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 genomes available at the UCSC Browser. These are small text files ending with “chrom.sizes” that can be found under the “Full data set” 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.
-
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”, “DNA microarray” and “Microarrays – DNA Chips” for a quick introduction to the microarrays technology.
- Learn about the MIAME (Minimum Information About a Microarray Experiment) project.
- Read about design, normalization methods, and exploratory analysis in a microarray experiment.
Weeks 6-7 – RNA-seq
- Watch “Illumina sequencing by Synthesis” and “Illumina sequencing technology” for a quick introduction to Illumina’s NGS technology.
- Read all about RNA-seq on RNA-seqlopedia an easy to read online resource by the University of Oregon.
- Read the introduction to RNA-sequencing by Illumina
- Watch the video “A gentle introduction to RNA-seq”
- Read the publication Wang, Zhong et al. “RNA-Seq: a revolutionary tool for transcriptomics.” Nature reviews. Genetics vol. 10,1 (2009): 57-63. doi:10.1038/nrg2484
- Follow the Galaxy tutorial on RNA-seq https://galaxyproject.org/tutorials/rb_rnaseq/
