Bioinformatics Seminar
Time: 11AM
Venue: Hybrid
5 September 2023
Exploring human CD4+ T cell activation using T2T reference
Xueyi DongWEHI ACRF Cancer Biology and Stem Cells/Bioinformatics
Lupus, or systemic lupus erythematosus (SLE), is a chronic autoimmune disease where the body's immune system attacks its own tissues and organs. Lupus has a higher prevalence in females than in males. Due to the presence of two X chromosomes in females, one X chromosome is inactivated within cells to prevent excessive expression of genes located on the X chromosome. We hypothesis that the different prevalence of lupus between males and females may be due to reactivation of immune-potent genes on the silenced X chromosome that escape the silencing as the immune cells get activated. To study the change of gene expression and alternative splicing in human immune cells during activation and compare the difference between male and female, we designed an RNA-seq experiment of resting (0h) and activated (9h and 38h) CD4+ T cells from 10 healthy donors. For the RNA-seq analysis, we used the human Telomere-to-Telomere (T2T) genome assembly as the reference and compared it with GRCh38 (hg38) reference genome. Using this data, we demonstrated how to perform differential gene expression, differential transcript expression and differential transcript usage analysis using human T2T reference.