Authors:
- Konstantin Demin, Almazov National Medical Research Centre (supervisor)
- Allan Kalueff, Sirius University of Science and Technology (supervisor)
- Nikita Ilyin, Almazov National Medical Research Centre (S)
- Anton Shevlyakov, Sirius University of Science and Technology (A)
We analysed gene expression changes after Traumatic Brain Injury (TBI) and subsequent exposure to ISRIB nootrope in the brain of Danio rerio. In general we had 4 groups: control (C), fish with TBI (T), fish with ISRIB injection (I) and fish with TBI and ISRIB injection (TI). In order to determine the main molecular responses of the ISRIB action, RNA-seq was used, followed by differential expression genes identification and pathway analysis. The results of the DESeq2 analysis were divided into three main parts corresponding to the predictors of the regression model (2 factors and their interaction). Each of the three results was analysed independently. The first factor (T) describes the influence of TBI on transcriptomic brain changes, the second (I) - the effect of ISRIB injection, and their interaction determines the difference between T and I.
Danio rerio brain samples were collected for bulk RNA sequencing on HiSeq2500 platform. Overall 27 samples were prepared for analysis (7 - C; 7 - T; 5 - I; 7 - TI). After quality control and trimming, one control sample was removed due to small number of readings. Total of 26 samples were used for analysis.
Aim: Identify the main molecular response of ISRIB action on Danio rerio brain afer TBI.
Objectives:
- Data preparation and develop design of analysis
- Differnetial expression analysis by DESeq2
- Gene set enrichmant analysis (GSEA), pathways identification and their annotation in the contest of ISRIB action
- Identification of co-expression clusters by WGCNA and their annotation by overrepresented analysis (GO and KEGG)
Workflow:
