Fig. 4
From: The impact of RNA sequence library construction protocols on transcriptomic profiling of leukemia
Validation by quantitative reverse transcription PCR (qRT-PCR). Normalized fold expression values represented on the X-axis were calculated by the ΔΔCt method using four reference genes (B2M, GAPDH, PGK1, RPLP0) and then normalized to total RNA as control. Error bars represent the standard error of the mean ΔCt values across all cell lines. Student’s T-test showing significant differences (P < 0.05). a, b The qRT-PCR log2-fold change expression of 5 genes in two leukemia patient samples (ALL 542 and AML 800) using PA and RD protocols compared to total RNA, showing the PA protocol prepared RNA is closer to total RNA. c, d The log2-fold expression of AML compared to ALL samples from both PA and RD libraries demonstrates the higher agreement of RNA-seq (log2 RPKM) and qRT-PCR (log2-fold expression) expression estimates in the PA than RD protocol. e, f The bar plots show the log2-fold change expression of 9 genes in four breast cancer cell lines MCF7, SKBR3, KPL1, BT474 using PA and RD protocols compared to total RNA. g, h The log2-fold expression of 18 s and 28 s rRNA compared to the expression in total RNA in ALL 542 and AML 800 patient samples, depicting higher efficiency of the RD protocol at removing rRNAs compared to the PA protocol. The log2-fold expression of 4 non-coding RNA in two cell lines (MCF7 and SKBR3) showing higher efficiency for the non-coding RNAs of the RD protocol compared to the PA protocol