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m6A RNA modification controls cell fate transition in mouse embryonic stem cells

GSE52681 Mus musculus (mouse) Expression microarray 17 samples Submitted 2014/10/16 Platform GPL6193Platform GPL13112
At a glance

Expression microarray · mouse · 17 samples

What it is
Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
Organism
Mus musculus (mouse)
Samples
17 samples: 7 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get
A processed expression table (series matrix) and the array files, from NCBI.
SuperSeries — this record groups several sub-series.
Summary (written by the submitters)
This SuperSeries is composed of the SubSeries listed below.
This dataset
Open GSE52681 in finder → Find more mouse microarray 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 GSE52681_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: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.

Also filed as BioProject PRJNA229784 and SRA study SRP033269. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 25456834) ↗
Study design
7 conditions, mostly in duplicate
mESC luciferase shRNA, replicate # ×3 mESC Mettl3 shRNA #1 replicate # ×2 mESC Mettl3 shRNA #2 replicate # ×2 mESC Input sample, ×2 mESC m6A IP sample, ×2 mESC mettl3 KO Input sample, ×2 mESC mettl3 KO m6A IP sample, ×2 mESC Input sample ×1 +1 more

Supports a between-group comparison across 15 samples.

How we read this: 7 replicated groups read from 17 sample titles; they account for 15 of them. 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.

Samples in this study
Datasets on a similar topic

Search all mouse microarray 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.