Alexis Hucteau PhD project
Notes about all the project advances and researches during the PhD
2021 Todo lists
18.10.2021 - 22.10.2021
IDH PhD project
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Look at clinical data from Verhaak cohort & do OS IDHwt analysis
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Look at cell lines previous analysis
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Make a signature of response
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Make a poster
Splicing project
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Look at rMATS code [DONE]
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Read rMATS paper [DONE]
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Learn how to use rMATS [DONE]
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Learn how to use rmatsashimiplot [DONE]
Wet-lab
- Do a clear recap on upcoming experiments [DONE]
Deconvolution
- Try to find a way to investigate on the 40 genes
Biblio
- Make a summary of a paper [3/3]
- Genome_wide_analysis_of_focal_DNA_hypermethylation_in_IDH_mutant_AML_samples [DONE]
- The_implications_of_IDH_mutations_for_cancer_development_and_therapy [AML part DONE]
- The STAT3-MYC Axis Promotes Survival of Leukemia Stem Cells by Regulating SLC1A5 and Oxidative Phosphorylation [DONE]
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Look at paper already found on RELA
- Read paper on MYC
Scripting
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Create Github.io? [DONE]
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Remake a clear rmd file [DONE]
25.10.2021 - 29.10.2021
Communication
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Make a part of the Team 18 poster [DONE]
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Redesign pictures and text for Cancer cell symposium poster
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Prepare a flash talk for Cancer cell symposium
IDH PhD project
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Look at clinical data from Verhaak cohort & do OS IDHwt analysis
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Continue to look at cell lines previous analysis [DONE]
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Make a signature of response
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Start wet-lab [DONE]
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Look at Koichi RNAseq if bam files available [DONE]
Biblio
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Find 3 papers [4/3] [DONE]
- Make a summary of a paper [0/3]
- Metabolic reprogramming and epigenetic modifications on the path to cancer
- Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease
- Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
- EXTRA already read: Rewiring of the Transcription Factor Network in Acute Myeloid Leukemia [DONE]
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Do a thesis introduction [will never ends]
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Look at CHO abstracts
- Do method and team method bibliography
Scripting
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Create Github.io? [DONE]
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Remake a clear rmd file
02.11.2021 - 05.11.2021
IDH PhD Project
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Put tables of DEG, Mviper etc. on git .io
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Find datasets on glioma IDH
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Continue Introduction
Communication
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Make poster for Cancer cell symposium
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Record a flash talk for Cancer cell symposium
Deconvolution
- Redo Venn diagram and analyze results
Wet lab
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Wednesday –> Subculture 1:30pm –> 2:30pm
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Thursday –> Make “ampoule de congélation” 4:00pm –> 6:00pm
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Friday –> test mycoplasme –> 1:30pm –> 2:30pm
Bibliography
- Make a summary of a paper [0/3]
- Metabolic reprogramming and epigenetic modifications on the path to cancer
- Genetic perturbation of PU.1 binding and chromatin looping at neutrophil enhancers associates with autoimmune disease
- Mapping long-range promoter contacts in human cells with high-resolution capture Hi-C
08.11.2021 - 10.11.2021
Team 18 Informatic park
- Install computer for new person
- Buy some screens for the PC of the salle commune
Deconvolution
- Redo Venn diagram and heatmap
Communication
- CDRC poster presentation on Monday
IDH PhD Project
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Put tables of DEG, Mviper etc. on git .io
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Find datasets on glioma IDH
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Continue Introduction
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Compare 56-11 to Molm14
Wet lab
Monday –> Subculture (3 samples)
Tuesday –> Subculture + Dox +/- AGI
Wednesday –> Subculture (5 samples)
Conferences
- Cell symposium
15.11.2021 - 19.11.2021
Team 18 Informatics
- Buy some screens and stuff for the PC of the salle commune [DONE]
- Test PC commun and find out what happen to Thomas’s computer [DONE]
Deconvolution
- Redo figure 2 of the paper [DONE]
IDH PhD Project
- Put tables of DEG, Mviper etc. on git .io
- Redo DNA methylation analysis [DONE]
- From differences between Molm and HL60 [DONE]
- Make a signature to compare Good versus bad responders
- Find datasets on glioma IDH
- Continue Introduction
- Check gene expression variability through cell lines & Patient response [DONE]
Wet lab
- ATP [DONE]
- Scenith [DONE]
- Rhod2 [DONE]
- Subcultures [DONE]
- Analysis of the data [DONE]
Bibliography
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Find a paper on methods for analysis of DNA met and/or RNAseq data
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Make a summary of a paper [0/1]
- Non-genetic mechanisms of therapeutic resistance in cancer
Formations
- Thursday –> Programme mentorat [DONE]
22.11.2021 - 26.11.2021
IDH PhD Project
- Put tables of DEG, Mviper etc. on git .io
- Make a signature to compare Good versus bad responders
- Find datasets on glioma IDH
- Continue Introduction
- Add statistical comparisons on boxplots
Wet lab
- Continue biblio of the wetlab experiments
- Culture to redo experiments
- Monday afternoon:
- “Dosage protéines”
- Tuesday morning:
- “dépôt des gels migration/transfert/saturation et incubation des Ac primaires”
- Wednesday:
- “lavages/Ac secondaires/lavages/revélation”
- Analysis of the results
Bibliography
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Find a paper on methods for analysis of DNA met and/or RNAseq data
- Make a summary of a paper [0/1]
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Non-genetic mechanisms of therapeutic resistance in cancer
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- Look at wet lab results to confirm ours.
Communication
29.11.2021 - 02.12.2021
IDH PhD Project
- Make a signature to compare Good versus bad responders
- Find datasets on glioma IDH
- Continue Introduction
Deconvolution
- High priority Finish empirical test DONE
Wet lab
- Continue subculture
- Monday: induction Dox in Molm14
- Wednesday: Subculture
- Analysis of the results of WB
Bibliography
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Find a paper on methods for analysis of DNA met and/or RNAseq data
- Make a summary of a paper [0/1]
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Non-genetic mechanisms of therapeutic resistance in cancer
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- Look at wet lab results to confirm ours.
Communication
- High priority Prepare 02.12.2021 Groupe meeting project presentation
13.12.2021 - 17.12.2021
IDH PhD Project
- Test expression variability
- Download Koichi fastq/bam for rMATS analysis
Wet lab
- Monday: Subculture
- Tuesday: Extractions-cytometry
Bibliography
- Add biblio on Introduction
- Reading
- Non-genetic mechanisms of therapeutic resistance in cancer
- A darwinian and physical look at stem cell biology helps understanding the role of Stochasticity in development
Others
- Wednesday: Marie’s thesis
- Thursday: Mentorat