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Sample GSM575881 Query DataSets for GSM575881
Status Public on Nov 15, 2010
Title liver_Trim28+/+ _rep1
Sample type RNA
Source name liver, Trim28+/+
Organism Mus musculus
Characteristics genetic background: FVB/NJ
gender: male
age: 4 weeks
tissue: liver
genotype: Trim28+/+
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol RNA was extracted using the QIAGEN Rneasy-Plus kit in accordance with the prescribed protocol. All RNA samples were checked on Agilent’s Bioanalyzer (Agilent RNA 6000 Nano) and had RNA Integrity Numbers (RINs) greater than 8.
Label biotin
Label protocol Biotinylated cRNA was prepared using the Illumina TotalPrep RNA Amplification Kit (Ambion).
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description replicate 1
Data processing Illumina GenomeStudio software was used according to the recommendations of the manufacturer. Data was grouped (wildtype versus heterozygotes), background corrected, and normalised (average normalisation). Significantly differentially expressed genes were identified using Illumina's differential expression analysis.
Submission date Aug 09, 2010
Last update date Nov 15, 2010
Contact name Suyinn Chong
Organization name Queensland Institute of Medical Research
Department Division of Genetics and Population Health
Lab Epigenetics Laboratory
Street address 300 Herston Rd
City Herston
State/province Queensland
ZIP/Postal code 4006
Country Australia
Platform ID GPL6885
Series (1)
GSE23512 Reduced levels of two modifiers of epigenetic gene silencing, Dnmt3a and Trim28, cause increased phenotypic noise.

Data table header descriptions
VALUE average normalisation
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 1633.088 0
ILMN_2721178 431.1429 0
ILMN_3033922 682.9214 0
ILMN_3092673 2712.84 0
ILMN_2816356 28.97364 0.002506266
ILMN_2808939 850.0144 0
ILMN_2634564 186.5965 0
ILMN_2737647 7.17799 0.09774436
ILMN_2734484 96.43484 0
ILMN_2952292 28.23317 0.003759399
ILMN_2699078 -2.621868 0.6428571
ILMN_1213681 200.6254 0
ILMN_2735413 332.268 0
ILMN_2735415 404.2295 0
ILMN_2891688 195.6178 0
ILMN_2637698 348.9106 0
ILMN_2674228 130.4406 0
ILMN_2601546 6.193187 0.1102757
ILMN_1230831 3.3555 0.2180451
ILMN_2848071 606.1101 0

Total number of rows: 25697

Table truncated, full table size 747 Kbytes.

Supplementary data files not provided
Raw data are available on Series record
Processed data included within Sample table

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