Dataset features

Specifications


Application: RNA-seq analysis
Number of samples: 131
Release date: Oct 13 2011
Last update date: Nov 14 2017
Access: Public
Taxon: Homo sapiens
Dataset link The evolution of gene expression levels in mammalian organs

Experimental Protocol


To study mammalian transcriptome evolution at high resolution, we generated RNA-Seq data (∼3.2 billion Illumina Genome Analyser IIx reads of 76 base pairs) for the polyadenylated RNA fraction of brain (cerebral cortex or whole brain without cerebellum), cerebellum, heart, kidney, liver and testis (usually from one male and one female per somatic tissue and two males for testis) from nine mammalian species: placental mammals (great apes, including humans; rhesus macaque; mouse), marsupials (gray short-tailed opossum) and monotremes (platypus). Corresponding data (∼0.3 billion reads) were generated for a bird (red jungle fowl, a non-domesticated chicken) and used as an evolutionary outgroup. Important note: Fluorophore intensity files were processed with the Ibis base caller (version 1.11). As illustrated in Supplementary Note Table 1 and Supplementary Note Figure 1 of Brawand et al. (Nature 2011), we found that Ibis significantly increased the number of usable reads and drastically reduced the error rate. However, Ibis quality values are not comparable to those from Illumina values, which should be taken into account when using our data and interpreting their quality relative to data established using other base calling approaches.

Repositories


GEO

GSE30352

ArrayExpress

E-MTAB-3718

ArrayExpress

E-MTAB-3717

ArrayExpress

E-MTAB-3716

ArrayExpress

E-GEOD-30352

ArrayExpress

E-MTAB-3719

ENA

SRP007412

BioProject

PRJNA143627

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