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Sample GSM575884 Query DataSets for GSM575884
Status Public on Nov 15, 2010
Title liver_Trim28+/+ _rep4
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 4
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 1397.296 0
ILMN_2721178 334.6097 0
ILMN_3033922 598.4184 0
ILMN_3092673 2597.146 0
ILMN_2816356 16.13383 0.02005013
ILMN_2808939 940.979 0
ILMN_2634564 199.8628 0
ILMN_2737647 1.126967 0.3433584
ILMN_2734484 114.1123 0
ILMN_2952292 35.93319 0
ILMN_2699078 0.1345668 0.4172932
ILMN_1213681 176.0432 0
ILMN_2735413 372.3925 0
ILMN_2735415 508.9098 0
ILMN_2891688 279.4512 0
ILMN_2637698 332.6408 0
ILMN_2674228 131.8661 0
ILMN_2601546 5.807228 0.1328321
ILMN_1230831 2.150833 0.2706767
ILMN_2848071 478.9138 0

Total number of rows: 25697

Table truncated, full table size 750 Kbytes.




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

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