Genomics

Dataset Information

26

ChIP-Chip tiling array for CTCF and Rad21 in mouse β-TC3 cells (pancreatic insulinoma) MV+ (lens epithelium) and RAG cells (renal adenocarcinoma) over panel of genes including Pax6, Sox2, Otx2, Sox9.


ABSTRACT: CTCF and Rad21 ChIP-ChIP in mouse pancretic cells, pancreatic β-TC3 cells, lens epithelium MV+ cells and renal adenocarcinoma RAG cells, 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: Three cell lines, with two biological replicates of β-TC3, MV+ and RAG with both CTCF and Rad21 ChIP hybrisdised verus input DNA. CTCF (Antibody Cell signalling, D31H2) and Rad21 (Antibody Ab992).

INSTRUMENT(S): NimbleGen 110505_AB_MM9_regions_ChIP tiling array

SUBMITTER: nick gilbert  

PROVIDER: GSE119658 | GEO | 2018-10-18

REPOSITORIES: GEO

Dataset's files

Source:
Action DRS
GSE119658_MV+_CTCF_2rep.bedgraph.gz Bedgraph
GSE119658_MV+_Rad21_2rep.bedgraph.gz Bedgraph
GSE119658_RAG_CTCF_2rep.bedgraph.gz Bedgraph
GSE119658_RAG_Rad21_2rep.bedgraph.gz Bedgraph
GSE119658_RAW.tar Raw
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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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