Alternate splicing of transcripts shape macrophage response to Mycobacterium tuberculosis infection
Fig 2
Gene level quantification differs considerably from isoform level quantification.
(A) Fold change in the expression was calculated at gene level as well as isoform levels. Gene level changes in expression across the time points for eight genes (as mentioned) in H37Ra (blue) or H37Rv (red) infected macrophages are plotted as line graph. (B) Expression values at isoform levels for the respective genes under H37Ra (left) or H37Rv (right) infected conditions were normalized to 100% and contribution from different isoforms were plotted as different sub-bars. The black arrowheads indicate the transcript and the time point that was selected to validate the RNA-seq data using Q-PCR (shown at the right in Fig 2C). (C) cDNAs from uninfected (UI), H37Rv infected (H37Rv) and H37Ra infected (H37Ra) macrophages at the mentioned time points were analyzed by quantitative PCR using isoform specific primers (see methods). Plots represent fold-change with respect to uninfected control (Values ±S.D.). (D) Corresponding FPKM values for the transcripts at the time points validated in 2C were plotted separately here for the ease of comparison.