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GEO help: Mouse over screen elements for information. |
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| Status |
Public on May 09, 2014 |
| Title |
Widespread contribution of transposable elements to the innovation of gene regulatory networks [human ENCODE] |
| Project |
ENCODE
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| Organism |
Homo sapiens |
| Experiment type |
Methylation profiling by high throughput sequencing
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| Summary |
Transposable elements (TE) have been shown to contrain functional transcription factor (TF) binding sites for long, but the extent to which TEs contribute TF binding sites is not well know. Here, we comprehensively mapped binding sites for 26 pairs of orthologous TFs, in two pairs of human and mouse cell lines (i.e., leukemia, and lymphoblast), along with epigenomic profiles representing DNA methylation and six histone modifications. We found that on average, 20% of TF binding sites were embedded in TEs. We further identified 710 TF-TE relationships in which certain TE subfamilies enriched for TF binidng sites. TE-derived TF binding peaks were also strongly associated with decreased DNA methylation and increased enhancer-associated histone marks. Most of the TE-derived TF binding sites were species-specific, but we also identified conserved binding sites. Additionally, 66% of TE-derived TF binding events were cell-type specific, associated with cell-type specific epigenetic landscape.
For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf
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| Overall design |
To evaluate the contribution of transposable elements (TE) to transcription factor (TF) binding landscapes, we profiled ChIP-seq datasets for 26 TFs in two cell lines in human and mouse, generated by the ENCODE and MouseENCODE consortia. The epigenomic profiles were evaluated from six histone modification in each of the cell lines, also generated by the consortia. We added DNA methylation to the epigenomic profiles, using two complementary techniques, MeDIP-seq and MRE-seq.
The mouse data related to this study are available through GSE57230:
http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE57230
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| Web link |
http://www.ncbi.nlm.nih.gov/geo/info/ENCODE.html
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| Contributor(s) |
Sundaram V, Cheng Y, Li D, Xing X, Snyder M, Wang T |
| Citation(s) |
25319995 |
| BioProject |
PRJNA63443 |
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| Submission date |
Apr 14, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Daofeng Li |
| E-mail(s) |
lidaof@gmail.com
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| Phone |
(314) 286-0866
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| Organization name |
Washington University in St. Louis
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| Department |
Genetics
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| Lab |
Ting Wang Lab
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| Street address |
4515 McKinley Avenue
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| City |
SAINT LOUIS |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platforms (1) |
| GPL15433 |
Illumina HiSeq 1000 (Homo sapiens) |
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| Samples (4)
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| Relations |
| SRA |
SRP041158 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE56774_RAW.tar |
1.2 Gb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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