GEO series

Genome Wide Characterization of Genome Organization in Mouse ES cells

GSE64881 Mus musculus (mouse) Genome variation profiling by high throughput sequencing; Other 477 samples Submitted 2017/03/08 Platform GPL19736Platform GPL13112

At a glance

mouse · 477 samples

Organism: Mus musculus (mouse)
Samples: 477 samples
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.

Summary (written by the submitters)

The three-dimensional folding of genomes in the eukaryotic nucleus can influence the expression of genes. We used a new method to determine interactions between different chromatin regions genome-wide. Using a simple statistical model, we determine the subset of those interactions which represent stable contacts. We find an enrichment in contacts between active genes, between Polycomb-repressed genes, between enhancer elements and between enhancers and active genes.

This dataset

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Download · which file do I need?

Direct links to NCBI and ENA, 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, or the whole study as GSE64881_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

Also filed as BioProject PRJNA272507 and SRA study SRP052060. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28273065) ↗

Samples in this study

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

+ 477 more — browse all 477 samples with per-sample file links →

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.