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Sample GSM575887 Query DataSets for GSM575887
Status Public on Nov 15, 2010
Title liver_Trim28+/+ _rep7
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 7
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 1242.315 0
ILMN_2721178 290.0753 0
ILMN_3033922 377.7494 0
ILMN_3092673 2231.224 0
ILMN_2816356 25.00966 0.005012531
ILMN_2808939 1014.036 0
ILMN_2634564 247.498 0
ILMN_2737647 6.22528 0.131579
ILMN_2734484 203.4197 0
ILMN_2952292 30.12275 0.002506266
ILMN_2699078 0.06763346 0.3759398
ILMN_1213681 106.7494 0
ILMN_2735413 345.6333 0
ILMN_2735415 385.1164 0
ILMN_2891688 307.5327 0
ILMN_2637698 319.7473 0
ILMN_2674228 106.2645 0
ILMN_2601546 8.405544 0.08646616
ILMN_1230831 0.9478586 0.3358396
ILMN_2848071 616.8844 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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