GEO series

Genome-wide analysis of chromatin state in extended pluripotent stem cells, primed pluripotent stem cells, and naïve pluripotent stem cells

GSE89301 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 10 samples Submitted 2017/04/06 Platform GPL17021Platform GPL16791

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 10 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: Homo sapiens (human)
Samples: 10 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)

Among all known cultured stem cell types, pluripotent stem cells (PSCs) sit atop the landscape of developmental potency and are characterized by their unrestricted developmental potential, able to generate all cell types of an adult organism. However, PSCs show limited contribution to the extraembryonic (ExEm) tissues, in particular, those giving rise to the placenta in vivo.

Read the full summary ↓

To date, it remains unknown whether stem cells with both embryonic and extraembryonic developmental potency can be captured and maintained in vitro. Here, we identify a new chemical cocktail that allows for the generation of stem cells with extended developmental potency from mouse and human, designated as extended pluripotent stem (EPS) cells, which is capable of chimerizing both embryonic and extraembryonic tissues. Importantly, a single mouse EPS (mEPS) cell shows widespread contribution to both embryonic and extraembryonic lineages in chimeric mouse conceptuses at late-gestation stages, and permits generation of high-grade germline competent chimeras as well as single EPS-derived viable mice by tetraploid complementation. Furthermore, human EPS (hEPS) cells contribute to embryonic and extraembryonic tissues in interspecies chimeric mouse conceptuses. Compared to known PSCs, EPS cells show unique gene modules that upregulate in embryonic cells from early preimplantation development. Further analysis shows that PARP1 inhibition is required for maintaining EPS potency. Our findings constitute a first step towards capturing pluripotent stem cells with extraembryonic developmental potentials in culture, and open new avenues for generating mammalian PSCs with robust chimeric competency for basic and translational research.

This dataset

Open GSE89301 in finder → Find more ChIP / ATAC / CUT&Tag datasets →

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 GSE89301_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 ↗

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 PRJNA351267 and SRA study SRP092260. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 28388409) ↗

Samples in this study

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

+ 10 more — browse all 10 samples with per-sample file links →

Datasets on a similar topic

GSE80732 Global transcriptional analysis of human extended pluripotent stem cells, human primed pluripotent stem cells, mouse extended pluripotent stem cells, and mouse embryonic stem cells by RNA-seq 10 samples shares pluripotent, extended, primed, stem
GSE52824 Derivation of novel human ground state naïve pluripotent stem cells. 71 samples shares pluripotent, state, stem
GSE52617 Derivation of novel human ground state naïve pluripotent stem cells [ChIP-seq; RRBS-seq] 59 samples shares pluripotent, state, stem
GSE320163 Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity [ATAC-Seq] 377 samples shares chromatin, stem
GSE324892 Systematic Benchmarking of CUT&Tag Improves the Reliability and Reproducibility of Chromatin Analysis II 35 samples shares chromatin, stem
GSE292571 SUMOylation orchestrates a metastable heterochromatin state on a MORC3-responsive element to silence IFNB1 at a distance [ChIP-seq] 116 samples shares chromatin, state
GSE269958 Chromatin-associated LTR RNA m5C oxidation by TET2 regulates chromatin state and leukemogenesis [seq_DNA-ATAC_set2] 54 samples shares chromatin, state
GSE320165 Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity [Cut&Tag] 46 samples shares chromatin, stem

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

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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.