Transcriptome analyses of Leishmania donovani promastigotes depleted of SET7 and SET29 proteins, under normal and oxidative growth environment [exp1]

This study was performed with the goal of understanding the roles of Leishmania donovani SET7 and SET29 proteins in gene regulation. Using homologous recombination to knock out set7 and set29 genes, set7 and set29 mutant parasites were created. This was folllowed by transcriptome analyses of wild type parasites, set7 mutant parasites and set29 mutant parasites, that were carried out using RNA-seq. In the first experimental set, transcriptomes of wild type parasites cultured under normal conditions as well as under hydrogen peroxide (H2O2) -induced oxidizing conditions were analysed, along with transcriptomes of set7 mutant parasites that were similarly grown under normal growth conditions as well as under H2O2-induced oxidizing conditions. Using the data obtained, the transcriptome of wild type parasites exposed to H2O2 has been compared with the transcriptome of wild type parasites grown under normal conditions. The transcriptome of set7 mutant parasites grown under H2O2-induced oxidizing conditions versus normal conditions have been similarly compared. In addition, the transcriptome of set7 mutant parasites grown under normal conditions has been compared to that of similarly grown wild type parasites. In the second experimental set, transcriptomes of wild type parasites cultured under normal growth conditions, set29 mutant parasites grown under normal conditions, as well as set29 mutant parasites grown under H2O2-induced oxidizing conditions, were analysed. Using the data obtained, the transcriptome of set29 mutant parasites grown under normal conditions has been compared to that of similarly grown wild type parasites. The transcriptome of set29 mutant parasites grown under H2O2-induced oxidizing conditions versus normal conditions have been similarly compared. Our data reveals, that knock out of set7 modulates transcription of specific clusters of genes on particular chromosomes, with almost 10 % of the total genes being regulated. On the other hand, depletion of SET29 modulates transcription of a very small set of genes distributed primarily in two clusters. This datasheet is for first experimental set. Two experimental sets were performed, each with two biological replicates of all samples. For transcriptome analysis, we first depleted the cells of LdSET7 and LdSET29 expression by sequentially knocking out two alleles of both the genes, which led to creation of set7-/- and set29-/-/+ cell lines. In the first experimental set, RNA was isolated from logarithmically growing wild type and set7-/- promastigotes (two biologicals). RNA was also isolated from logarithmically growing wild type and set7-/- promastigotes (two biologicals) that had been exposed to H2O2 (100 µM) for 5h followed by transfer of cells into fresh medium for 3 hours. In the second set of experiments, RNA was isolated from logarithmically growing wild type and set29-/-/+ promastigotes (two biologicals). RNA was also isolated from logarithmically growing set29-/-/+ promastigotes (two biologicals) that had been exposed to H2O2 (100 µM) for 5h followed by transfer of cells into fresh medium for 3 hours.This was followed by RNA sequencing. We then performed comparative gene expression profile analysis, among different samples. This datasheet is for first experimental set