Dataset Information

TempO-Seq S1500+ Platform Gene Expression of Rat Liver Mode of Action Samples

ABSTRACT: Using the TempO-Seq rat S1500+ platform we performed gene expression analysis of using 63 purified RNA samples from the livers of rats exposed to controls or chemicals that fall into one of five modes of action (MOAs): constitutive androstane receptor/pregnane X receptor (CAR/PXR) activation, aryl hydrocarbon receptor (AhR) activation, peroxisome proliferator-activated receptor-alpha (PPARA) activation, cytotoxicity or DNA damage. The TempO-Seq data generated was used to compare to gene expression data acquired from the same samples run on Affymetrix microarays (GEO: GSE47875) and Illumina RNA-Seq (GEO: GSE55347, SRA:SRP039021).

ORGANISM(S): Rattus norvegicus

PROVIDER: GSE118956 | GEO | 2018/08/24

REPOSITORIES: GEO

ACCESS DATA

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Project description:The use of gene expression signatures to classify compounds, identify efficacy or toxicity, and differentiate close analogs relies on the sensitivity of the method to identify modulated genes. We used a novel ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq®, to determine whether previously unreported compound-responsive genes could be identified and incorporated into a broad but specific compound signature. TempO-Seq exhibits 99.6% specificity, single cell sensitivity, and excellent correlation with fold differences measured by RNA-Seq (R2 = 0.9) for 20,629 targets. Unlike many expression assays, TempO-Seq does not require RNA purification, cDNA synthesis, or capture of targeted RNA, and lacks a 3′ end bias. To investigate the sensitivity of the TempO-Seq assay to identify significantly modulated compound-responsive genes, we derived whole transcriptome profiles from MCF-7 cells treated with the histone deacetylase inhibitor Trichostatin A (TSA) and identified more than 9,000 differentially expressed genes. The TSA profile for MCF-7 cells overlapped those for HL-60 and PC-3 cells in the Connectivity Map (cMAP) database, suggesting a common TSA-specific expression profile independent of baseline gene expression. A 43-gene cell-independent TSA signature was extracted from cMAP and confirmed in TempO-Seq MCF-7 data. Additional genes that were not previously reported to be TSA responsive in the cMAP database were also identified. TSA treatment of 5 cell types revealed 1,136 differentially expressed genes in common, including 785 genes not previously reported to be TSA responsive. We conclude that TSA induces a specific expression signature that is consistent across widely different cell types, that this signature contains genes not previously associated with TSA responses, and that TempO-Seq provides the sensitive differential expression detection needed to define such compound-specific, cell-independent, changes in expression.

Dataset Information

TempO-Seq S1500+ Platform Gene Expression of Rat Liver Mode of Action Samples

Dataset's files

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets