Weeks 1-2 – DNA and RNA
- Explore DNAs of different organisms in the UCSC Genome Browser.
- You can download the files containing the lengths of the chromosomes of multiple genomesĀ available at theĀ UCSC Browser. These are small text files ending with āchrom.sizesā that can be foundĀ under the āFull data setā link at each genome.
- Obtain 50K base pairs of DNA in the beta globin locus on human chromosome 11 (exercise from the Pevsner textbook).
- Read about the ENCODE (Encyclopedia of DNA elements) project.
- Explore the most widely used data file formats in bioinformatics and genomics.
- Explore miRBase, the microRNA database.
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GEO is a public functional genomics data repository for array-based and sequence-based datasets. Follow this tutorial to learn how to download fastq format data from published papers.
Weeks 3-5 – Microarrays
- Watch “DNA microarrays”,Ā “DNA microarray”Ā and “Microarrays – DNA Chips”Ā for a quick introduction to the microarrays technology.
- Learn about the MIAME (Minimum Information About a Microarray Experiment) project.Ā
- Read about design, normalization methods, and exploratory analysis in a microarray experiment.
Weeks 6-7 – RNA-seq
- Watch “Illumina sequencing by Synthesis”Ā and “Illumina sequencing technology” for a quick introduction to Illumina’s NGS technology.
- Read all about RNA-seq on RNA-seqlopediaĀ an easy to read online resource by the University of Oregon.
- Read the introduction toĀ RNA-sequencingĀ by Illumina
- Watch the video “A gentle introduction to RNA-seq”
- Read the publication Wang, Zhong et al. āRNA-Seq: a revolutionary tool for transcriptomics.āĀ Nature reviews. GeneticsĀ vol. 10,1 (2009): 57-63. doi:10.1038/nrg2484
- Follow the Galaxy tutorial on RNA-seq https://galaxyproject.org/tutorials/rb_rnaseq/Ā
