TrainMALTA Summer School on Epigenomics

Transcription

1 TrainMALTA Summer School on Epigenomics th July 2018, University of Malta

2 TrainMALTA Partners: University of Malta University of Cambridge Katholieke Universiteit Leuven This project has received funding from the European Union s Horizon 2020 research and innovation programme under grant agreement No Page 2 of 9

3 TrainMALTA Summer School 2018 Timetable Time 09:00-10:00 10:00 11:00 11:00 12:00 Group A only: Introduction to ChIP Group A only: Introduction to the practicals Monday 23 rd July Day 1 Group B only: Review and discuss sonicated chromatin and run additional QC checks Practical 1: Antibody-Bead Binding (Direct method) and Chromatin Pre-clearing Tuesday 24 th July Day 2* Practical 4: ChIP Washes and Elution + Practical 5: Input Preparation and Reverse Crosslink Train the Trainer Workshop Wednesday 25 th July Day 3 Talks Talks Talks Group B: Practical 7: Microplex Library Preparation Thursday 26 th July Day 4 Unix and R recap Friday 27 th July Day 5 Alignment and peak calling 12:00 13:00 Lunch Lunch Lunch Lunch Lunch 13:00 14:00 14:00 15:00 15:00 16:00 16:00 17:00 17:00 18:00 Practical 2: Recover Pre-cleared Chromatin and Wash Loaded Beads Practical 3: Prepare Chromatin Immunoprecipitation Journal Club Practical 6: RNase, Proteinase K, Recover ChIP DNA, and quantify Train the Trainer Workshop Practical 8: Library Size Selection Bioanalyzer Runs Practical Sum-up and discussion FastQC and IGV recap Chip-seq results integrative analysis Group A: Introduction to ChIP and Library Prep group Group B: Performing ChIP on own Samples group All summer school participants *The Train the Trainer workshop and the Summer School will run in parallel on Day 2.

4 Day 1 - Monday, 23 rd July 2018 Lab 307 Premise: Group One will use the chromatin and antibodies prepared in Cambridge and will involve a step by step guide to the process in the ChIP process, including a introduction etc. Group Two will be supplying their own chromatin and antibodies, so they will have a load of home-work prior to the practicals; this will also require at least some basic knowledge of the process to complete it. Notably group two will do the entire process, whilst certain aspects of the process will be gratuitous and be missed out for group one :30 Welcome and Brief Introduction and Division into Two Groups Group 1: 09:30-10:00 Talk: Introduction to ChIP 10:00-11:00 Talk: Introduction to Practicals Group 2: 09:30-11:00 Open forum to discuss the home-work and review all quality control etc. It is also to gauge the quantity of samples each person wants to process etc. and to clear up exactly what they should be doing. It will be desired that each person in this group has an outline of their experimental design (ideally in excel) and should be happy for it to be modified nothing complicated but a template of the practical objective (no need for the hypothesis/question) 11: Lab practical (Groups 1+2): Chromatin Pre-clearing and Bead-Antibody Preparation Lunch 13:00 15:00 Lab practical (Groups 1+2): Recover Chromatin and Wash Beads 15:00-17:00 Lab practical (Groups 1+2): Prepare Overnight Chromatin Immunoprecipitation Page 4 of 9

5 Day 2 - Tuesday, 24 th July 2018 Lab 307 9:00 12:00 Lab practical (Groups 1+2): ChIP Washes and Elution + Input Preparation + Reverse Crosslink 12:00 15:00 Extended Lunch and Simultaneous Journal Club We have a 4 hour incubation (so at least 3 hours free for everyone). We plan to include a form of Journal Club were every participant is expected to review the articles (2-3) that we supply, and groups will be made to present the work in an open discussion. 15:00 17:00 Lab practical (Groups 1+2): Rnase, Proteinase K, Recover ChIP DNA, and Quantify. Page 5 of 9

6 Train the Trainer Workshop - Tuesday, 24 th July 2018 Room :00 13:00 Lunch Page 6 of 9

7 Day 3 - Wednesday, 25 July 2018 Lab 307 Group 1: Either come in late (e.g. 12:00 or we can have talks or open discussions) - the Library Prep kit being used is a straight forward and completely gratuitous process if the samples are not being sequenced; the method itself is guaranteed to work if manufacturer's instructions are followed. Later in the day, participants will be supplied with a completed library to finished the Practicals. 09:00 12:00 Lab Practicals: Group 2 only! (earlier the better!) Microplex Library Preparation 12:00 13:00 Lunch 13:00 15:00 Lab practical (Groups 1+2): Library Size Selection Bioanalyzer Run (Coffee break for most) 15:00 16:00 Talk: Practical Sum-up Page 7 of 9

8 Day 4 - Thursday, 26 July 2018 Room :00 12:00 Recap of R and unix command line tools 12:00 13:00 Lunch 13:00 14:45 FastQC practical 14:45 15:00 Coffee break 15:00 17:00 IGV practical Page 8 of 9

9 Day 5 - Friday, 27 July 2018 Room :00 12:00 Alignment and Peak calling 12:00 13:00 Lunch 13:00 14:45 Motif analysis 14:45 15:00 Coffee break 15:00 17:00 Integrative analyses Page 9 of 9