Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of human neural stem and neuroblastoma cells

ABSTRACT: Both in situ synthesized long oligo arrays from Agilent Technologies and short oligo arrays from Affymetrix were used to meausre differential gene expression in RNA samples generated from (1) human neural stem cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 20ÂµM) for 24h, and (2) neuroblastoma cells treated with vehicle (EtOH, 0.01%) and tert-butylhydroquinone (tBHQ, 10ÂµM) for 24h. This SuperSeries is composed of the following subset Series:; GSE759: Long oligonucleotide arrays verse short oligonucleotide arrays-CTX066; GSE761: Long oligonucleotide arrays verse short oligonucleotide arrays -IMR32 cells Experiment Overall Design: Refer to individual Series

ORGANISM(S): Homo sapiens

SUBMITTER: Jiang Li

PROVIDER: E-GEOD-768 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Dissecting tBHQ induced ARE-driven gene expression through long and short oligonucleotide arrays.

Li Jiang J Spletter Maria L ML Johnson Jeffrey A JA

Physiological genomics 20041221 1

This paper compares the gene expression profiles identified by short (Affymetrix U95AV2) or long (Agilent Hu1A) oligonucleotide arrays on a model for upregulation of a cluster of antioxidant responsive element-driven genes by treatment with tert-butylhydroquinone. MAS 5.0, dCHIP, and RMA were applied to normalize the Affymetrix data, and Lowess regression was considered for Agilent data. SAM was used to identify the differential gene expression. A set of biological markers and housekeeping genes ...[more]

PMID: 15613614

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Project description:Oxidative stress is an important mechanism of chemical toxicity, contributing to teratogenesis as well as to cardiovascular and neurodegenerative diseases. Developing animals may be especially sensitive to chemicals causing oxidative stress. To assess the response to chemicals at different stages of development, zebrafish (Danio rerio) embryos at 1, 2, 3, 4, 5, and 6 days post-fertilization (dpf) were exposed to 0.1% dimethyl sulfoxide (DMSO), 2 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), or 10 uM tert-butylhydroquinone (tBHQ) for 6 hr. Transcript abundance was assessed by real-time qRT-PCR and microarray (Agilent 22k). By microarray, 1477 probes were significantly different among the DMSO-, tBHQ-, and TCDD-treated embryos at 4 dpf. Of these, 220 were 2-fold or greater up-regulated and 108 were 2-fold or greater down-regulated by tBHQ. For TCDD, 17 probes were 2-fold or greater up-regulated and 6 were 2-fold or greater down-regulated. Genes induced by tBHQ, included genes involved in glutathione synthesis and utilization, signal transduction, and DNA damage / stress response. Keywords: Danio rerio, TCDD, tBHQ, oxidative stress, gene expression Separate groups of 30 embryos generated from TL adults were placed in 15 ml egg water in a 10-cm glass petri and at 1, 2, 3, 4, 5, and 6-dpf were exposed for 6 hr to 0.1% dimethyl sulfoxide (DMSO), 2 nM 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), or 10 uM tert-butylhydroquinone (tBHQ) (4 replicates per compound per time point). Embyros were frozen immediately after the 6 hr exposure and RNA isolated for microarray analysis. A Universal RNA Reference Sample was created by mixing equal amounts of total RNA from 2 replicates each from all toxicants (TCDD, tBHQ, DMSO) and timepoints (1, 2, 3, 4, 5, 6-dpf). Based on qRT-PCR results, the 4 dpf timepoint was selected for microarray analysis, in which the RNA samples (4 replicates per compound) were Cy3 labeled and co-hybridized with Cy5 labeled Universal RNA Reference Sample to generate data for analysis of variance.

Dataset Information

Transcription profiling of human neural stem and neuroblastoma cells

Publications

Dissecting tBHQ induced ARE-driven gene expression through long and short oligonucleotide arrays.

Similar Datasets

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