PhD and postdoc training school on ChIP-seq (wet-lab) and basic functional animal genome analysis (24-28 June 2019)

Course

PhD and postdoc training school on ChIP-seq (wet-lab) and basic functional animal genome analysis (24-28 June 2019)

Organised by Wageningen Institute of Animal Sciences (WIAS), Animal Breeding and Genetics
Date

Mon 24 June 2019 until Fri 28 June 2019

Venue Orion, building number 103
Bronland 1
103
6708 WH Wageningen
+31 (0) 317 48 87 77
Room Orion building Rooms: C4030, P5009 and P5010, PC3031 and C1040

For the Training School leaflet with all information, please click here:

Preliminary programme

Monday 24th June: ‘intro group and wet-lab’

Start: 09:30 hour

9h30 – 10h30: Outline of the week

Introduction of trainee’s

10h30-11h30: technical presentation about ChIP and organization of the practicals

Afternoon: Chromatin preparation - duration:  ~ 3h30  

and Start Immunoprecipitation – duration ~ 30-45 min

 

Tuesday 25th June: ‘start up analysis’

Morning:

9h – 10h30 : Group 1: ChIP (washes, elution and start cross-link reversion)

Group 2:  Analysis: Intro Linux and data sets

10h45 – 12h15 : Group 2: ChIP (washes, elution and start cross-link reversion)

Group 1:  Analysis: Intro Linux and data sets

Afternoon session: Seminar

4 speakers: national and international specialists connected to the topic

  • Dr Diego Villar (Queen Mary University of London, UK)
  • Dr Lucia Daxinger (Leiden University and Medical Centre, The Netherlands)
  • Prof. Dr Marianne Rots (University Medical Centre Groningen, the Netherlands)
  • Dr Sylvain Foissac (INRA, France)

Evening: network dinner

 

Wednesday 26th June: ‘data quality’

Morning:

DNA purification (1 h) + Qubit quantification  + qPCR (2-3 h) ;

during qPCR – talk: Tools to decode Epigenetics – Jerome Kroonen

Afternoon session:

Analysis: data quality, trimming, aligning RNA seq, Chip-seq and methylation

 

Thursday 27th June: ‘start up analysis’

Morning:

Wet-lab: qPCR analysis

Analysis: peak calling, gene expression calling, methylation calling

Afternoon session:

Computer practical: Biosamples and data submission FAANG by EBI, UK

Pizza evening

 

Friday 28th June: ‘integration of data’

Wet-lab: discus results and wrap-up

Analysis: Integration of data and wrap-up.

End: 13:00 hour