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| Status |
Public on Jan 24, 2012 |
| Title |
CD4_H3K4me2_ChIAPET_Exp1_Seq2 |
| Sample type |
SRA |
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| Source name |
CD4+ T cells
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| Organism |
Homo sapiens |
| Characteristics |
cell type: CD4+ T cells
antibody: H3K4me2
vendor: Millipore, 07-030
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
100 million CD4+ T cells were isolated from human blood as previous described (Barski et al., 2007). Cells were then cross-linked with 1% formaldehyde for 10 minutes at room temperature, followed by sonication of the cells to obtain chromatin fragments ranging in size from 150 to 300 bp. The ChIP assay was carried out using the antibody against H3K4me2 (Millipore, 07-030) and the immunoprecipitated chromatin was stored in TE buffer. ChIA-PET libraries were prepared as described (Fullwood et al., 2009. Nature 462, 58-64.) and pair-end sequencing was carried out using Illumina Hi-seq sequencer.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The raw sequences were trimmed to the first 36-bp and the linker sequences from the 36-bp reads were removed. The sequences of the two ends of PETs were separately mapped to the hg18 human genome using the bowtie algorithm (Langmead et al., 2009. Genome Biol 10, R25) ensuring that only uniquely mapped reads with zero mismatches to the reference genome were retained and taking into account the base-quality values. To identify long-range chromatin interactions, we represented paired-end tags by points in the 2-dimensional space Genome × Genome and identified regions with significantly enriched points
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| Submission date |
Oct 06, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Iouri Chepelev |
| E-mail(s) |
ichepelev@gmail.com
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| Organization name |
US Department of Veterans Affairs Medical Center
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| Street address |
3200 Vine St
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45220 |
| Country |
USA |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE32677 |
Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization |
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| Relations |
| SRA |
SRX100689 |
| BioSample |
SAMN00738590 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM811037_CD4_H3K4me2_ChIAPET_Exp1_Seq2.txt.gz |
404.6 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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