Expression studies

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In my course “From Genome Sequence towards Analysis of the Transcriptome” I will teach to the students today’s different technologies for transcriptome analysis and explain on selected publications how these technologies are used and what are the results one can obtain. An important aspect of my lecture will be to explain that there are “biased” methods, where we look at what we know from annotation (known genes) and that there are “unbiased” methods where we take the sequence information of the entire genome and interrogate for transcripts. The latter methods have revealed an unexpected complexity of the transcriptome which is far beyond the classical model of gene-transcript-protein.

Part A) Gene centered microarrays

Microarrays which are designed based on the annotation of the genome

Examples of their use in research:

a) Understanding complex biological processes

Article: A transcriptional Program Mediating Entry into Cellular Quiescence PLoS Genetics (2007), 3, e91

b) Use as a diagnostic tool

Article: Gene Expression Profiling Predicts Clinical Outcome of Breast Cancer Nature (2002), 415, 530

Part B) Quantitative real-time PCR: a sensitive tool for medium to high throughput transcript analysis

Basics of RT-qPCR, relative and absolute quantification, applications

Part C) Non gene-centered microarrays: tiling arrays

Examples for their use in research:

a) Analysis of the transcriptome of the human genome

Article: Novel RNAs identified from in-depth analysis of the transcriptome of human chromosomes 21 and 22 Genome Research (2004) 14, 331

Article: Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution Science (2005) 308, 1149

b) Identification of unannotated transcripts in Drosophila and their possible function

Article: Biological function of unannotated transcription during the early development of Drosophila melanogaster Nature (2006) 38, 1151

Part D) Ultra High Throughput Sequencing

Short introduction to UHTS (will be discussed in very much detail by Keith Harshman in semester 8), comparison of UHTS mRNAseq to microarray based approaches

NOTE: although the concept of the course will be certainly maintained there may be small changes, e.g. selection of other articles