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Sample GSM575876 Query DataSets for GSM575876
Status Public on Nov 15, 2010
Title liver_Trim28MommeD9/+ _rep3
Sample type RNA
 
Source name liver, Trim28MommeD9/+
Organism Mus musculus
Characteristics genetic background: FVB/NJ
gender: male
age: 4 weeks
tissue: liver
genotype: Trim28MommeD9/+
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 3
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
ID_REF
VALUE average normalisation
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_2896528 1404.885 0
ILMN_2721178 353.1395 0
ILMN_3033922 667.4876 0
ILMN_3092673 3051.793 0
ILMN_2816356 13.4434 0.02380952
ILMN_2808939 853.5848 0
ILMN_2634564 237.4388 0
ILMN_2737647 0.963878 0.3295739
ILMN_2734484 108.4458 0
ILMN_2952292 25.81008 0.006265664
ILMN_2699078 -1.920597 0.5726817
ILMN_1213681 170.908 0
ILMN_2735413 298.9995 0
ILMN_2735415 447.9181 0
ILMN_2891688 223.5987 0
ILMN_2637698 297.4815 0
ILMN_2674228 137.0883 0
ILMN_2601546 6.081574 0.1140351
ILMN_1230831 7.438307 0.08646616
ILMN_2848071 658.7664 0

Total number of rows: 25697

Table truncated, full table size 756 Kbytes.




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

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