It has been a good week for RNA-seq enthusiasts. First, Kallisto, a new way to quantify transcript expression, happened at BOG15. And this weeks’ Science magazine has three interesting papers on the GTEx (Genotype-Tissue Expression) Project, dealing with boatload of RNA-seq data, a whopping 1641 human RNA-seq samples to be precise. In addition, there are three more papers in Genome Research, Bioinformatics, and PLoS Computational Biology.
The GTEx project originally started as pilot project in 2010 with the goal of creating a resource of genotypes and gene expression in multiple tissues, understanding the how variants regulates gene expression in multiple tissues, and potentially its association to human diseases.
Over the last few years, GTEx has collected massive amounts of RNA-seq data from multiple tissues and genotyped the same individuals. The three papers in Science present the results from pilot analysis looking at expression landscape across human tissues, allele-specific expression, genomic imprinting expression QTLs, and the effect of protein truncating variants in transcriptome.
- The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans
- The human transcriptome across tissues and individuals
- Effect of predicted protein-truncating genetic variants on the human transcriptome
- The landscape of genomic imprinting across diverse adult human tissues
- Assessing allele-specific expression across multiple tissues from RNA-seq read data
The Science magazine also has commentary on the three paper
This month’s Nature Genetics paper also uses the GTEx data to look at imprinting across tissues in human (and mouse). Here is the link to the blog post on the paper.