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Sample GSM1375128 Query DataSets for GSM1375128
Status Public on Oct 15, 2014
Title Fasted liver double knockout rep2
Sample type RNA
 
Source name Liver, 2-month old male, fasted, macroH2A1/2 double knockout
Organism Mus musculus
Characteristics gender: Male
strain: 129/S6 (taconic)
tissue: Liver
animal age: 2-months
nutritional status: Overnight fast (~16 hours)
genotype/variation: macroH2A1 macroH2A2 double knockout
Treatment protocol Mice were fasted overnight for ~ 16 hours and sacrificed between 9 and 10 AM.
Growth protocol Mice were maintained on a 12 hr day/night cycle with the lights coming on a 8 AM. They were given water and low fat rodent chow Ad libitum. They were killed mid-morning.
Extracted molecule total RNA
Extraction protocol Total liver RNA was extracted with Trizol (life technologies) following standard protocol
Label Biotin
Label protocol Labeled cDNA was prepared from 250 ng of total RNA using the standard procedure of the Ambion WT Expression Kit (Life Technologies)
 
Hybridization protocol Five and a half micrograms of labeled cDNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Mouse Gene 2.0 ST GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A GeneChip 3000 7G scanner was used to collect fluorescence signal.
Scan protocol A GeneChip 3000 7G scanner was used to collect fluorescence signal.
Description Fasted_liver-7
Data processing Affymetrix Command Console and Expression Console were used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Border pixels were removed, and the average intensity of pixels within the 75th percentile was computed for each probe. The average of the lowest 2% of probe intensities occurring in each of the microarray sectors was set as background and subtracted from all features in that sector.
 
Submission date Apr 25, 2014
Last update date Oct 15, 2014
Contact name John Pehrson
E-mail(s) pehrson@vet.upenn.edu
Organization name University of Pennsylvania
Street address 3800 Spruce Street
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL16570
Series (2)
GSE57088 Expression data from fasted macroH2A1/2 double knockout adult mouse liver
GSE57089 Role of MacroH2A core histone variants in liver

Data table header descriptions
ID_REF
VALUE Log2-transformed, RMA normalized intensities

Data table
ID_REF VALUE
17200001 7.6854
17200003 8.2227
17200005 4.97104
17200007 5.96772
17200009 6.8227
17200011 5.95966
17200013 6.40563
17200015 6.5162
17200017 4.50148
17200019 5.11035
17200021 6.16187
17200023 7.76217
17200025 8.14052
17200027 7.31889
17200029 5.78643
17200031 4.82997
17200033 4.88965
17200035 5.05081
17200037 6.18436
17200039 4.25557

Total number of rows: 41345

Table truncated, full table size 681 Kbytes.




Supplementary file Size Download File type/resource
GSM1375128_4912_51826_DKO2_MoGene2.0ST.CEL.gz 9.7 Mb (ftp)(http) CEL
Processed data included within Sample table

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