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Sample GSM181386 Query DataSets for GSM181386
Status Public on Mar 08, 2010
Title Ntg sham 416
Sample type RNA
 
Source name Non-transgenic (Ntg) mice - sham (control group) heart tissue - array 416
Organism Mus musculus
Characteristics Organism: Mus musculus
Strain: FVB/N
Source organ: heart
Ntg-sham: Normal function, histology and molecular signature. Some gene changes reflecting stress of surgical
procedure.
Biomaterial provider Dr. Julie McMullen, Baker Heart Institute, Melbourne, Australia
Treatment protocol The sham (control) operation was performed on mice at 4 months of age. After 8 weeks, cardiac function of the mice were measured by echo cardiograph and heart was removed. Total RNA was extracted following the removal.
Growth protocol The mice were on a standard chow diet, and were kept in temperature controlled cages (21 - 23 degree celcius) and maintained a 12 hour light/dark cycle.
Extracted molecule total RNA
Extraction protocol Heart was homogenized individually using motar and pestile in liquid nitrogen.
Total RNA from the samples was collected by the addition of of TRIzol® Reagent (Invitrogen).
Cells suspended in TRIzol® reagent were disrupted by repeated pipetting and then transferred into microfuge tubes.
This protocol was modified
from manufacturer’s instructions and is described here. The lysate was further homogenized
using syringe and needle for 30 s and incubated at room temperature (~21ºC) for 5 min, and
200 l of chloroform was added. The tubes were shaken vigorously µ for 15 s to mix the
phases and incubated for 3 min at room temperature. The phases were separated by
centrifugation at 12,000 x g for 15 min at 4ºC. The upper aqueous phase was transferred
into a fresh microfuge tube and 500 µl of ice cold isopropanol added to precipitate the
RNA. The contents were mixed by gentle inversion and then incubated for 10 min at room
temperature. The RNA was recovered by centrifugation at 12,000 x g for 10 min at 4ºC. A
gelatinous pellet was left on the side of the tube after removal of the supernatant. The RNA
pellet was washed with 1 ml of 75% ethanol and the tube was vortexed briefly to resuspend
the pellet. The RNA was recovered by centrifugation at 7,500 x g for 5 min at 4ºC. This
washing step was repeated twice. After removal of the supernatant, the RNA pellet was airdried
briefly and then resuspended in 20 µl Nuclease-free H2O (Ambion Inc., Austin, TX,
USA) and stored in -80ºC for further processing.
Label biotin
Label protocol cRNA targets for the Affymetrix arrays were synthesized, labeled, and purified according to vendor's (Affymetrix)
instructions.
Please refer to Expression Analysis Technical Manual available from Affymetrix website
(GeneChip® Expression Manual, Affymetrix, Inc., Santa Clara, CA)
 
Hybridization protocol The Affymetrix arrays were hybridized and washed using the manufacturer's protocol. The arrays were then stained with streptavidin-phycoerythrin using the standard antibody amplification protocol.
Please refer to Expression Analysis Technical Manual available from Affymetrix website
(GeneChip® Expression Manual, Affymetrix, Inc., Santa Clara, CA)
Scan protocol Affymetrix arrays were scanned with the Affymetrix GeneArray scanner.
Please refer to Expression Analysis Technical Manual available from Affymetrix website
(GeneChip® Expression Manual, Affymetrix, Inc., Santa Clara, CA)
Description Non-transgenic mice treated with sham operation to serve as controls
Data processing The images were analyzed using Microarray Suite 5.0 software (MAS5.0; Affymetrix Inc., Santa Clara, CA). Expression ratios were computed by comparative analysis of MAS5 values. The data were filtered using MAS5's signal detection and change calls generated at recommended default settings. The ratios included were those that had present calls for signal detection or an increase or decrease call associated with the ratio


 
Submission date Apr 09, 2007
Last update date Aug 28, 2018
Contact name Ruby CY Lin
E-mail(s) rubyl@unsw.edu.au, ruby.lin@sydney.edu.au
Organization name The Westmead Institute for Medical Research
Street address 176 Hawkesbury Road, Westmead
City Sydney
State/province NSW
ZIP/Postal code 2145
Country Australia
 
Platform ID GPL1261
Series (1)
GSE7487 Gene profiling of pathological cardiac hypertrophy vs physiological hypertrophy
Relations
Reanalyzed by GSE119085

Data table header descriptions
ID_REF
VALUE Signal, a measure of the abundance of the transcript. Signal count data is normalized by the Affymetricx Microarray
ABS_CALL The call in an absolute analysis that indicates whether a transcript is reliably detected (Present, P) or not
DETECTION P-VALUE p-value that indicates the significance level of the detection (ABS_CALL) call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 992.221 P 0.000662269
AFFX-BioB-M_at 1306.83 P 4.42873e-05
AFFX-BioB-3_at 914.518 P 4.42873e-05
AFFX-BioC-5_at 3165.97 P 6.02111e-05
AFFX-BioC-3_at 3537.08 P 4.42873e-05
AFFX-BioDn-5_at 7373.64 P 4.42873e-05
AFFX-BioDn-3_at 17130.6 P 5.16732e-05
AFFX-CreX-5_at 43514.5 P 5.16732e-05
AFFX-CreX-3_at 46633.2 P 4.42873e-05
AFFX-DapX-5_at 4462.7 P 4.42873e-05
AFFX-DapX-M_at 6970.65 P 0.000126798
AFFX-DapX-3_at 8824.67 P 4.42873e-05
AFFX-LysX-5_at 324.804 P 4.42873e-05
AFFX-LysX-M_at 554.012 P 0.000224668
AFFX-LysX-3_at 1370.71 P 8.14279e-05
AFFX-PheX-5_at 864.175 P 4.42873e-05
AFFX-PheX-M_at 737.343 P 0.000146581
AFFX-PheX-3_at 858.24 P 5.16732e-05
AFFX-ThrX-5_at 903.078 P 5.16732e-05
AFFX-ThrX-M_at 1198.29 P 4.42873e-05

Total number of rows: 45101

Table truncated, full table size 1370 Kbytes.




Supplementary file Size Download File type/resource
GSM181386.CEL.gz 3.7 Mb (ftp)(http) CEL
GSM181386.CHP.gz 243.5 Kb (ftp)(http) CHP
Processed data provided as supplementary file

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