Genomics

Dataset Information

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ChIP-Chip tiling array for H3k27ac in mouse MV+ (lens epithelium) and RAG cells ( renal adenocarcinoma) over panel of genes including Pax6, Sox2, Otx2, Sox9.


ABSTRACT: Enhancer identification using H3k27ac ChIP-ChIP in mouse MV+ and RAG, using custom tilling array covering a 66 Mb region around Pax6 (Chr2:75,000,000-141,000,000) mm9. Additional loci and regions, Sox2 (chr3:32,000,000-37,000,000), Otx2 (chr14:48,500,000-50,500,000), Rax (chr18:65,500,000-68,000,000), Hba a-globin (chr11:32,050,000-32,450,000), Six3 (chr17:85,200,000-86,700,000), Sox1 (chr8:11,800,000-12,800,000), Mab21L2 (chr3:85,850,000-86,850,000), Bmp4 (chr14:46,500,000-47,500,000), NeuroD1 (chr2:79,050,000-79,600,000), Prox1 (chr1:191,700,000-192,700,000), Hmx1 (chr5:34,700,000-36,200,000), H19-Igf2 (chr7:149500000-150500000), Sox9 (chr11:110000000-116000000). Overall design: Two cell lines, with two biological replicates of MV+ and RAG H3K27ac ChIP hybrisdised verus input DNA.

INSTRUMENT(S): NimbleGen 110505_AB_MM9_regions_ChIP tiling array

SUBMITTER: nick gilbert  

PROVIDER: GSE119659 | GEO | 2018-10-18

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE119659_MV+_H3K27ac_2rep.bedgraph.gz Bedgraph
GSE119659_RAG_H3K27ac_2rep.bedgraph.gz Bedgraph
GSE119659_RAW.tar Raw
filelist.txt Txt
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Publications

Polymer Simulations of Heteromorphic Chromatin Predict the 3D Folding of Complex Genomic Loci.

Buckle Adam A   Brackley Chris A CA   Boyle Shelagh S   Marenduzzo Davide D   Gilbert Nick N  

Molecular cell 20181018 4


Chromatin folded into 3D macromolecular structures is often analyzed by chromosome conformation capture (3C) and fluorescence in situ hybridization (FISH) techniques, but these frequently provide contradictory results. Chromatin can be modeled as a simple polymer composed of a connected chain of units. By embedding data for epigenetic marks (H3K27ac), chromatin accessibility (assay for transposase-accessible chromatin using sequencing [ATAC-seq]), and structural anchors (CCCTC-binding factor [CT  ...[more]

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