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Sample GSM159308 Query DataSets for GSM159308
Status Public on May 12, 2010
Title IRA_12
Sample type RNA
 
Source name Infrarenal region of abdominal aorta
Organism Mus musculus
Characteristics ApoE-/- (C57B6 background), male mouse, 14 weeks old
Biomaterial provider Animal Resource Centre (http://www.arc.wa.gov.au/) PO Box 1180, Canning Vale WA 6970, Australia
Extracted molecule total RNA
Extraction protocol RNA was extracted from excised artery segments by tissue disruption in Tri-Reagent (Sigma) and extraction as per manufacturers instructions. Isolated RNA was further purified on RNeasy columns (Qiagen) as per manufacturers instructions. The concentration and quality of total RNA was measured by spectrophotometry at OD260/280 and the quality of the total RNA sample was assessed using an Agilent Bioanalyser and Agilent RNA6000 Nano Lab Chip.
Label biotin, Cy5-Streptavidin
Label protocol Biotin-labeled cRNA was prepared by linear amplification of the Poly(A)+ RNA population within the total RNA sample. Briefly, 0.51 µg of total RNA was reverse transcribed after priming with a DNA oligonucleotide containing T7 RNA polymerase promoter 5' to a d(T)24 sequence. After second-strand cDNA synthesis and purification of double-stranded cDNA, in vitro transcription was performed using T7 RNA polymerase in the presence of biotinylated UTP.
 
Hybridization protocol 10 µg of purified cRNA was fragmented to uniform size and applied to CodeLink Bioarrays (GE Healthcare) in hybridization buffer. Arrays were hybridized at 37ºC for 18 hrs in a temperature-controlled shaking incubator. Arrays were washed in 0.75x TNT at 46º C for 1 hr and stained with Cy5-Streptavidin dye conjugate for 30 min.
Scan protocol Arrays were scanned with a GenePix™ 4000B scanner.
Description -
Data processing Array data was processed with CodeLink Expression Analysis software (GE Healthcare) and data was analyzed with GeneSpring software (Silicon Genetics). To compare individual expression values across arrays, raw intensity data (generated from CodeLink Expression 2 software) from each gene was normalized to the median intensity of the array. Only genes which had values greater than the background intensity in at least one condition were used for further analysis.
 
Submission date Jan 29, 2007
Last update date May 04, 2009
Contact name Jonathan Golledge
E-mail(s) jonathan.golledge@jcu.edu.au
Phone +67 7 47814730
Fax +61 7 4781 6986
URL http://www.jcu.edu.au/school/medicine/VBU.htm
Organization name James Cook University
Department School of Medicine
Lab Vascular Biology Unit
Street address School of Medicine
City Townsville
State/province Queensland
ZIP/Postal code 4811
Country Australia
 
Platform ID GPL2897
Series (1)
GSE7006 Comparison of infrarenal and suprarenal sections of mouse ApoE-/- abdominal aorta

Data table header descriptions
ID_REF
Raw_intensity Fluorescence intensity
VALUE Normalized Intensity = Raw_intensity/median intensity value {81.46117401}
Quality_flag

Data table
ID_REF Raw_intensity VALUE Quality_flag
1001 4568.5850 56.0830 G
1002 812.4054 9.9729 G
1003 15.8750 0.1949 L
1004 73.6393 0.9040 G
1005 17.8750 0.2194 L
1006 18.9444 0.2326 L
1007 4256.8750 52.2565 G
1008 4042.6917 49.6272 G
1010 155.3529 1.9071 G
1012 128.7385 1.5804 G
1013 36.1957 0.4443 G
1014 4355.5825 53.4682 G
1015 4070.0835 49.9635 G
1017 7.1936 0.0883 L
1018 17.1714 0.2108 L
1019 27.7692 0.3409 G
1020 23.7879 0.2920 L
1021 4091.8750 50.2310 G
1022 4001.0715 49.1163 G
1024 12.4717 0.1531 L

Total number of rows: 36227

Table truncated, full table size 862 Kbytes.




Supplementary data files not provided

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