GEO series

Poly(A)-tail profiling reveals an embryonic switch in translational control

GSE52809 Arabidopsis thaliana; Drosophila melanogaster; Xenopus laevis; Mus musculus; Homo sapiens; Saccharomyces cerevisiae; Schizosaccharomyces pombe; Danio rerio RNA-seq (gene expression) 64 samples Submitted 2014/01/29 Platform GPL9453Platform GPL17682Platform GPL9115Platform GPL9302Platform GPL14875Platform GPL9408Platform GPL11154Platform GPL9319Platform GPL13112Platform GPL9250Platform GPL9061Platform GPL9377Platform GPL13988

At a glance

RNA-seq (gene expression) · Arabidopsis thaliana; Drosophila melanogaster; Xenopus laevis; Mus musculus; Homo sapiens; Saccharomyces cerevisiae; Schizosaccharomyces pombe; Danio rerio · 64 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Arabidopsis thaliana; Drosophila melanogaster; Xenopus laevis; Mus musculus; Homo sapiens; Saccharomyces cerevisiae; Schizosaccharomyces pombe; Danio rerio
Samples: 64 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)

Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater understanding of poly(A)-tail function. Here we describe poly(A)-tail length profiling by sequencing (PAL-seq) and apply it to measure tail lengths of millions of individual RNAs isolated from yeasts, cell lines, Arabidopsis thaliana leaves, mouse liver, and zebrafish and frog embryos.

Read the full summary ↓

Poly(A)-tail lengths were conserved between orthologous mRNAs, with mRNAs encoding ribosomal proteins and other 'housekeeping' proteins tending to have shorter tails. As expected, tail lengths were coupled to translational efficiencies in early zebrafish and frog embryos. However, this strong coupling diminished at gastrulation and was absent in non-embryonic samples, indicating a rapid developmental switch in the nature of translational control. This switch complements an earlier switch to zygotic transcriptional control and explains why the predominant effect of microRNA mediated deadenylation concurrently shifts from translational repression to mRNA destabilization.

This dataset

Open GSE52809 in finder → Find more RNA-seq 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 GSE52809_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 RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA230112 and SRA study SRP033369. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 24476825) ↗

Samples in this study

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+ 64 more — browse all 64 samples with per-sample file links →

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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.