Alexis Hucteau PhD project
Notes about all the project advances and researches during the PhD
Weekly advances
2021
2022
18.10.2021 - 22.10.2021
18.10.2021
- Made a todo list
- Looked at papers
- Selected 3 papers
- Install rMATS
19.10.2021
- Biblio on Genome_wide_analysis_of_focal_DNA_hypermethylation_in_IDH_mutant_AML_samples
- Installing rMATS
- Testing the scripts of rMATS
- Understanding results and try to understand how to interpret its
20.10.2021
- Biblio on The STAT3-MYC Axis Promotes Survival of Leukemia Stem Cells by Regulating SLC1A5 and Oxidative Phosphorylation
- Try to use rmatsashimiplot
- Know how to use rmatsashimiplot
21.10.2021
- Try to download .bam file from GDC portal (need token)
- Split BEATAML patient using HighOXPHOS vs RNAsplicing 18 genes
25.10.2021 - 29.10.2021
25.10.2021
- Make a todo list
- Make a quick picture about my project for the team poster
- Work on the thesis introduction
- Defrost 56-11 HL60 & MOLM14 IDHm cells
26.10.2021
- Team 21 Journal club [11am-12.30pm]
- Correct cell lines analysis to make a .md result file
- Starting a git pages
- Do method bibliography
27.10.2021
- Rearrange code of cell lines analysis
- Reorganize Git pages
- Observation of cell culture
- Rearrange code of Patients samples analysis
28.10.2021
- Rearrange code of Patients samples analysis
- Upload all on the git pages
- Team 18 lab meeting [11am-12.30pm]
- COMET journal Club [1pm-1.30pm]
- Team 21 lab meeting [2pm-3.30pm]
- Tutorial Github pages [3.30pm-4pm]
- Wetlab
- Counting
- Subculture HL60
29.10.2021
- Wetlab
- Counting
- Centri MOLM14
- Subculture HL60
- Downloading bam files from Koichi’s experiment
- Need storage
02.11.2021 - 05.11.2021
02.11.2021
- Make a To do list
- Start poster
- Making network representations for poster
03.11.2021
- Work on poster
- Wet-lab
04.11.2021
- Working on poster
- Team 18 Meetings (11:00am - 12:45pm)
- Team 21 Meetings (2:00pm - 4:00pm)
- Wet lab (4:00pm - 6:00pm)
05.11.2021
- Working on poster
- Wet lab (1:30pm - 3:30pm)
- Working on Poster + Flash talk
08.11.2021 - 10.11.2021
08.11.2021
- Finishing the poster
- Wet-lab (Sub culture HL60, M14 - Dox, M14 + Dox) (2:00pm - 3:30pm)
- Preparing poster session
09.11.2021
- Looking at HL60 vs M14 (Possible Bad responders vs Good responders)
- Journal club (11:00am - 12:15pm)
- Wet lab (2:30 - 4:00pm)
15.11.2021 - 19.11.2021
15.11.2021
- Making a todo list
- Do some informatic management for team 18
- Jean-Pascal CAPP talk
- Wet lab subculture
- Preparation of read-out
16.11.2021
- Read-out the whole day
17.11.2021
- Redo figure 2 of deconv paper
- Do some bioinfo & info stuff for team 18
- Rerun Methylation analysis on Koichi patient
- Add variability of gene expression through patient samples
18.11.2021
- Meeting “Programme mentorat”
- Biblio on Wetlab experiment to prepare analysis of cytometry
- Redo figure 2
19.11.2021
22.11.2021 - 26.11.2021
22.11.2021
23.11.2021
- Wet lab WB the whole day
24.11.2021
*
25.11.2021
- Revelation WB
- Meetings
26.11.2021
- Make a randomization algorithm for empirical test
29.11.2021 - 2.12.2021
29.11.2021
- Making a To do list
- Making a fast function for deconvolution empirical test still not finished yet
30.11.2021
- Finished the randomization function
- Continuing group meeting presentation
13.12.2021 - 17.12.2021
- Find 1To data storage in the computer
- Downloading PDXRNAseq for Margherita’s project
- Doing a fastqc analysis
- Downloading Koichi’s fastq for splicing analysis
- Look at Expression variability
- Subculture
10.01.2022 - 14.01.2022
10.01.2022
- Rescue the 1To data storage with all the data downloaded
- Create Project in cahier de laboratoire électronique
- Start reading Universal annotation of the human genome through integration of over a thousand epigenomic datasets
24.01.2022 - 28.01.2022
24.01.2022
- In vitro subculture
- Making a todo and dbd list
- Reading Experimental_and_bioinfo_DNA_met paper
- Reparing thunderbird to send mail
- Look at DSS package tuto
- Look at RELA
- Downloading Coverage Methylation data
- Converting into bed files [In progress]
25.01.2022
- Finishing in vitro protocols
- Organize thesis Commitee.
31.01.2022 - 04.02.2022
31.01.2022
- Biblio on Rela
- Prepare Western blot experiments
- Continuing managing WGBS data
01.02.2022
- Helping Emeline with her mice experiments
- Protein quantification