EPA Science Inventory

Evaluation of Sequencing Approaches for High-Throughput Transcriptomics - (BOSC)

Citation:

Martin, M., J. Harrill, A. Karmaus, AND R. Thomas. Evaluation of Sequencing Approaches for High-Throughput Transcriptomics - (BOSC). Presented at BOSC CSS Meeting, RTP, NC, November 16 - 18, 2016. https://doi.org/10.23645/epacomptox.5180668

Description:

Whole-genome in vitro transcriptomics has shown the capability to identify mechanisms of action and estimates of potency for chemical-mediated effects in a toxicological framework, but with limited throughput and high cost. The generation of high-throughput global gene expression profiles using RNA-sequencing technologies for the evaluation of chemically-mediated effects could greatly advance the current toxicogenomics knowledgebase. We present the evaluation of three transcriptomics platforms for potential application to high-throughput screening: 1. TempO-Seq utilizing custom designed paired probes per gene; 2. Targeted sequencing utilizing Illumina’s TruSeq RNA Access Library Prep Kit containing tiled exon-specific probe sets; 3. Low coverage whole transcriptome sequencing using Illumina’s TruSeq Stranded mRNA Kit. In summary, the three transcriptomics platforms showed the ability to measure whole-genome transcript levels with good technical reproducibility and show promise for the integration of transcriptomics into high-throughput screening.

Purpose/Objective:

Poster presented at BOSC CSS meeting in RTP, NC

URLs/Downloads:

CSS BOSC_TRANSCRIPTOMICS_NOV2016_V3.PDF   (PDF,NA pp, 2336.825 KB,  about PDF)

Record Details:

Record Type: DOCUMENT (PRESENTATION/POSTER)
Start Date: 11/18/2016
Completion Date: 11/18/2016
Record Last Revised: 02/12/2018
Record Created: 12/18/2017
Record Released: 12/18/2017
OMB Category: Other
Record ID: 338796

Organization:

U.S. ENVIRONMENTAL PROTECTION AGENCY

OFFICE OF RESEARCH AND DEVELOPMENT

NATIONAL CENTER FOR COMPUTATIONAL TOXICOLOGY