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Sample GSM1198697 Query DataSets for GSM1198697
Status Public on Nov 25, 2013
Title WT liver, biological rep2
Sample type RNA
 
Source name Liver, wild-type (AAV-GFP)
Organism Mus musculus
Characteristics genotype: wild-type
age: 3-month old
Treatment protocol Livers were put into liquid nitrogen immediately after mice euthanization
Growth protocol Mice were maintained on normal chow and the normal 24-hr light/dark cycle
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions.
Label biotin
Label protocol GeneChip WT Terminal Labeling and Control Kit (Affymetrix)
 
Hybridization protocol RNA were hybridized to the Mouse Gene 2.0 ST Array (Affymetrix).
Scan protocol GeneChips were scanned using the Hewlett-Packard GeneArray Scanner GCS3000.
Description wild-type (AAV-GFP)
Data processing Microarray image analysis was carried out using Partek Genomics Suite software. Subsequent analysis was carried out using BioConductor. Data from the 8 samples were subjected to background subtraction, quantile normalization, log2 transformation and probeset summarization using the RMA (Robust Multichip Average) algorithm. Only the probe sets that interrogate genes were retained and those meant for QC and normalization purposes were excluded from further analysis. The SAM procedure was then used to obtain multiple test corrected q-values for differential expression of genes between the hearts from MCH3-KO mice and control.
 
Submission date Jul 31, 2013
Last update date Nov 25, 2013
Contact name Zheng Sun
E-mail(s) zheng.sun@bcm.edu
Organization name Baylor College of Medicine
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
 
Platform ID GPL16570
Series (2)
GSE49387 Gene expression profiling of liver-specific NCOR knockout mice
GSE49388 Gene expression profiles in mouse livers depleted of HDAC3 or NCOR1

Data table header descriptions
ID_REF
VALUE RMA data

Data table
ID_REF VALUE
AFFX-CreX-5_st 33.67997121
17318118 116.3469031
AFFX-r2-P1-cre-5_st 51.98541453
AFFX-r2-P1-cre-3_st 37.30523005
AFFX-CreX-3_st 71.63670125
17464654 298.3233308
17235511 154.2144347
17548717 144.8175863
17548238 148.7134166
17284349 150.3115437
17444697 394.6984381
17475385 173.7961123
17373634 70.59930127
17335467 902.906007
17365410 457.3132787
17514326 201.0506235
17425202 178.0721389
17231571 53.72720936
17481960 97.51674053
17396056 85.15161574

Total number of rows: 41345

Table truncated, full table size 845 Kbytes.




Supplementary file Size Download File type/resource
GSM1198697_4842_49943_WT2_MoGene2.0__28MoGene-2_0-st_29.CEL.gz 9.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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