E-GEOD-12724 - Transcription profiling of rat Adamts16 variants linked to inherited hypertension: knockdown of Adamts16 in NRK-52E cells

Status
Submitted on 10 September 2008, released on 13 November 2008, last updated on 1 May 2014
Organism
Rattus norvegicus
Samples (7)
Array (1)
Protocols (6)
Description
We used Affymetrix GeneChips to expression profile rat kidney NRK-52E cells treated with control scrambled siRNA or siRNA specifically targeting Adamts16. The goal of this project was to identify the downstream genes regulated by Adamts16 (the function of Adamts16 has yet to be fully delineated). Gene expression differences resulting from these siRNA-mediated gene knockdown experiments will be compared to the gene expression profiling experiments comparing kidneys from Dahl salt-senstive hypertensive inbred strain versus less hypertensive S.LEW(D1MCO4x1x3Bx1) congenic strain. The S.LEW(D1MCO4x1x3Bx1) congenic animal is an S rat containing the LEWIS allele for Adamts16 instead of the S allele. Gene expression differences in the kidneys of S.LEW(D1MCO4x1x3Bx1) versus S are hypothesized to result from sequence differences between the S and LEWIS alleles for Adamts16. It is further hypothesized that allelic differences in Adamts16 in inbred rats is responsible for blood pressure variance. The downstream genes regulated by Adamts16 may provide insight pertaining to the mechanism of blood pressure differences. Experiment Overall Design: RNA from 3 independent cultures of NRK-52E cells treated with scrambled control siRNA was extracted for target preparation and hybridization onto Affymetrix GeneChips. We also isolated RNA from NRK-52E cells treated with two different siRNAs targeting Adamts16 (n=2 independent cultures for each siRNA) for target preparation and hybridization onto Affymetrix GeneChips.
Experiment types
transcription profiling by array, unknown experiment type
Contact
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-12724.idf.txt
Sample and data relationshipE-GEOD-12724.sdrf.txt
Raw data (1)E-GEOD-12724.raw.1.zip
Processed data (1)E-GEOD-12724.processed.1.zip
Array designA-AFFY-43.adf.txt
R ExpressionSetE-GEOD-12724.eSet.r
Links