Data Set Group2: MDC/CAS/UCL Heart 230_V2 (Dec08) RMA

Data Set: MDC/CAS/UCL Heart 230_V2 (Dec08) RMA GN Accession: GN221 GEO Series: Title: Genome-wide co-expression analysis in multiple tissues. Organism: Rat (Rattus norvegicus, mRatBN7.2/rn7) Group: HXBBXH Tissue: Heart mRNA Dataset Status: Public Platforms: Affy Rat Genome 230 v2.0 (GPL1355) Normalization: RMA

Contact Information Timothy Aitman Imperial College London Imperial College London, South Kensington Campus, London SW7 2AZ London, London 2AZ UK Tel. 44 (0)20 3313 4253 t.aitman@imperial.ac.uk Website Download datasets and supplementary data files GN221_MeanDataAnnotated_rev081815.txt (N/A) GN221_StdError_rev081815.txt (N/A)

Specifics of this Data Set:

None

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.

About the cases used to generate this set of data:

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 the tissue used to generate this set of data:

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. Strain SampleID HSR HSR1 HSR HSR2 HSR HSR3 HSR HSR4 BN BN1 BN BN2 BN BN3 BN BN4 BN BN5 HXB1 RI 01-1 HXB1 RI 01-2 HXB1 RI 01-3 HXB1 RI 01-4 HXB2 RI 02-1 HXB2 RI 02-2 HXB2 RI 02-3 HXB2 RI 02-4 HXB3 RI 03-1 HXB3 RI 03-2 HXB3 RI 03-3 HXB3 RI 03-4 HXB4 RI 04-1 HXB4 RI 04-2 HXB4 RI 04-3 HXB4 RI 04-4 HXB5 RI 05-1 HXB5 RI 05-2 HXB5 RI 05-3 HXB5 *RI 05-4 HXB7 RI 07-1 HXB7 RI 07-2 HXB7 RI 07-3 HXB7 RI 07-4 HXB10 RI 10-1 HXB10 RI 10-2 HXB10 RI 10-3 HXB10 RI 10-4 HXB15 RI 15-1 HXB15 RI 15-2 HXB15 RI 15-3 HXB15 RI 15-4 HXB17 RI 17-1 HXB17 RI 17-2 HXB17 RI 17-3 HXB17 RI 17-4 HXB18 RI 18-1 HXB18 RI 18-2 HXB18 RI 18-3 HXB18 RI 18-4 HXB20 RI 20-1 HXB20 RI 20-2 HXB20 RI 20-3 HXB20 RI 20-4 HXB21 RI 21-1 HXB21 RI 21-2 HXB21 RI 21-3 HXB21 RI 21-4 HXB22 RI 22-1 HXB22 RI 22-2 HXB22 RI 22-3 HXB22 RI 22-4 HXB23 RI 23-1 HXB23 RI 23-2 HXB23 RI 23-3 HXB23 RI 23-4 HXB24 RI 24-1 HXB24 RI 24-2 HXB24 RI 24-3 HXB24 RI 24-4 HXB25 RI 25-1 HXB25 RI 25-2 HXB25 RI 25-3 HXB25 *RI 25-4 HXB26 RI 26-1 HXB26 RI 26-2 HXB26 RI 26-3 HXB26 RI 26-4 HXB27 RI 27-1 HXB27 RI 27-2 HXB27 RI 27-3 HXB27 RI 27-4 HXB29 RI 29-1 HXB29 RI 29-2 HXB29 RI 29-3 HXB29 RI 29-4 HXB31 RI 31-1 HXB31 RI 31-2 HXB31 RI 31-3 HXB31 RI 31-4 BXH2 RI 02c-1 BXH2 RI 02c-2 BXH2 RI 02c-3 BXH2 RI 02c-4 BXH3 RI 03c-1 BXH3 RI 03c-2 BXH3 RI 03c-3 BXH3 RI 03c-4 BXH5 RI 05c-1 BXH5 RI 05c-2 BXH5 RI 05c-3 BXH5 RI 05c-4 BXH6 RI 06c-1 BXH6 RI 06c-2 BXH6 RI 06c-3 BXH6 RI 06c-4 BXH8 RI 08c-1 BXH8 RI 08c-2 BXH8 RI 08c-3 BXH8 RI 08c-4 BXH9 RI 09c-1 BXH9 RI 09c-2 BXH9 RI 09c-3 BXH9 RI 09c-4 BXH10 RI 10c-1 BXH10 RI 10c-2 BXH10 RI 10c-3 BXH11 RI 11c-1 BXH11 RI 11c-2 BXH11 RI 11c-3 BXH11 RI 11c-4 BXH12 RI 12c-1 BXH12 RI 12c-2 BXH12 RI 12c-3 BXH12 RI 12c-4 BXH13 RI 13c-1 BXH13 RI 13c-2 BXH13 RI 13c-3 BXH13 RI 13c-4

About the array 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 values and 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.

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.

Experiment Type:

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.

Contributor:

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.

Data source 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.

Study Id:

69

• The UT Center for Integrative and Translational Genomics
• NIGMS Systems Genetics and Precision Medicine project (R01 GM123489, 2017-2021)
• NIDA NIDA Core Center of Excellence in Transcriptomics, Systems Genetics, and the Addictome (P30 DA044223, 2017-2022)
• NIA Translational Systems Genetics of Mitochondria, Metabolism, and Aging (R01AG043930, 2013-2018)
• NIAAA Integrative Neuroscience Initiative on Alcoholism (U01 AA016662, U01 AA013499, U24 AA013513, U01 AA014425, 2006-2017)
• NIDA, NIMH, and NIAAA (P20-DA 21131, 2001-2012)
• NCI MMHCC (U01CA105417), NCRR, BIRN, (U24 RR021760)