Weekly Todo list

2021

2022

• Week 02
• Week 03
• Week 04
• Week 05
• Week 06
• Week 07

10.01.2022 - 14.01.2022

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

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

• Continue reading “Experimantal and bioinformatic Approaches to Studying DNA methylation in Cancer”

Communication

• Prepare 20.01.2022 presentation

---

24.01.2022 - 28.01.2022

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

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

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

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