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Weekly Todo list

2021

2022

10.01.2022 - 14.01.2022 {#week-02}

IDH Project

  • Analyse DNA methylation from Koichi data with the Focal_disruption_of_DNA_methylation approach
    • Compare Good and Bad responder at Baseline -> DMR_Response
    • Compare Baseline and CD34+ -> DMR IDH
    • Response specific DMR
    • Compare Good and Bad responder at post treatment -> DMR residuel
    • Compare Post and Baseline -> DMR treatment
    • (DMR residuel - DMR traitement) union with Response specific DMR
    • Compare Response specific DMR with IDH specific DMR from Focal_disruption_of_DNA_methylation WGBS.

Wet lab

  • Monday: Subculture
  • Wednesday: Subculture
  • Friday: Subculture
  • Prepare experiments protocol for next week

17.01.2022 - 21.01.2022 {#week-03}

IDH project

  • Change DMRs threshold
  • Change overlap parameters
  • Associate genes and DMRs from both analysis
  • Analyse IDH1 & IDH2 mutation separately
  • Investigate DMRs location and compare to their DMR WGBS analysis

Wet lab

  • Monday: Subculture [DONE]
  • Tuesday: +/- AGI
  • Wednesday: Subculture
  • Friday: Subculture +/- AGI

Biblio

Communication

  • Prepare 20.01.2022 presentation

24.01.2022 - 28.01.2022 {#week-04}

IDH project

  • Biblio on specific genes like:
    • RELA / NFkB
    • MYC
  • Biblio on how to analyse WGBS data
    • Experimental and Bioinformatic Approaches to Studying DNA Methylation in Cancer and relative papers
  • Look at WGBS data

Wet lab

  • Write clear protocols

    • facs preparation
    • Western blot

  • Read Scenith paper

  • Monday: Subculture

  • Thursday: Cell seeding

  • Friday (The whole day):

    • Facs preparation
    • Protein pellet preparation

Others

  • Setting date up ave les membres du Comité de thèse

31.01.2022 - 04.02.2022 {#week-05}

IDH project

  • Biblio:
    • Continue looking at RelA and MYC
  • Continue managing WGBS data.
    • Compute with DSS package the input data made

In vitro experiments

  • Analyse data with FlowJo
  • Finish preparing Western blot for Tuesday
  • Analyse results of Western blots
  • Help Emeline with mice experiments

Thesis committee

  • End of the week: ask news about the doodle
  • Prepare some presentation plan
  • List biblio to read for thesis committee.

07.02.2022 - 11.02.2022 {#week-06}

IDH project

  • Biblio:
    • Continue looking at RelA and Myc
  • Continue managing WGBS data
    • Compute WGBS data

Wet lab manips

  • Look at last week results
  • Redo secondary AA on NF-kB prots

Thesis committee

  • Prepare some presentation plan
  • List biblio to read for thesis committee
  • Start using Prism
  • List figures done

14.02.2022 - 18.02.2022 {#week-07}

Committee presentation

  • Make the presentation
    • Have a clear plan (not too long not too short)
  • Redo some figures with Prism (if it takes not too long time)
  • Make a summary of DNA methylation analysis

Bibliography

  • Read paper on Scenith
  • Reread paper on viper and MSviper
  • Reread paper on ChAMP
  • Reread Lucille Paper
  • Continue biblio on Myc and its targets, CREB1, STAT3, HIF1a, SREBP1, BCL2
  • Make back-up slides

Others

  • Formation k-mers
  • Do some literature on k-mers