Blog Series: WoG, Cesky Krumlov: Day 8: Transcriptomics

Where did days 6 and 7 go??? 

Lost inevitably in the chaos of RStudio Lab tutorial, Python Lab Tutorial, Cesky Krumlov Castle touring and wine tasting followed by copious amounts of wandering, eating, more wandering, snow ball fights, freezing feet, beer drinking and sleeping.

The tutorials are well written, given there was no lecture for these, I've simply linked the tutorials...go nutz.

Remember I've discussed python in previous blogs in the programming prep blog for instance and linked Tyghe's website for further tutorials using python--the resources are at your fingertips, have at it! Feel free to direct python related questions to Tyghe's blog or if you happen to know Daniel McDonald from the Univ. of Colorado feel free to harass him as well...I will not link his email in case he hunts me down for giving you all his information and challenges my husband to a python duel--coding at dawn!

Now...on to week 2!!!

Blog Series: Workshop on Genomics, Cesky Krumlov; Preparation--Transcriptomics

Section 3: Transcriptomics

Four readings were suggested for this section which sadly are not open access, I'll link them below and then we'll dive into some crash-course transcriptomics and explore other resources available to round out your knowledge base on the subject.

• Garber, M et al., 2011. Computational methods for transcriptome annotation and quantification using RNA-seq. Nature Methods. 8:469-477.
• Pepke, S; B Wold and A Mortazavi. 2009. Computation for ChIP-seq and RNA-seq studies. Nature Methods. 6(11 Suppl):S22-S32.
• Mortazavi, A et al., 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods. 5:621-628.
• Johnson, DS et al., 2007. Genome-wide mapping of in vivo protein-DNA interactions. Science. 316:1497-1502.

Richard Twyman writes a nice short sum up of Transcriptomics and it's applications on the Wellcome Trust site. He defines transcriptomics as the global study of gene expression at the RNA level. So now we are not only talking about genes and their nucleotides, we are now talking about what those genes are doing, when those genes are active and to what degree those genes are active and regulated. All of this is measured through various forms of RNA (mRNA, tRNA, rRNA, ncRNA, siRNA or total RNA). The type of RNA you are interested in depends on what question are you asking. Richard Twyman has assisted in many research publications involving bioinformatic analysis and his recent publications can be found on the writescience site.

In terms of more articles to sift through that explore transcriptomics you can try the OmicsGateway with subject: Transcriptomics through Nature Publishing, though I cannot guarantee they'll be open access. Alternatively you can go to BMC Genomics which has a whole section on Transcriptomics where many of the articles are open access.