Fig 2. RBP6OE differentiation transcriptome and proteome.
(A) Scheme of the differentiation process and the experimental time points. The RBP6-induced cells were harvested and analyzed by RNA-Seq and label-free quantitative mass spectrometry at different time points, as indicated. The table contains an overview of the number of differentially expressed transcripts and proteins. (B) Gene expression profile of transcripts encoding surface glycoproteins GPEET (Tb927.6.510), BARP (Tb927.5.15530, Tb927.5.15550, Tb927.5.15560, Tb927.5.15600, Tb927.5.15590), and T. brucei 427 mVSG (Tb427_000106600.1, Tb427_000524500.1, Tb427_000173600.1, Tb427_000288600.1, Tb427_000304300.1, Tb427_000108300.1, Tb427_000627000.1, Tb427_000615900.1). (C) Time-course expression profiling of transcriptomic data based on K-medoids clustering. (D) Gene Ontology (GO) term analysis applied to all four transcriptomics clusters. Significant levels are depicted as follows **P < 0.01, ***P < 0.0001. (E) Volcano plots showing a comparison of protein expression levels (5,227 protein groups) between day 0 and day 2 (left panel) or day 6 (right panel) upon RBP6 induction. Log2 fold change values of averaged LFQ intensities from quadruplicate experiments are plotted against the respective −log10-transformed P values. Significantly down-regulated proteins are depicted in blue, while significantly up-regulated proteins are depicted in red. RBP6, AOX, and surface glycoproteins BARP (day 2) and metacyclic (m)VSGs (day 6) are highlighted. (F) Time-course expression profiling of proteomic data based on K-medoids clustering. (G) GO term analysis of Clusters 1, 3, and 4 showing a significant enrichment. **P < 0.01, ***P < 0.001. Underlying data plotted in panel B are provided in S1 Data. AOX, alternative oxidase; BARP, brucei alanine-rich protein; EP, procyclin rich in Glu-Pro repeats; GO, Gene Ontology; GPEET, procyclin rich in Gly-Pro-Glu-Glu-Thr repeats; k, kinetoplast; LC-MS/MS, liquid chromatography tandem mass spectrometry; LFQ, label-free quantification; mVSG, metacyclic-like variable surface glycoprotein; n, nucleus; RBP6, RNA binding protein 6.