• Suggested reading
• Campus Map

• 9:30am Register
• 9:30 - 9:45 introduction to the course.
• 9:45 - 10:45 Seminar Introduction to genomics and genotyping.
• 10:45 - 11:00 Coffee
• 11:00 - 12:30 Seminar Introduction to transcriptomics
• Resource: A short video on RNAseq analysis at DNA subway
• 12:30 - 1:00 Practical Introduction to GEO, File formats, and selection of experiments **
• Resource: Paper: Crowdsourcing transcriptomic data
• Resource: Cartoon: The importance of data deposition
• 1:00 - 2:00 Lunch - Sutton Bonington facilities or bring your own
• 2:00 - 3:15 Practical - Partek transcriptomics PtI (Marcos Castellanos-Uribe).
  • Resource: Folder of data for practical
• 3:15 - 3:30 Coffee
• 3:30 - 4:30 Practical - Partek transcriptomics ptII (Marcos Castellanos-Uribe).

Homework

• 9:30 Register
• 9:35 - 10:30 Seminar Sequencing methods.
• Resource: NextGen sequencing videos
• Resource: Early history (-2007) of sequencing [poster]
• 10:30 - 10:45 Coffee
• 10:45 - 11:30 Familiarisation Practical
• How to exploit genome database resources using basic sequence analysis tools such as BLAST
• 11:30 - 12:00 Team building: Gene function: Groups of ~5 students will prepare for the mini-group-project using the techniques learned so far, find out the gene name/locus and GO functions for as many of these genes as possible in the time allocated.
• 12:00 - 1:00 Practical tour (Castellanos & May)
• 1:00 - 2:00 Lunch - Sutton Bonington facilities or bring your own
• 2:00 - 3:15 Guided practical - Demonstration of transcriptome data in R/Bioconductor (May/Castellanos) followed by YOUR OWN ANALYSIS in Partek and/or Bioconductor
• Your specific dataset is downloadable from: GEO experiment accession
• Additional options to unarchive these data:
  1. The data as a zip archive
     An 'untaring' and 'ungzipping' site can be found here
  2. The same data as plain CEL files
• 3:15 - 3:30 Coffee
• 3:30 - 4:30 Experimental design (esp. for transcriptomics)
• Resource: Cartoon - Biologist vs statistician
• Optional: Transcript silencing (RNAi, miRNA)

Homework

• 9:30 Start
• 9:35 - 11:00 Interactive seminar Standards, bias and ontologies
• Crowdsourcing wisdom
• 11:00 - 11:15 Coffee
• 11:15 - 11:45 Seminar - A practical approach to phenomics (Darren Wells)
• 11:45 - 1:00 Tour of local Phenomics facilities
• 1:00 - 2:00 Lunch - Sutton Bonington facilities or bring your own
• 2:00 - 3:15 Practical
• Student preparation of transcriptomics data finishing with a round up of student results
• 3:15 - 3:30 Coffee
• 3:30 - 4:00 Seminar Practical use of transcriptomics
• 4:00 - 4:30 DNA barcoding (Marcos Castellanos-Uribe)