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Fig. 7 | BMC Genomics

Fig. 7

From: Trypanosoma cruzi specific mRNA amplification by in vitro transcription improves parasite transcriptomics in host-parasite RNA mixtures

Fig. 7

T7SL IVT DEGs detection on mixtures and limiting mass samples. a Hierarchical clustering of all DEGs (FDR < 0.01) when comparing all epimastigotes samples (mixtures and limiting mass) to the trypomastigote stage. Blue/black/yellow color code is log2 of expression fold change of epimastigote to trypomastigote). Supra Gene expression level is rainbow color coded based on log2 of counts per million reads (log2 CPM). Heatmap was created using Euclidian distance, average linkage clustering method and MeV (Multiple Experiment Viewer) v. 4.8.1 software. Note that, in general, all epimastigote samples show a similar fold change pattern for the great majority of genes, independent of initial mass used for amplification (limiting mass samples) or percentage of parasite RNA on host-parasite mixtures (mixture samples). b Principal Component Analysis (PCA) of the same samples used in a. The first component represents 84% of the total variation and is mainly due to epimastigote to trypomastigote differences; the second component represents 9% of the total variation and is mainly due to epimastigote transcriptome differences between the limiting mass experiments. PCA graph was created using Perseus v.1.5.0.31 software. c Euler diagram showing the number and overlap of detected DEGs for epimastigote to trypomastigote comparison using five different groups: (i) Poly(A)+: both parasite stages analyzed by Poly(A) + RNA; (ii) T7SL: both parasite stages analyzed by T7SL IVT amplification method from 100 ng of initial mass; (iii) Epi_3ng: limiting mass of 3 ng for epimastigote T7SL IVT; (iv) Epi_0.1%: mixture of host-parasite RNA containing only 0.1% of parasite RNA; (v) Epi_Sort: amplification of RNA obtained from 105 sorted epimastigotes

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