MRes Course on Post-genomics, Transcriptomics and bio-informatics - D2DPG1

MRes in Advanced Genomic and Proteomic Sciences (AGPS)
UoN Module: D2DPG1 Genomics/Transcriptomics/Bioinformatics.

Location: The Limes Computer Room

Monday 20th Oct

09:00 - 10:00 Study Time : Day-paper for afternoon tutorial – “crop circles”
10:00 - 10:15 Introduction to module.
10:15 - 11:00 Introduction to genomics
11:30 - 12:00 Introduction to genome databases
12:00 - 13:00 QTLs - Kamal Swarup
14:00 - 15:00 Practical: How to exploit genome database resources using basic sequence analysis tools such as BLAST
Tools to exploit genome database resources for investigating gene function
15:00 - 16:00 Practical: Individual assignment to investigate gene function.
16:00 - 17:00 Tutorial on paper 1.
Tuesday 21st Oct
09:00 - 10:00 Study Time : Day-paper for afternoon tutorial – “allergy arrays”
10:00 - 12:30 Introduction to general transcriptomics / array analysis
Basic concept movie
14:00 - 15:00 Introduction to Affymetrix GeneChips
15:30 - 16:30 Tutorial on paper 2.
Wednesday 22nd Oct
09:30 - 12:15 ***Experimental Design Module ***
14:00 - 17:00 Tour of Genomics facilities including films
Spotting and Agilent movies
Nanodrop film
Thursday 23rd Oct
09:00 - 10:00 Study Time :Day-paper for afternoon tutorial – “How to decide”
10:00 - 11:00 Authentigene - a genomics spin-out company
11:30 - 12:30 Xspecies - a novel research application of transcriptomics
14:00 - 15:00 Next-gen sequencing technologies
From making libraries to sequencing the 'old' way.
454 summary
Illumina/Solexa
PacBio - Single Molecule Real Time
15:30 - 16:30 Tutorial on paper 3.
Friday 24th Oct
09:00 - 14:00 Study Time : Day-paper for afternoon tutorial – “Homotopic filter”
14:00 - 15:00 Research applications of trancriptomics (Chungui Lu)
15:30 - 16:30 Tutorial on paper 4.
Monday 27th Oct
09:30 - 12:30 Introduction to Affy datasets
Including Study Time: choice of dataset.
14:00-15:00 Study Time: background on choice of Affy datasets (first 2 slides of talk).
Tuesday 28th Oct
09:30 - 12:00 Introduction to Genespring Workgroup (Neil Graham)
Including Practical: training session in Genespring (Neil Graham).
12:00 - end Study Time: analysis of Affy datasets.
Wednesday 29th Oct
09:30 - 12:15 ***Experimental Design Module ***
14:00-15:30 Social context of genomics.
1. The film GATTACA will be shown
2. 'Background' Times article 24th Oct 2008
Resource : Genespring tutorial
15:30-end Study Time: Affy data analysis and talk preparation.
Thursday 30th Oct
ALL DAY - Study Time: Affy data analysis and talk preparation.
Friday 31st Oct
09:30 - 12:15 Study Time: Affy data talk preparation.
12:15 - 12:30 HAND-IN of presentations - MUST be PowerPoint format.
14:00 - 16:00 Assessment: 12 student presentations & discussion.
Alphabetical by surname.
10 slides in 15 minutes all students as individuals
student deliverable - please provide a single file powerpoint talk on CD or USB
The Marking Criteria
1. Elekwachi, Chijioke - AtGenExpress: Basic hormone treatment of seeds (184)
2. Emmerson, Zoe - Circadian gene expression under different light treatments (196)
3. Devenport, Neil - AtGenExpress: Stress Treatments (Salt stress) (140)
4. Hickman, Graham - Low chronic exposure of Arabidopsis thaliana to Caesium-137 (324)
5. Lai, Hung-Ming - Systemic signalling of irradiance and CO2 concentration in Arabidopsis (Treatment 2: Elevated CO2 and Ambient Light) (157)
6. Lunn, Daniel - AtGenExpress: Effect of auxin inhibitors on seedlings (186)
7. Manocha, Mansi - Transcriptional profiling of laser-capture micro-dissected embryonic tissues (55)
8. Pan, Yu - Ethylene induced hyponastic growth in Arabidopsis thaliana (32)
9. Sood, Deepti - AtGenExpress: Stress Treatments (Cold stress) (138)
10. Vadakekolathu, Jayakumar - Transcriptome changes of Arabidopsis during pathogen and insect attack (330)