Next Generation DNA sequencing is revolutionizing transcriptome analysis and giving us much deeper insights into the ways in which genes are expressed. Next Wednesday, December 17th, Geospiza will host a webinar on how FinchLab and GeneSifter simplify complex data analyses to turn millions of reads into informative datasets that can yield scientific insights.
Next Gen sequencing is quickly becoming an attractive option for gene expression analysis because the vast numbers of sequences that can be obtained provide a highly sensitive way to evaluate the RNA population inside of a cell. In addition to rRNA, tRNA, and mRNA, new assays are quickly emerging to measuring non-coding RNA and multiple classes of small RNAs as well. Moreover, as we obtain deeper information, largely through Next Gen, we learn that even mRNA is more complicated than previously thought. In yeast, 85% of the genome might be transcribed and new reports indicate that 92-97% of human genes undergo alternative splicing.
Next Gen sequencing applications such as RNA-Seq, Tag Profiling, and Small RNA Analysis allow whole genome analysis of coding as well as non-coding RNA at an unprecedented level. Current technologies can generate 200 million data points in a single instrument and can completely characterize all known RNAs in a sample, and identify novel RNAs and novel splicing events for known RNAs.
Join us next Wed. Dec 17 at 10:00 am (PDT) as we provide an overview of two applications, RNA-Seq and miRNA-Seq, using examples from publicly available datasets. The presentation will include a discussion of the challenges and solutions for how sequence data from the transcriptome can be analyzed in routine ways with Geospiza’s products.
Castle J.C., Zhang C., Shah J.K., Kulkarni A.V., Kalsotra A., Cooper T.A., Johnson J.M., 2008. Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines. Nat Genet 40, 1416-1425.
David L., Huber W., Granovskaia M., Toedling J., Palm C.J., Bofkin L., Jones T., Davis R.W., Steinmetz L.M., 2006. A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A 103, 5320-5325.
Mortazavi A., Williams B.A., McCue K., Schaeffer L., Wold B., 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 5, 621-628.
Seila A.C., Calabrese J.M., Levine S.S., Yeo G.W., Rahl P.B., Flynn R.A., Young R.A., Sharp P.A., 2008. Divergent Transcription from Active Promoters. Science.
Wang E.T., Sandberg R., Luo S., Khrebtukova I., Zhang L., Mayr C., Kingsmore S.F., Schroth G.P., Burge C.B., 2008. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476.
Wold B., Myers R.M., 2008. Sequence census methods for functional genomics. Nat Methods 5, 19-21.
Zamore P.D., Haley B., 2005. Ribo-gnome: the big world of small RNAs. Science 309, 1519-1524.