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Comparing RNA-seq and TempO-seq mRNA data sets: a case study
Citation:
Taylor, L., L. Everett, J. Harrill, I. Shah, AND R. Judson. Comparing RNA-seq and TempO-seq mRNA data sets: a case study. Society of Toxicology 62nd Annual Meeting and ToxExpo 2023, Nashville, TN, March 19 - 23, 2023. https://doi.org/10.23645/epacomptox.22782854
Impact/Purpose:
Platform Presentation to the Society of Toxicology 62nd Annual Meeting and ToxExpo March 2023. This work helps validate the use of TempO-seq for transcriptomics research.
Description:
There are multiple technological platforms available for quantifying mRNA levels to use for transcriptomics studies. With the increase in TempO-seq generated mRNA data, it is important to determine whether TempO-seq and RNA-seq generated data are comparable and/or can be combined. For this analysis, two different TempO-seq data sets (Cell Atlas and Tox21 CPP2) were compared to each other using principal component analysis (PCA) for four overlapping cell types (Daudi, HepG2, MCF-7, and U-2 OS) and the PCA showed that the data sets could be combined. The TempO-seq data were then compared to RNA-seq data for 12 cell types (A549, Daudi, HBEC3-KT, HepG2, HME-1, HUVEC, MCF-7, RPE-1, RPTEC, TIME, U-2 OS, and T47-D) using PCA. For the four overlapping cell types within both Cell Atlas and Tox21 CPP2 data, the average of all replicates per cell type were used for this comparison to RNA-seq. Statistical testing using PCA on TempO-seq versus RNA-seq mRNA expression data for the 19,119 overlapping genes showed that there was a clear platform divergence pattern within the first principal component (PC1) for all cell types evaluated. This meant that these TempO-seq and RNA-seq data should not be combined without further steps. Normalizing the data by calculating the relative log expression (RLE) compared to the average expression level across cell types in each platform removed the platform divergence observed in PC1. Removing genes with large differences in expression levels between the technological platforms was also found to be effective in resolving platform divergence. Here, we describe a workflow process for evaluating whether and how mRNA data sets can be combined when comparing and/or aggregating data generated by TempO-seq versus RNA-seq. This work should help increase scientific confidence when using TempO-seq data for conducting transcriptomics research. The views expressed are those of the authors and do not necessarily represent the views or the policies of the U.S. EPA.
URLs/Downloads:
DOI: Comparing RNA-seq and TempO-seq mRNA data sets: a case study
PLATFORM PRESENTATION_RNA SEQUENCING METHODS COMPARISON_LAURA TAYLOR.PDF (PDF, NA pp, 5721.837 KB, about PDF)