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Summary
This December 2008 data set provides estimates of mRNA expression in normal hearts of 31 strains of rats including the hypertensive SHR strain (aka HSR), the normotensive BN strain, and 29 HXB/BXH recombinant inbred strains. Most strains were sampled in quadruplicate (6-week-old males). Animals and tissues were generated by Michal Pravenec and colleagues at the Czech Academy of Sciences (CAS). RNA samples were processed at the Max-Delbrück-Center (MDC), Berlin Buch by Norbert Hübner and colleagues. Transcriptome mapping was carried out by Timothy Aitman and colleagues at the Imperial College, London (ICL). Samples were hybridized individually to a total of approximately XXX Affymetrix RAE230A array processed using the RMA protocol. The expression values of each array have been logged and adjusted to a mean of 8 and a standard deviation of 2 (mean and variance stabilized). This data set complements the kidney and fat data set exploited by Hübner and colleagues 2005.
These data may also be viewed using the eQTL Explorer Java application by John Mangion, Tim Aitman, and colleagues (Mueller et al. 2006).
Genome-wide co-expression analysis in multiple tissues.
And see closely associate set of papers:
- Integrated transcriptional profiling and linkage analysis for identification of genes underlying disease.
- Heritability and tissue specificity of expression quantitative trait loci.
- Integrated genomic approaches implicate osteoglycin (Ogn) in the regulation of left ventricular mass.
- New insights into the genetic control of gene expression using a Bayesian multi-tissue approach.
- The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance.
- A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.
- Integrated genomic approaches to identification of candidate genes underlying metabolic and cardiovascular phenotypes in the spontaneously hypertensive rat.
- Systems-level approaches reveal conservation of trans-regulated genes in the rat and genetic determinants of blood pressure in humans.
Experiment design
RNA processing:RNA was extracted using Trizol reagent (Invitrogen) and purified using an RNeasy Mini kit from Qiagen. Double-stranded cDNA was generated without pooling. The Ambion MEGAscript T7 kit from Ambion was used to generate biotinylated cRNA for kidney. See Hübner et al. 2005 for additional detail. One-hundred and twenty eight samples passed RNA quality control steps.
About cases
Data were generated using the HXB/BXH recombinant inbred strains of rats generated over the past 20 years in Prague. The parental strains from which all HXB lines are derived are SHR (SHR/OlaIpcv, abbreviated SHR or HSR = H) and Brown Norway (BN-Lx/Cub= B). These strains have been used extensively to study cardiovascular system physiology and genetics.
The HXB strains were bred by Michal Pravenec at the Institute of Physiology, Czech Academy of Sciences. The BXH strains were bred by Vladimir Kren (see Pravenec et al. 1989, 2004) at a similar animal facility at the Institute of Biology and Medical Genetics, 1st Medical Faculty, Charles University. These strains are at approximately the 6oth generation of continuous inbreeding (F60).
Animals used in the transcriptome analyses of multiple tissues (Hübner and colleagues, 2005) were weaned at 4 weeks. Those born at the Charles University were transferred to the Institute of Physiology. Animals were reared on a commerical rat chow (ST-1 from VELAZ, Czech Republic). Four males were house per cage. Cages were made of polystyrene and have a floor size of 22 x 38 cm and height of 23 cm. The bedding was changed twice a week. Light cycle was 12:12 on-off. Vivarium rooms were maintained at 23 deg. C. Rats were sexually naive. All males used in the initial transcriptome studies (Hübner et al., 2005) were born between May and August 2002. They were sacrificed unfastged by rapid cervical dislocation between 9 and 10 AM, following an approved animal protocol (Ethics Committee of the Institute of Physiology, Czech Academy of Sciences, Prague; Animal Protectiion Law of the Czech Republic (311/1997).
About tissue
All tissues were collected at the age of 6 weeks. Hearts and other organs were rapidly dissected and cleaned of fat, inserted into a vial, and immersed in liquid nitrogen for storage until RNA extraction. THIS IS AN OLD TABLE FOR THE KIDNEY DATA IN THIS INFO FILE ONLY AS A PLACEHOLDER. The table below lists the arrays by strain and sample identifier. Each array was hybridized with mRNA from a single young male rat.
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About platform
Affymetrix 230Av2 GeneChip: Expression data were generated using the Affymetrix 230Av2 array (GEO_GPL341). The chromosomal locations of probe sets were determined by BLAT analysis of concatenated probe sequences using the Rat Genome Sequencing Consortium assembly.
About data processing
Probe (cell) level data from the CEL file: These CEL values produced by GCOS are 75% quantiles from a set of pixel measured in each cell.Probe set data: The original CEL values were processed using RMA and log2 transformed using our standard 2z +8 transform. This recenters each array to a mean of 8 units and a SD of 2 units. Probe set values are typically the averages of four biological replicates within strain.
Contributors
Grieve IC1, Dickens NJ, Pravenec M, Kren V, Hubner N, Cook SA, Aitman TJ, Petretto E, Mangion J. Author information 1MRC Clinical Sciences Centre, Imperial College, Hammersmith Hospital, London, United Kingdom.
Citation
PLoS One. 2008;3(12):e4033. doi: 10.1371/journal.pone.0004033. Epub 2008 Dec 29.
Acknowledgment
This work was supported with funds to TJA by the MRC Clinical Sciences Centre, the British Heart Foundation, and the Wellcome Trust Cardiovascular Functional Genomics Initiative; to NH from the German Ministry for Science and Education (National Genome Research Network); to MP and Vladimir Kren from the Grant Agency of the Czech Republic; to MP and TJA from the Wellcome Trust Collaborative Research Initiative grant, to Theodore W Kurtz from the NIH, to TWK and MP from a Fogarty International Research Collaboration Award. Microarrays were a generous donation of Affymetrix Inc. Michal Pravenec thanks the Howard Hughes Medical Institute for its support to him as an international research scholar.
Notes
Heart Left Ventricle
http://www.expressionanalysis.com/pdf/Affymetrix/GXRat230v2.pdf
GEO platform id http://www.ncbi.nlm.nih.gov/projects/geo/query/acc.cgi?acc=GPL1355
Data entered by Evan Williams and Rob Williams, Jan 2, 2009.
Mapping of probes http://compbio.dcs.gla.ac.uk/sf/index.html#230map
Entered by Arthur Centeno, Dec 18, 2008. Data from Herbert Schulz. CEL files processed by AC. Data normalized by AC and RWW (2z+8).
Access to this data set is currently limited to the three teams of researchers who generated the data: Norbert Hübner (MDC, Berlin), Timothy Aitman (UC London), and Michal Pravenec (CAS, Prague). For access to data please contact N. Hübner by email.
The text below was copied from the INFO file for the older (2005) kidney gene expression data set by RWW (Dec 20, 2008). It contains errors and will need to be corrected with the guidance of the data generators and owners.
This text file originally copied from the old kidney INFO file that was generated by Robert Williams, Norbert Hübner, Michal Pravnec, Timothy Aitman. This version entered into the adrenal INFO file, December 19, 2008, by RWW, Kathrin Saar Dec 23.