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Sample GSM80557 Query DataSets for GSM80557
Status Public on Nov 01, 2005
Title MKK3bE transgenic male replicate 3 late timepoint
Sample type RNA
 
Source name Mouse cardiac left ventricle
Organism Mus musculus
Characteristics Adult mouse, C57black background, left ventricle of heart
Biomaterial provider Yibin Wang
Treatment protocol Tamoxifen(20mg/KgBW)
Extracted molecule total RNA
Extraction protocol RNA extration was accomplished using TRIzol reagent(http://www.invitrogen.com/content/sfs/manuals/15596026.pdf) and purified using Qiagen Rneasy Mini Kit (http://www1.qiagen.com/literature/protocols/pdf/RY20.pdf)
Label biotin
Label protocol standard affymetrix protocol http://www.affymetrix.com/support/downloads/manuals/10k_manual.pdf
 
Hybridization protocol standard affymetrix protocol http://www.affymetrix.com/support/downloads/manuals/10k_manual.pdf
Scan protocol standard affymetrix protocol-GeneChip Scanner 3000 using the protocol http://www.affymetrix.com/support/downloads/manuals/10k_manual.pdf
Description The mouse strains for all the transgenic lines are C57black background and established after nearly 2 years of cross-breeding between the floxed alleles and the MCM strain. ?MHC-floxed-HRas-v12/MKK3bE/MKK7D transgenic mice were established as reported previously(19, 20, 36, 37, 40). They were bred with ?MHC-Mer-Cre-Mer (MCM) mice (from Dr. J. Molkentin, Cincinnati Children’s Hospital)(32) to generate double transgenic animals harboring both floxed transgenes and Mer-Cre-Mer transgene. At 12 weeks of age the double transgenic mice and non-transgenic littermate controls were treated via i.p. injection of tamoxifen at a dosage of 20mg/kgBW once a day for 3 consecutive days as reported. The hearts were harvested at an early (4-7 days post first tamoxifen injection) and a late (2-4 weeks) time point. Left ventricles were dissected and rapidly frozen in liquid nitrogen and stored at -80?C prior to protein and RNA analysis.
Data processing Affymetrix MAS5.0 gene expressions are normalized with median invariant method. To filter out significant genes, we adapted two approaches. A primary filtering method we used the standard two samples t-test in pair-wise comparisons involving gender (male or female), animal types (control, JNK, RAS, p38) and different time points (0, 1, 3, 4, 5, 9, 14). The selection criteria are as follows: |the fold change >2, |difference|>100, and p-value < 0.05
 
Submission date Oct 28, 2005
Last update date Oct 31, 2005
Contact name Scherise Mitchell
E-mail(s) smitc003@umaryland.edu
Organization name UCLA
Department Anesthesiology
Lab Dr. Yibin Wang
Street address 650 Charles E Young Dr, BH 569 CHS
City Los Angeles
State/province CA
ZIP/Postal code 90095
Country USA
 
Platform ID GPL1261
Series (1)
GSE3530 Distinct Gene Expression Profiles in Adult Mouse Heart Following Targeted MAP Kinase Activation

Data table header descriptions
ID_REF
VALUE MAS5-calculated Signal intensity
ABS_CALL the call in an absolute analysis that indicates if the transcript was present (P), absent (A), marginal (M), or no call (NC)
DETECTION P-VALUE 'detection p-value', p-value that indicates the significance level of the detection call

Data table
ID_REF VALUE ABS_CALL DETECTION P-VALUE
AFFX-BioB-5_at 3436.2 P 0.000754
AFFX-BioB-M_at 8391.9 P 0.000044
AFFX-BioB-3_at 2922.3 P 0.000195
AFFX-BioC-5_at 10227.6 P 0.00006
AFFX-BioC-3_at 12167.3 P 0.000044
AFFX-BioDn-5_at 10758.7 P 0.000044
AFFX-BioDn-3_at 48701.3 P 0.00007
AFFX-CreX-5_at 129091.5 P 0.000052
AFFX-CreX-3_at 149267.3 P 0.000044
AFFX-DapX-5_at 33.5 A 0.686277
AFFX-DapX-M_at 185.3 A 0.39692
AFFX-DapX-3_at 29.5 A 0.921998
AFFX-LysX-5_at 121.9 A 0.368438
AFFX-LysX-M_at 379 A 0.440646
AFFX-LysX-3_at 168.9 A 0.078002
AFFX-PheX-5_at 35.2 A 0.9273
AFFX-PheX-M_at 30.2 A 0.910522
AFFX-PheX-3_at 74 A 0.617401
AFFX-ThrX-5_at 27.4 A 0.916408
AFFX-ThrX-M_at 104.4 A 0.58862

Total number of rows: 45101

Table truncated, full table size 1250 Kbytes.




Supplementary data files not provided

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