{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Fiona Crawford"],"disease":["short day torpor"],"organism":["Phodopus sungorus"],"software":["GenePix Pro [Axon Instruments]"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MEXP-1185"],"description":["Heart cDNA from torpid and normothermic male hamsters is compared at five different time-points every three hours, starting from 2h prior to lights on and finishing 10h after lights on."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Labeling - In vitro transcription using double-stranded cDNA as a template in the presence of Cy3-dUTP, using Superscript II Reverse Transcriptase kit (Invitrogen) according to the manufacturer’s instructions. Unincorporated fluorescent nucleotides were removed using an AutoSeqG-50 column (Amersham Biosciences), following the manufacturer's protocol. Labelled cDNA was ethanol precipitated and resuspended in nuclease-free water.","Labeling - In vitro transcription using double-stranded cDNA as a template in the presence of Cy5-dUTP, using Superscript II Reverse Transcriptase kit (Invitrogen) according to the manufacturer’s instructions. Unincorporated fluorescent nucleotides were removed using an AutoSeqG-50 column (Amersham Biosciences), following the manufacturer's protocol. Labelled cDNA was ethanol precipitated and resuspended in nuclease-free water.","Growth Protocol - Temperature 18 °C, Food and Water ad libitum, Individually housed in cages according to German legislation, Lighting decreasing one hour per week from 16h light and 8h dark per day (16L:8D) to 8L:16D, then remaining at 8L:16D until culling.","Sample Processing - Hamsters were culled by C02 inhalation. Hearts were immediately removed and frozen on dry ice. Tissue was maintained at -80 degrees Centigrade.","Nucleic Acid Extraction - Total RNA extracted with TRIzol reagent (Invitrogen) according to the manufacturer’s instructions.","Hybridization - Cy3 and Cy5 labelled probes (10ul each) were mixed and 20ul 2x hybridisation buffer added (49% formamide (Sigma), 9.8x SSC, 0.2% SDS). Probe mixture was pipetted onto array and covered with polyethylene hydrophobic coverslip (BDH) and incubated as above."],"figure_sub":["MIAME Score","Raw Data","Organization","Assays and Data","MAGE-TAB Files","Array Designs"],"data_protocol":["Feature Extraction - Arrays were kept in the dark prior to scanning. They were scanned with the above scanner and software. Overall levels of Cy3 and Cy5 were balanced and the image of each slide saved as a TIFF file."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["GenePix 4000A [Axon Instruments]"],"pubmed_abstract":["The Siberian hamster exhibits the key winter adaptive strategy of daily torpor, during which metabolism and heart rate are slowed for a few hours and body temperature declines by up to 20 degrees C, allowing substantial energetic savings. Previous studies of hibernators in which temperature drops by >30 degrees C for many days to weeks have revealed decreased transcription and translation during hypometabolism and identified several key physiological pathways involved. Here we used a cDNA microarray to define cardiac transcript changes over the course of a daily torpor bout and return to normothermia, and we show that, in common with hibernators, a relatively small proportion of the transcriptome (<5%) exhibited altered expression over a torpor bout. Pathways exhibiting significantly alter"],"study_type":["transcription profiling by array"],"species":["Phodopus sungorus"],"pubmed_title":["The influence of torpor on cardiac expression of genes involved in the circadian clock and protein turnover in the Siberian hamster (Phodopus sungorus)."],"pubmed_authors":["Fiona IJ Crawford, Cassandra L Hodgkinson, Elena Ivanova, Larisa B Logunova, Gary J Evans, Stephan Steinlechner, Andrew SI Loudon","Fiona Crawford"],"additional_accession":[]},"is_claimable":false,"name":"Transcription profiling of heart from torpid and normothermic male Siberian hamsters compared at five different time-points","description":"Heart cDNA from torpid and normothermic male hamsters is compared at five different time-points every three hours, starting from 2h prior to lights on and finishing 10h after lights on.","dates":{"release":"2007-12-05T00:00:00Z","modification":"2022-02-03T09:07:15.513Z","creation":"2022-02-03T09:07:15.513Z"},"accession":"E-MEXP-1185","cross_references":{"pubmed":["17848604"],"EFO":["EFO_0002768"],"doi":["17848604"]}}