Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of rat liver throughout the day

ABSTRACT: One Âµg of total RNA from either an; individual rat or from a pooled sample was amplified and labeled with a; fluorescent dye (either Cy3 or Cy5) using the Low RNA Input Linear Amplification Labeling kit (Agilent Technologies, Palo Alto, CA) following the manufacturerâ??s protocol. The amount and quality of the resulting fluorescently labeled cRNA was assessed using a Nanodrop ND-100 spectrophometer and an Agilent; Bioanalyzer. Equal amounts of Cy3- or Cy5-labeled cRNA were hybridized to the Agilent Rat Oligo Microarray (Agilent Technologies, Inc., Palo Alto, CA) for 17 hrs, prior to washing and scanning. Data was extracted from the resulting; images using Agilentâ??s Feature Extraction Software (Agilent Technologies, Inc., Palo Alto, CA). For day/night comparisons, two types of complementing hybridizations were performed: hepatic RNA from individual day rats was hybridized against a pool made up of RNA from 12 hour offset night rats, and RNA from individual night rats was hybridized against a pool made up of RNA from 12-hour offset day rats. Specifically, hepatic RNA samples from three individual day rats collected ten hours after light on (CT10) were hybridized against a pooled RNA sample composed of equal aliquots of RNA from the livers of six night rats collected ten hrs after lights off (CT22); and RNA samples from three individual night rats collected at CT22 were hybridized against a pooled RNA sample composed of equal aliquots of RNA from the livers of six day rats collected at CT10. This was replicated in a second study for a total of 24 hybridizations of 12 hour offset samples. For time of day comparisons, equal aliquots of RNA from the livers of six; rats collected at each of four different times of the circadian day (CT4, CT10, C16 and CT22) were pooled. The two replicate studies thus resulted in 8 pools (two replicate pools/time point times four time points); each pool was hybridized against a Universal Rat Reference RNA Standard (Stratagene, La Jolla, CA).

ORGANISM(S): Rattus norvegicus

SUBMITTER: Gary Boorman

PROVIDER: E-GEOD-2441 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Hepatic gene expression changes throughout the day in the Fischer rat: implications for toxicogenomic experiments.

Boorman Gary A GA Blackshear Pamela E PE Parker Joel S JS Lobenhofer Edward K EK Malarkey David E DE Vallant Molly K MK Gerken Diane K DK Irwin Richard D RD

Toxicological sciences : an official journal of the Society of Toxicology 20050406 1

There is increasing use of transcriptional profiling in hepatotoxicity studies in the rat. Understanding hepatic gene expression changes over time is critical, since tissue collection may occur throughout the day. Furthermore, when comparing results from different data sets, times of dosing and tissue collection may vary. Circadian effects on the mouse hepatic transcriptome have been well documented. However, limited reports exist for the rat. In one study approximately 7% of the hepatic genes s ...[more]

PMID: 15814895

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Dataset Information

Transcription profiling of rat liver throughout the day

Publications

Hepatic gene expression changes throughout the day in the Fischer rat: implications for toxicogenomic experiments.

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