GEO series

The evolution of gene expression levels in mammalian organs

GSE30352 Pan troglodytes; Pongo pygmaeus; Gallus gallus; Ornithorhynchus anatinus; Macaca mulatta; Pan paniscus; Monodelphis domestica; Gorilla gorilla; Homo sapiens; Mus musculus RNA-seq (gene expression) 131 samples Submitted 2011/10/13 Platform GPL13801Platform GPL13798Platform GPL13800Platform GPL13797Platform GPL13766Platform GPL13803Platform GPL13802Platform GPL13799Platform GPL10999Platform GPL11002

At a glance

RNA-seq (gene expression) · Pan troglodytes; Pongo pygmaeus; Gallus gallus; Ornithorhynchus anatinus; Macaca mulatta; Pan paniscus; Monodelphis domestica; Gorilla gorilla; Homo sapiens; Mus musculus · 131 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: Pan troglodytes; Pongo pygmaeus; Gallus gallus; Ornithorhynchus anatinus; Macaca mulatta; Pan paniscus; Monodelphis domestica; Gorilla gorilla; Homo sapiens; Mus musculus
Samples: 131 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)

Changes in gene expression are thought to underlie many of the phenotypic differences between species. However, large-scale analyses of gene expression evolution were until recently prevented by technological limitations. Here we report the sequencing of polyadenylated RNA from six organs across ten species that represent all major mammalian lineages (placentals, marsupials and monotremes) and birds (the evolutionary outgroup), with the goal of understanding the dynamics of mammalian transcriptome evolution.

Read the full summary ↓

We show that the rate of gene expression evolution varies among organs, lineages and chromosomes, owing to differences in selective pressures: transcriptome change was slow in nervous tissues and rapid in testes, slower in rodents than in apes and monotremes, and rapid for the X chromosome right after its formation. Although gene expression evolution in mammals was strongly shaped by purifying selection, we identify numerous potentially selectively driven expression switches, which occurred at different rates across lineages and tissues and which probably contributed to the specific organ biology of various mammals. Our transcriptome data provide a valuable resource for functional and evolutionary analyses of mammalian genomes.

This dataset

Open GSE30352 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 GSE30352_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 PRJNA143627 and SRA study SRP007412. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 22012392) ↗

Samples in this study

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

+ 131 more — browse all 131 samples with per-sample file links →

Share this dataset

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.