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Sample GSM1055966 Query DataSets for GSM1055966
Status Public on Jan 01, 2014
Title KO- zt9 [206]
Sample type RNA
 
Source name heart, KO- zt9
Organism Mus musculus
Characteristics gender: Male
strain: C57/Bl6
zt time: 9
Growth protocol Male CBK (on the C57Bl/6J background), as well as littermate controls, were housed at the Center for Comparative Medicine at the University of Alabama at Birmingham, under temperature-, humidity-, and light- controlled conditions. A strict 12-hour light/12-hour dark cycle regime was enforced (lights on at 6AM; zeitgeber time [ZT] 0); the light/dark cycle was maintained throughout these studies, facilitating elucidation of the potential roles for the cardiomyocyte circadian clock under physiological conditions (as such, diurnal variations were investigated). Mice received food and water ad libitum.
Extracted molecule total RNA
Extraction protocol A standard RNA extraction protocol using Tri-reagent was used.
Label Cy3
Label protocol Total RNA was converted to cDNA by reverse transcription using ArrayScript reverse transcriptase and T7-(dT)24 primers, followed by second-strand synthesis to generate double-stranded cDNA (Ambion). After purification, the cDNA was converted to biotin-labeled cRNA, hybridized to the BeadChip (Illumina), and stained with strepavidin-Cy3 for visualization.
 
Hybridization protocol See above
Scan protocol BeadChips were visualized using an iScan system (Illumina, Inc.).
Description KO- zt9
Ad libitum feeding, standard chow
Data processing Stata version IC10.0 (Stata Corp., San Antonio, TX) was used to perform two-way ANOVA to investigate main effects of time and/or genotype, followed by Bonferroni post hoc analyses for pair-wise comparisons. Rhythmic parameter comparisons of were calculated using Stata version IC10.0 to perform cosinor analysis. The cosinor analyses were performed based on the assumption that the free-running period is fixed at 24 h. Data was considered rhythmic if the p-value of the R2 of the linearized cosinor function of f(t) = M + Cos(2πt/24) + Sin(2πt/24) was less than 0.05. In all analyses, the null hypothesis of no model effects was rejected at p<0.05.
 
Submission date Dec 20, 2012
Last update date Jan 01, 2014
Contact name Molly Bray
E-mail(s) mbray@uab.edu
Phone 205-975-7651
Fax 205-934-8665
Organization name University of Alabama at Birmingham
Department Genetics
Street address 1720 2nd Avenue N, RPHB 230H
City Birmingham
State/province AL
ZIP/Postal code 35294
Country USA
 
Platform ID GPL6885
Series (1)
GSE43073 IMPACT OF CARDIOMYOCYTE-SPECIFIC BMAL1 DELETION ON MYOCARDIAL GENE EXPRESSION, METABOLISM, AND CONTRACTILE FUNCTION

Data table header descriptions
ID_REF
VALUE Average signal intensity data were quantile normalized using GenomeStudio V2011.1 software.
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 5212.14 0
ILMN_2721178 1311.73 0
ILMN_3033922 412.3094 0
ILMN_3092673 2624.73 0
ILMN_2816356 16.223 0.05012531
ILMN_2808939 131.2425 0
ILMN_2634564 178.6086 0
ILMN_2737647 1.754258 0.3721805
ILMN_2734484 465.4879 0
ILMN_2952292 30.64115 0.01253133
ILMN_2699078 -5.897249 0.6967419
ILMN_1213681 1019.399 0
ILMN_2735413 1.914077 0.3621554
ILMN_2735415 7.094313 0.1804511
ILMN_2891688 856.8568 0
ILMN_2637698 669.7716 0
ILMN_2674228 136.5968 0
ILMN_2601546 11.33738 0.1015038
ILMN_1230831 11.1651 0.10401
ILMN_2848071 14.94787 0.06015038

Total number of rows: 25697

Table truncated, full table size 739 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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