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Sample GSM572294 Query DataSets for GSM572294
Status Public on Dec 31, 2013
Title striatum-HI-24h-Rep1
Sample type RNA
 
Source name Infarct striatum
Organism Mus musculus
Characteristics strain: C57/Bl6
age: 8 days
treatment: Hypoxic ischemia
time point: 24h
tissue: brain striatum
Treatment protocol Pups were anesthetized with 1.5% isoflurane in 30% O2/70% N2 mixture and underwent unilateral HI. The right common carotid artery was exposed through a ventral midline neck incision and permanently occluded by electrocoagulation (Aaron Medical Industries Inc, Florida, USA), where the occlusion was verified The wound was sutured and mouse pups were returned to their mother for 1.5–2 h. Sham control rats (n = 4) underwent the identical procedure, without carotid artery occlusion. Pups were then placed in an 8% O2/92% N2 humidified chamber at 37°C for 1 h. This combined procedure results in select neuronal damage or infarction in the hemisphere ipsilateral to the carotid occlusion, whereas hypoxia alone (contralateral hemisphere) does not produce any significant brain injury (reference). Following the HI or sham surgery procedure, all pups were returned to their dam and kept under standard housing conditions for the remainder of the study.
Growth protocol All animal work conducted in this study was approved by the University of New South Wales (UNSW) Animal Ethics and Experimentation Committee and performed in accordance with the guidelines of the National Health and Medical Research Council (Australia). C57 Black 6 mouse pups were obtained from Animal Resources Centre (Perth, WA) and were housed under standard housing conditions in the UNSW Biological Resources Centre animal facility throughout experiments.
Extracted molecule total RNA
Extraction protocol RNA was extracted and cleaned up with QIAGEN miRNeasy mini kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with E-gene HDA-GT12 genetic analyzer.
Label biotin
Label protocol Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays
 
Hybridization protocol Standard Illumina hybridization protocol with a hybridization duration of 17h.
Scan protocol Standard Illumina scanning protocol with a pmt value=478
Description Replicate 1
4514990161_F
Data processing The data were normalised using median normalisation with GeneSpring Ver 7.3
 
Submission date Jul 29, 2010
Last update date Dec 31, 2013
Contact name Minghui Jessica Chen
Organization name Menzies Research Institute
Department Neuroscience group
Lab A/P Steve Cheung
Street address Menzies Research Institute, University of Tasmania, Private Bag 24
City Hobart
State/province Tasmania
ZIP/Postal code 7001
Country Australia
 
Platform ID GPL6885
Series (2)
GSE23319 Global transcriptomic profiling of hypoxic ischemia in an in vivo neonatal mouse model: Striatum
GSE23333 Global transcriptomic profiling of hypoxic ischemia in an in vivo neonatal mouse model

Data table header descriptions
ID_REF
VALUE Median normalisation

Data table
ID_REF VALUE
ILMN_1248788 0.8725344
ILMN_2707227 1.0323459
ILMN_2896528 0.9442937
ILMN_2721178 0.75365007
ILMN_1227723 0.8177257
ILMN_3033922 0.8849326
ILMN_3092673 0.8964307
ILMN_2730714 0.98638976
ILMN_3162224 1.0227093
ILMN_2816356 0.97555417
ILMN_2808939 0.9567714
ILMN_2634564 0.80389655
ILMN_1216623 0.82753694
ILMN_1215157 0.8648831
ILMN_1228777 1.083121
ILMN_2737647 1.2067742
ILMN_1216425 1.1386333
ILMN_2734484 0.809017
ILMN_2652961 1.0695193
ILMN_2952292 0.79269844

Total number of rows: 25697

Table truncated, full table size 578 Kbytes.




Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table
Processed data are available on Series record

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