← BioTransfer GEO Dataset Finder
GEO series

ChIP-chip from mouse embryonic stem (mES) cells

GSE20551 Mus musculus (mouse) ChIP-seq / ATAC-seq (genome binding and open chromatin) 7 samples Submitted 2010/10/14 Platform GPL5811
At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 7 samples

What it is
ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism
Mus musculus (mouse)
Samples
7 samples
Data you can get
A processed table (series matrix) and supplementary files from NCBI.
Summary (written by the submitters)
c-Myc (Myc) is an important transcriptional regulator in embryonic stem (ES) cells, somatic cell reprogramming, and cancer, yet functionally differs from the core pluripotency transcription factors, such as Oct4, Sox, and Nanog. Here, we identify a Myc-centered regulatory network in ES cells by combining protein-protein interaction and protein-DNA interaction studies, and show that Myc interacts with the NuA4 histone acetyltransferase complex, previously identified as a critical regulator in ES cell identity.
Read the full summary ↓
In combination with previously studied transcriptional regulatory network information, we construct three ES cell modules (Core, Polycomb, and Myc) and show that these modules are functionally separable in ES, iPS, MEFs, and partial iPS cells, suggesting that the overall ES cell transcription program is comprised of distinct functional units. With these regulatory modules as an analytical tool, we have reassessed data suggesting that cancer cells reactivate an ES cell-like transcriptional program. We find that the Myc module, independent of the Core module, is active in various cancers and predicts cancer outcome. These observations argue against the hypothesis linking an embryonic gene expression signature with cancer or cancer stem cells. The apparent similarity of cancer and ES cell signatures reflects in large part the pervasive nature of Myc regulatory network. Keywords: Biotin-mediated Chip-chip, Antibody ChIP-chip, Mouse embryonic stem cells
This dataset
Open GSE20551 in finder → Find more mouse ChIP / ATAC / CUT&Tag datasets →
Download · which file do I need?

Direct links to NCBI, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓
2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need.

All supplementary files ↗
3 · The original raw files

Whole study · RAW.tar

Everything the authors deposited as one archive (GSE20551_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.

Whole study · RAW.tar ↓

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA125311. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 20946988) ↗
Samples in this study

The sample list for this study is not cached yet. Press Load samples and it will be fetched from NCBI.

+ 7 more — browse all 7 samples with per-sample file links →

Datasets on a similar topic

Search all mouse ChIP / ATAC / CUT&Tag datasets in GEO →

Share this dataset

Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.