Introduction to general transcriptomics / array analysis
NOTE for 2012 - shrink this - too long!!!
small array animation
11:00 - 11:30 Break
11:30 - 12:30 PRACTICAL: Introduction to Bioconductor (Estrogen arrays)
affylmGUI notes
Estrogen data (48MB)
12:30 Lunch break
Afternoon - ***Experimental Design Module***
Wednesday 5th Oct
09:00 - 10:00 UNSUPERVISED Study Time :Paper for today's tutorial – “Equine transcriptome”
10:00 - 10:30 Introduction to Affymetrix GeneChips
10:30 - 11:00 Break
11:00 - 12:30 Q & A with an Affymetrix operator (Zoe Emmerson) including lab tour and videos:
ALL VIDEOS IN ONE
12:30 - 13:30 Lunch break
13:30 - 14:30
Experiment design and Xspecies - a research hack for transcriptomics
14:30 - 15:00 TUTORIAL on equine transcriptomics (paper 3).
15:00 - 15:30 Break
15:30 - 16:30 PRACTICAL: Rubber xspecies transcriptomics with Bioconductor.
Rubber notes
Rubber data (43MB)
Thursday 6th Oct
09:00 - 11:00 UNSUPERVISED Study Time : Day-paper for today's tutorial – "biophysics of arrays"
11:00 - 11:30 Break
11:30 - 12:30Authentigene - a genomics spin-out company
12:30 - 13:30 Lunch break
13:30 - 16:00 Social context of genomics.
- The film GATTACA will be shown
- 'Background' Times article from 2008
- ~15:00-15:30 TUTORIAL on biophysics of arrays (paper 4).
Friday 7th Oct
09:00 - 10:00 UNSUPERVISED
Study Time : day-paper for today's tutorial – “RNAseq”
possible paper for 2012
10:00 - 11:00 TUTORIAL: RNAseq (paper5)
11:00 - 11:30 Break
11:30 - 12:30 Next-gen sequencing technologies Including sequencing 'game'.
OPTION: From making libraries to sequencing the 'old' way.
13:00 - 14:00 Lunch break
14:00 - 14:30 Description of the PROJECT and introduction to GEO.
14:30 - 15:30 Research applications of Transcriptomics (Chungui Lu)
15:30 - 16:00 Break
16:00 - 16:30Time to select your PROJECT DATA
Monday 10th Oct
09:30 - 12:00 UNSUPERVISED Final selection of your INDIVIDUAL PROJECT DATA.
Including Study Time: choice of dataset.
You should be studying IN THE LIMES
12:00 - 12:30 REGISTRATION of choice of dataset.
12:30 - 13:30 Lunch break
13:30 - end Study Time: biological background on choice of Affy datasets (first 2 slides of talk).
Tuesday 11th Oct
AM - personal study time: analysis of Affy datasets.
Youshould be studying IN THE LIMES
11:30 - 12:30 - Partek experience.
Link to software - please install 6.6 Beta
The licence server is 27000@128.243.222.222
the software will ask for this on startup
You will also have to set the proxy (mainproxy.nottingham.ac.uk) and proxy port (8080) under preferences.
Suggested work: Loading data, constructing experiment table, generating QC data (slides 3 & 4).
Afternoon - ***Experimental Design Module***
Wednesday 12th Oct
ALL DAY - personal study time: analysis of Affy datasets.
You should be studying IN THE LIMES
Suggested work: Normalising and deriving contrasts, Analysing contrasts, producing toptables/plots (slides 5 & 6).
Thursday 13th Oct
ALL DAY - personal study time: analysis of Affy datasets.
You should be studying IN THE LIMES
Suggested work: Chasing differential genes, making biological inferences, following the literature (remaining slides).
Friday 14th Oct
09:30 - 10:45 Final Study Time: Affy data talk preparation.
You should be studying IN THE LIMES
10:45 - 11:00 HAND-IN of presentations - MUST be PowerPoint ppt format only.
11:00 - 11:30 Data Mining: Multiple Attributes and Feature Selection (Silang Luo).
11:30 - 13:00 Lunch and relax!
13:00-15:00 Assessment: Student presentations & discussion.
Alphabetical by name.
10 slides in 10 minutes + 2 minutes questions.
All students as individuals
student deliverable - please provide a single file powerpoint talk on CD or USB
The Marking Criteria (word document)
How to mark
Student talks
- Choulia Mola
presentation 1
- Faraz Khan
presentation 2
- Irene Nwajei
presentation 3
- Kidist Kibret
presentation 4
- Liana Kafetzopoulou
presentation 5
- Olubukola Ajigboye
presentation 6
- Presidor Kendabie
presentation 7
- Sajidah Chowdhury
presentation 8
- Xi Xu
presentation 9
- Zhuolin Sun
presentation 10
Late starter presentations given on 1st Feb 2012
- Sajidah Chowdhury
presentation 11
- Om Prakash
presentation 12
Extra files
