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Sample GSM88143 Query DataSets for GSM88143
Status Public on Dec 16, 2006
Title Wild Type replicate F14_2
Sample type RNA
 
Source name Aorta, male WT, ZT14
Organism Mus musculus
Characteristics Strain: C57Bl/6
Sex: male
Tissue: aorta
Circadian time: ZT14
Treatment protocol Mice were initially acclimatized for at least 2 weeks to a 12 hour light/dark cycle (light 7:00-19:00h or ZT0-ZT12; dark 19:00-7:00h or ZT12-ZT24). Mice were placed in constant darkness for at least 30 hours before sacrifice.
Extracted molecule total RNA
Extraction protocol Mice were anesthetized at the time of sacrifice. The abdomen and thorax were opened and a blood sample was taken from the vena cava. The animal was then perfused via the left ventricle with 10mls of phosphate buffered saline (PBS) (Fisher Scientific) followed by 5mls of DEPC treated water (Fischer Scientific). The aorta was exposed as close to the heart as possible at the aortic arch and to just beyond the femoral artery bifurcation, using a dissection microscope. It was then removed and immediately flash-frozen in liquid Nitrogen. Aortae were pulverized on dry ice with a Plattner’s diamond mortar and pestle set (Fisher Scientific). Total RNA was extracted using RNAqueous (Ambion, TX) and Trizol (Invitrogen, CA) and quantified by spectrophotometer.
Label Biotin
 
Hybridization protocol Target cRNA was prepared from total RNA and hybridized using 20ug of cRNA onto Affymetrix MOE 430V2 chips in accordance with protocols described in the Affymetrix Gene-Chip Expression Analysis Technical Manual.
Description After 2 week acclimation to 12 hr/12 hr light/dark regimen, mice were placed in constant darkness for at least 30 hours before sacrifice under anesthesia at ZT14. Thoracic aortae were harvested and the RNA extracted and hybridized to Affymetrix MOE 430V2 chips.
Data processing GCRMA normalization; Affymetrix Microarray Suite 5.0 normalization
 
Submission date Dec 16, 2005
Last update date Dec 19, 2005
Contact name Radu Daniel Rudic
E-mail(s) rudicrd@spirit.gcrc.upenn.edu
Phone 215 898-0255
Fax 215 573-9004
Organization name University of Pennsylvania
Department Center of Experimental Therapeutics
Lab Garret FitzGerald Lab
Street address 421 Curie Boulevard
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL1261
Series (1)
GSE3849 Differential transcript abundance in NPAS2 mutant mouse at ZT14

Data table header descriptions
ID_REF
STAT_PAIRS number of replicate PM/MM oligonucleotide pairs
STAT_PAIRS_USED number of oligonucleotide pairs used in MAS 5.0 analysis
MAS_5.0_SIGNAL MAS 5.0 normalized signal
ABS_CALL MAS 5.0 present/absent call
DETECTION P-VALUE MAS 5.0 detection p-value
VALUE GCRMA normalized signal

Data table
ID_REF STAT_PAIRS STAT_PAIRS_USED MAS_5.0_SIGNAL ABS_CALL DETECTION P-VALUE VALUE
1415670_at 11 11 390.4 P 0.000244 7.641211245
1415671_at 11 11 851 P 0.000732 8.360506301
1415672_at 11 11 1001.5 P 0.000732 9.190838038
1415673_at 11 11 154.3 P 0.005859 5.47493682
1415674_a_at 11 11 370 P 0.000244 7.075267326
1415675_at 11 11 249.5 P 0.000244 6.590085611
1415676_a_at 11 11 880.5 P 0.000244 8.991349118
1415677_at 11 11 199.9 P 0.018555 6.939592742
1415678_at 11 11 1087.6 P 0.000244 8.622440969
1415679_at 11 11 1131 P 0.000244 9.50587636
1415680_at 11 11 259.8 P 0.000244 6.740463661
1415681_at 11 11 347.8 P 0.000244 6.857599187
1415682_at 11 11 167.1 P 0.001953 4.855035397
1415683_at 11 11 617.5 P 0.000244 7.577341992
1415684_at 11 11 131.1 P 0.000732 4.874959124
1415685_at 11 11 381.2 P 0.000244 6.916374144
1415686_at 11 11 407 P 0.000244 6.959168456
1415687_a_at 11 11 1539.7 P 0.000244 9.723384515
1415688_at 11 11 855.3 P 0.000244 8.090352166
1415689_s_at 11 11 215.3 P 0.00293 5.677711447

Total number of rows: 45101

Table truncated, full table size 1986 Kbytes.




Supplementary data files not provided

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