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SRX10661560: GSM5259251: ATAC-seq from hematopoietic stem cell (ENCLB478MDQ); Mus musculus; ATAC-seq
2 ILLUMINA (Illumina HiSeq 2000) runs: 268.1M spots, 12.9G bases, 5.5Gb downloads

Submitted by: NCBI (GEO)
Study: GSE57230: Widespread contribution of transposable elements to the innovation of gene regulatory networks [mouse ENCODE]
show Abstracthide Abstract
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 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 human data related to this study are available through GSE56774: http://0-www.ncbi.nlm.nih.gov.brum.beds.ac.uk/geo/query/acc.cgi?acc=GSE56774
Sample: ENCODE biosample ENCBS301PDO: Hematopoietic stem cell (HSC)
SAMN18814564 • SRS8756299 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina HiSeq 2000
Strategy: ATAC-seq
Source: GENOMIC
Selection: other
Layout: SINGLE
Construction protocol: general protocol: https://www.encodeproject.org/documents/192f9cb2-7757-4695-846e-5fe0c20b1ead/@@download/attachment/ATACseq_PSUHardison_Mar2016.pdf general protocol: https://www.encodeproject.org/documents/192f9cb2-7757-4695-846e-5fe0c20b1ead/@@download/attachment/ATACseq_PSUHardison_Mar2016.pdf
Experiment attributes:
GEO Accession: GSM5259251
Links:
Runs: 2 runs, 268.1M spots, 12.9G bases, 5.5Gb
Run# of Spots# of BasesSizePublished
SRR14306140184,090,1378.8G2.9Gb2021-04-28
SRR1430613983,977,1684G2.5Gb2021-04-28

ID:
14158694

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