Investigation Title Transcription profiling of rat heart at several time points after either a myocardial infraction or sham operation Comment[Submitted Name] NTNU- Rat - Infarction and heart failure time course study Experimental Design time_series_design disease_state_design co-expression_design transcription profiling by array Experimental Design Term Source REF mo mo mo EFO Comment[ArrayExpressReleaseDate] 2006-11-10 Comment[AEMIAMESCORE] 3 Comment[ArrayExpressAccession] E-TABM-165 Comment[MAGETAB TimeStamp_Version] 2011-06-29 00:51:43 Last Changed Rev: 14857 Experimental Factor Name Time DiseaseState Experimental Factor Type time disease_state Experimental Factor Term Source REF Person Last Name Beisvag Person First Name Vidar Person Mid Initials Person Email vidar.beisvag@medisin.ntnu.no Person Phone Person Fax Person Address Department of Circulation and Medical Imaging, Medisinsk Teknisk Forskningssenter, Olav Kyrres gt 3, Trondheim, Norway Person Affiliation Norwegian University of Science and Technology Person Roles submitter Person Roles Term Source REF Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2006-11-10 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Experiment Description Myocardial Infarction Model: Sixty nine animals (252 ± 2 g) were randomized to either myocardial infraction (MI) or sham operation. MI were produced by partial ligation of the left coronary artery as described in detail by Loennechen et al. (Loennechen JP, Stoylen A, Beisvag V, Wisloff U, Ellingsen O: Regional expression of endothelin-1, ANP, IGF-1, and LV wall stress in the infarcted rat heart. Am J Physiol Heart Circ Physiol 2001, 280: H2902-H2910.). Animals with large infarctions (45 ± 2% of LV) were euthanized on one of the following days: day 1 (n = 6), 3(n = 5), 7 (n = 6), 14 (n = 6), 42 (n =6) and 91 (n = 4); and sham-operated animals were euthanized on one of the following days: 1 (n = 6), 3(n = 6), 7 (n = 6), 14 (n = 6), 42 (n =6) and 91 (n = 6). After sacrifice, heart tissue was removed, weighted and scored for size of the healed infarction. Infarct size was measured and the left ventricular myocardium stored on -80°C for preparation of RNA. Protocol Name P-TABM-836 P-TABM-835 P-TABM-833 P-TABM-830 P-TABM-832 P-TABM-831 P-TABM-834 Protocol Type specified_biomaterial_action specified_biomaterial_action pool nucleic_acid_extraction labeling hybridization image_acquisition Protocol Description Sample treatment sham operations: Sham operations were performed as described in detail by Loennechen et al. [21].(Loennechen JP, Stoylen A, Beisvag V, Wisloff U, Ellingsen O: Regional expression of endothelin-1, ANP, IGF-1, and LV wall stress in the infarcted rat heart. Am J Physiol Heart Circ Physiol 2001, 280: H2902-H2910.) Sample treatment myocardial infarction: MI were produced by partial ligation of the left coronary artery as described in detail by Loennechen et al.(Loennechen JP, Stoylen A, Beisvag V, Wisloff U, Ellingsen O: Regional expression of endothelin-1, ANP, IGF-1, and LV wall stress in the infarcted rat heart. Am J Physiol Heart Circ Physiol 2001, 280: H2902-H2910.) Pooling protocol form sham operated anaimals: Sham-operated animals were euthanized on one of the following days: 1 (n = 6), 3(n = 6), 7 (n = 6), 14 (n = 6), 42 (n =6) and 91 (n = 6). RNA from animals in the each grupe were pooled, resulting in 6 pools of RNA used as "controls" in the hybridization againts the infarcted heart samples at corrensponding time point. Samples were taken from the left ventricle free wall immediately after the rats were sacrified, snap frozen in liquid nitrogen and stored at ?80 C. Frozen tissue was homogenized using an Ultra-Turrax rotating knife homogenizer and total RNA extracted using a TRIzole reagent (GIBCO BRL Life Technologies, New York, NY, USA) followed by a second cleaning procedure using RNeasy midi kit (Quiagen Inc. CA, USA). Quantitation, purity and RNA integrity were evaluated by absorbance at 260 and 280 nm (Gene Quant, AmershamPharmacia, Buckinghamshire, UK), and agarose gel electrophoresis. High quality RNA with A260/A280 ratio above 1.8 and intact ribosomal 28S and 18S RNA bands was used for microarray. For the labelling reactions, five ?g total RNA was reverse transcribed and labelled with Cy3 or Cy5 attached dendrimers, respectively, using the Genisphere 3DNA kit as described in the manufacturer's one step protocol (Genisphere, Montvale, NJ, USA). Hybridization was performed at 60°C for 15hours using 0.25 M NaPO4, 1 mM EDTA, 4.5% SDS, 1X SSC and 0.5 ?g human Cot-1 DNA (GIBCO BRL, Life Technologies, Carlsbad, CL, USA) in a total volume of 35 ?l. Three 15 min post-hybridization washes were performed; first at 55°C with 2X SSC and 0.2% SDS, then at room temperature with 2X SSC, and finally at room temperature with 0.2X SSC. Scanning was done with fixed laser power (100%) and PMT gain adjusted to balance Cy3 and Cy5 signal intensities. Images were analyzed using ArraySuite version 2.0 extension of IPLab image processing software package (Scanalytics, Fairfax, VA, USA). Protocol Parameters Protocol Hardware Protocol Software Protocol Contact Protocol Term Source REF mo mo mo SDRF File E-TABM-165.sdrf.txt Term Source Name mo atcc ncbitax NCI_thesaurus The MGED Ontology ArrayExpress mo EFO Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.atcc.org/ http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html ncithesaurus.obo.alt http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/efo/ Term Source Version