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| Status |
Public on Oct 18, 2011 |
| Title |
Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells [new ChIP-Seq samples] |
| Organism |
Homo sapiens |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Cellular diversity in a multicellular organism like the human is achieved in part by distinct programs of gene expression at the level of transcription, which in turn are mediated by transcription factors (TFs). However, there are few systematic studies of the genomic binding of different types of TFs across a wide range of human cell types, especially in relation to gene expression. Using chromatin Immunoprecipitation followed by thigh-throughput sequencing (ChIP-seq) we identified an average of 45,000, 30,000 and 8,000 binding sites for CTCF, Pol2 and MYC respectively across eleven cell types.CTCF preferred to bind to intergenic regions while Pol2 and MYC tended to bind to core promoter regions. CTCF sites were highly conserved across diverse cell types, whereas MYC showed the greatest cell-type specificity. MYC co-localized with Pol2 at many of their binding sites and putative target genes. Cell-type specific binding sites, in particular for MYC and Pol II, were associated with cell-type specific functions. Patterns of binding in relation to gene features were generally invariant across different cell types. Pol II occupancy was higher over exons than adjacent introns, likely reflecting a link between transcriptional elongation and splicing. TF binding was positively correlated with the expression levels of their putative target genes, but combinatorial binding, in particular of MYC and Pol II was even more strongly associated with higher gene expression. Our ChIP-seq data sheds considerable light on how these transcription factors of different types function individually and in combination with one another to occupy target genomic loci and shape gene expression programs in a cell-type specific manner.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
Keywords: Genome binding/occupancy profiling by high throughput sequencing
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| Overall design |
ChIP-seq were performed on eleven human cell lines: GM12878 (lymphoblastoid), K562 (leukemia), HepG2 (hepatocellular carcinoma), HelaS3 (cervical carcinoma), HUVEC (human umbilical vein endothelial cells), NHEK (keratinocytes), H1-ES (embryonic stem cells), MCF7 (breast adenocarcinoma), FB8470 (Normal child fibroblasts), FB0167P (Progeria fibroblast), and H54 (glioblastoma). For each cell line, two or three replicates were independently grown and split into three, one for each of the three experimental methods. Control ChIP experiments were performed on five of the cell lines with NHEK and H1-ES being excluded due to lack of material.
Additional ChIP-Seq data mentioned in the 'overall design' but not included in this Series are contained in the GSE30226 SubSeries.
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| Web link |
http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/geo/info/ENCODE.html
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| Contributor(s) |
Furey TS, Iyer VR, Crawford GE |
| Citation(s) |
22090374 |
| BioProject |
PRJNA63447 |
| Submission date |
Oct 07, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Vishy Iyer |
| E-mail(s) |
iyerlab@gmail.com
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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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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (26)
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| This SubSeries is part of SuperSeries: |
| 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 |
SRP008801 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE32692_RAW.tar |
10.3 Gb |
(http)(custom) |
TAR (of BED, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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