GSE239776 EcoToxChip 2016 LSARP RNASeq database

Contributors : Niladri Basu ; Markus Hecker ; Natacha Hogan ; Jessica Head ; Doug Crump ; Jianguo Xia ; Krittika MittalSeries Type : Expression profiling by high throughput sequencingOrganism : Coturnix japonica ; Lithobates pipiens ; Oncorhynchus mykiss ; Phalacrocorax auritus ; Pimephales promelas ; Xenopus laevisAs part of the EcoToxChip project, 49 distinct exposure studies were conducted on three lab model species (Japanese quail, fathead minnow, African clawed frog) and three ecologically relevant species (double crested cormorant, rainbow trout, northern leopard frog), at multiple life stages (embryo, adult), exposed to eight chemicals of environmental concern (ethinyl estradiol-EE2, hexabromocyclododecane-HBCD, lead-Pb, selenomethionine-SeMe, 17 β trenbolone-TB, chlorpyrifos-CPF, fluoxetine-FLX, and benzo [a] pyrene-BaP. Whole transcriptome analyses were conducted on these samples resulting in a rich RNA seq dataset covering various species, life stages and chemicals, which is one of the largest purposeful complications of RNA seq data wit hin ecotoxicology. Recently, a unified bioinformatics platform of relevance to ecotoxicology, EcoOmicsAnalyst and ExpressAnalyst, was developed to facilitate RNA Seq analysis of non-model species lacking a reference transcriptome. The platform uses the Seq2Fun algorithm to map RNA-seq reads from euk aryotic species to an ortholog database comprised of protein sequences from>600 eukaryotic species (EcoOmicsDB) with a translat...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Coturnix japonica Lithobates pipiens Oncorhynchus mykiss Phalacrocorax auritus Pimephales promelas Xenopus laevis Source Type: research