GSE190909
RNA-seq of  CD4 T cells from the lungs of M. tuberculosis infected WT and vhl fl/fl cd4 cre mice
Purpose: We compared the transcriptomes of mouse CD4 T cells  lacking the vhl gene ( vhlfl/fl cd4 cre= vhl cKO)  with WT controls from the lungs of mice 8 weeks after aerosol infection with Mycobacterium tuberculosis. Results: Using an optimized data analysis workflow, between 40-55 million sequence reads per sample to the mouse genome (build mm10) and identified  14700  transcripts in the CD4 T cells  of WT and mutant mice after performing HISAT2 alignements to the mm10 reference. Conclusion: The  transcriptome of WT anf vhl cKO was compared. Groups did cluster differentially with regards to their transcript abundance. The WT group has enriched DNA synthesis/ proliferation pathways whereas the Vhl cKO was enriched in hypoxia pathways. Transcripts assocaited with T cell differentiation were increased in WT group while T cell inhibitory molecules was elevated in the transcriptome of vhl cKO CD4 T cells. Overall design: Biological Replicates: 5 WT and 6 vhl cKO CD4 T cells samples.