Global transcriptional analysis and genome-wide analysis of chromatin state in extended pluripotent stem cells, primed pluripotent stem cells, and naïve pluripotent stem cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 20 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
- 20 samples: 17 distinct titles, 3 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
- 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.
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.
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.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE89303_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA351266 and SRA study SRP074076. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 20 sample titles: 17 distinct titles with little repetition. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM2135522 H1-1
- GSM2135523 H1-2
- GSM2135524 H1-EPS-1
- GSM2135525 H1-EPS-2
- GSM2135526 ES1-EPS-1
- GSM2135527 ES1-EPS-2
- GSM2135528 mc2i
- GSM2135529 OG-2i
- GSM2135530 mc6-1
- GSM2135531 OG6-3
- GSM2365677 H1_H3K4me3
- GSM2365678 H1_H3K27me3
- GSM2365679 H1-EPS_H3K4me3
- GSM2365680 H1-EPS_H3K27me3
- GSM2365681 Human_input
- GSM2365682 mc2i_H3K4me3
- GSM2365683 mc2i_H3K27me3
- GSM2365684 mc6-1_H3K4me3
- GSM2365685 mc6-1_H3K27me3
- GSM2365686 Mouse_input
- GSE305653 Genome-wide chromatin recording resolves dynamic cell state changes 110 samples shares genome-wide, chromatin, state
- GSE243065 Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity 783 samples shares chromatin, stem
- GSE89309 Chromatin states of tumor-specific T cells 97 samples shares chromatin, state
- GSE291992 Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization 47 samples shares chromatin, state
- GSE291990 Z-DNA formation induces the totipotent-like state and primes Zscan4-dependent chromatin compartmentalization [scRNA-seq] 2 samples shares chromatin, state
- GSE304363 Paraspeckle Protein NONO Regulates Active Chromatin by Allosterically Stimulating NSD1 36 samples shares chromatin
- GSE255572 Chromatin remodeler CHD7 regulates neurogenic gene expression via controlling chromatin accessibility and modifications of histone marks H3K27me3 and H3K4me3 34 samples shares chromatin
- GSE291229 Reducing batch effects in single cell chromatin accessibility measurements by pooled transposition with MULTI-ATAC 19 samples shares chromatin
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.