Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Transcription profiling of response to chronic constant hypoxia in adult Zebrafish hearts

ABSTRACT: Gene expression profile of the response to chronic constant hypoxia in the heart of adult zebrafish Experiment Overall Design: 10 arrays (5 for hypoxia and 5 normoxia); in total 8 biological samples plus 2 technical replicates

ORGANISM(S): Danio rerio

SUBMITTER: Christoph Peter Bagowski

PROVIDER: E-GEOD-4989 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Transcriptome analysis of the response to chronic constant hypoxia in zebrafish hearts.

Marques Ines J IJ Leito Jelani T D JT Spaink Herman P HP Testerink Janwillem J Jaspers Richard T RT Witte Frans F van den Berg Sjoerd S van den Berg Sjoerd S Bagowski Christoph P CP

Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology 20070908 1

Insufficient blood supply during acute infarction and chronic ischemia leads to tissue hypoxia which can significantly alter gene expression patterns in the heart. In contrast to most mammals, some teleost fishes are able to adapt to extremely low oxygen levels. We describe here that chronic constant hypoxia (CCH) leads to a smaller ventricular outflow tract, reduced lacunae within the central ventricular cavity and around the trabeculae and an increase in the number of cardiac myocyte nuclei pe ...[more]

PMID: 17828398

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Project description:Adult zebrafish (TÃ¼bingen strain, sex not specified) at approximately 1 year of age were analysed. For experiments conducted under low oxygen conditions, nitrogen gas was bubbled through water to deplete oxygen before exposure of individual fish to the medium. Oxygen concentrations were measured using a dissolved oxygen meter (DO 6+, EUTECH instruments, Singapore). The dissolved oxygen level for hypoxia treatment was measured to be 1.20 Â± 0.6 mg/l, whereas normal ambient oxygen levels were 6.6 Â± 0.45 mg/l. Zebrafish were exposed to the hypoxic medium for 3 hours. Briefly, after each hypoxia trial, the animals were euthanized by hypothermic shock and then decapitated to remove the brain. Total RNA was extracted from samples mentioned above using the QIAGEN RNeasy mini kit (QIAGEN, GmbH, Hilden, Germany) and stored at â??80Â°C before further analysis. RNA concentration was determined with a NanoVueâ?¢ UVâ??vis spectrophotometer (GE Healthcare Life Sciences, Fairfield, USA). RNA integrity and quality were then estimated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and the RNA integrity number (RIN) index was calculated for each sample. Only RNAs with a RIN number >7.0 were processed further. Microarray analysis of gene expression was performed using the Zebrafish Gene 1.0 ST Array (Affymetrix Inc. Santa Clara, CA). Briefly, 300ng of total RNA derived from a single adult brain was converted to amplified sense strand cDNA using the Ambion WT Expression Kit (Life Technologies, Carlsbad, CA). The resulting sense cDNA was fragmented and Biotin end-labelled using the Affymetrix Genechip WT Terminal Labeling Kit prior to hybridisation to the array at 45 Â°C for 16 hours. Two treatments including hypoxia and normoxia were studied. Each treatment had three biological replicates (i.e. three fish exposed to hypoxia and three fish exposed to normoxia). Six samples were analysed. Microarray analysis of gene expression was performed using the Zebrafish Gene 1.0 ST Array. The signal intensity of the chip was scanned using a GeneChipR Scanner 3000TG and analysed using Expression Console software (www. Affymetrix.com). CEL files were imported and intensities adjusted by RMA background correction and quantile normalization.

Dataset Information

Transcription profiling of response to chronic constant hypoxia in adult Zebrafish hearts

Publications

Transcriptome analysis of the response to chronic constant hypoxia in zebrafish hearts.

Similar Datasets

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