncodeUtaChIPseqPeaksGm12878CtcfV2.narrowPeak_20.txt.gz |
1.1 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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