Random ramblings about some random stuff, and things; but more stuff than things -- all in a mesmerizing and kaleidoscopic soapbox-like flow of words.
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome -- Sultan et al. 321 (5891): 956 -- Science
A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome
This is another very interesting paper that uses the RNA-seq method to produce a very fine map of Alternative Splicing in the human genome. In this case, they've sequenced poly(A) RNA from human embryonic kidney cells and B cells. The authors use the term "digital transcript-counting approach
Digital expression levels were normalized (NE values) by taking into account the theoretical number of unique 27-mers (sequences that are 27 bases long) contained in each exon and the total number of reads generated in each experiment.
which in my mind translates to: sequence a shitload of 27mers (Illumina), map them to the reference genome, and count the amount of reads that stack up to the coding exons. If they don't map to currently predicted exons (about 25% of the reads), then have a look and see what is that region. A high proportion of these previously unknown exons were unique to one cell type and likely to be differentially expressed.
Some alternative splicing summary numbers: average of 7.2 junctions per gene with a mean density of 3.8 reads per junction (not that much?). The most common AS event is exon skipping, with events mostly affecting one or two exons.
I am loving all these RNA-seq experiments!