GEO series

Molecular Criteria for Defining the Naive Human Pluripotent State [methylation profiling]

GSE85708 Homo sapiens (human) DNA methylation 12 samples Submitted 2016/08/16 Platform GPL16791

At a glance

DNA methylation · human · 12 samples

What it is: DNA methylationChemical marks on DNA that help switch genes on or off.
Organism: Homo sapiens (human)
Samples: 12 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)

Naive human pluripotent cells have been isolated in culture, but it remains unclear to what extent they resemble pluripotent cells in vivo. Here we present three lines of evidence indicating that naive pluripotent stem cells generated by small molecules share defining molecular signatures with the human preimplantation embryo. First, a comprehensive analysis of the transposcriptome reveals that naive human cells display a unique transposon expression profile of cleavage stage embryos.

Read the full summary ↓

Second, induction of naive pluripotency is accompanied by a genome-wide depletion in DNA methylation that is reversible upon differentiation except at imprinted regions. Third, allele-specific analysis demonstrates that female naive cells exhibit an X chromosome signature of the human preimplantation embryo. However, when introduced into mouse embryos the naive cells failed to efficiently generate interspecies chimeras. Our work provides a set of molecular benchmarks for evaluating the developmental identity of distinct human pluripotent states captured in vitro.

This dataset

Open GSE85708 in finder → Find more human methylation 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 GSE85708_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 beta-value tables or raw IDAT files among the supplementary files.

Also filed as BioProject PRJNA339143 and SRA study SRP085035. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 27424783) ↗

Samples in this study

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

+ 12 more — browse all 12 samples with per-sample file links →

Datasets on a similar topic

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GSE319444 DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML [PrimaryAML_WGBS] 20 samples shares methylation
GSE271127 Substained DNA demethylation and discordant chromatin accessibility dynamics define enhancer regulation during neural progenitor cell differentiation [ATACme] 18 samples shares methylation
GSE319448 DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML [CellCulture_WGBS] 12 samples shares methylation

Search all human methylation 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.