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Sample GSM490127 Query DataSets for GSM490127
Status Public on Sep 30, 2010
Title testis-wildtype#2-rep2
Sample type RNA
 
Source name whole testes
Organism Mus musculus
Characteristics strain: 129SvEv
gender: Male
tissue: whole testes
genome/variation: wildtype
Growth protocol Testes from freshly euthanized adult male mice (strain 129S6 (129SvEv)) were flash frozen and stored at -80 °C.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from three frozen wild type and age-matched homozygous Mll5-/- testes using QIAzol™ lysis reagent (Qiagen, Maryland, USA). The tissues were homogenized in 800 µL QIAzol and transferred to Phase Lock Gel tubes (2 mL, heavy) (Eppendorf AG, Hamburg, Germany) to which 200 µL chloroform was added. Samples were centrifuged and the aqueous phase was removed and transferred to a new tube with an equal volume of isopropanol. After centrifugation, the supernatant was removed from the precipitated RNA pellets, and the pellets were washed with 70% ethanol. The air-dried RNA was dissolved in RNase/DNase free water and stored frozen at -80 °C. Total RNA samples were analyzed on a NanoDrop (Thermo Fisher Scientific, Waltham, MA) spectrophotometer to determine RNA quality and concentration. One µL of the RNA (was adjusted within a range of 25-500 ng/µL) was analyzed on the Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) using the RNA 6000 Nano kit.
Label biotin
Label protocol Samples with a resulting total RNA of 1 µg or greater and with a RNA integrity number (RIN) of 7.0 or greater were used and the whole transcript sense target labeling procedure followed the Affymetrix protocol, including the RiboMinus™ rRNA removal step. Three biological replicates were compared for each of the genotypes (wild type and homozygous Mll5-/-) for a total of six experiments.
 
Hybridization protocol Labelled RNA was probed on GeneChip Mouse Exon Array 1.0 ST chips (Affymetrix, Santa Clara, California) for gene expression analysis and scanned at the CTAG Facility of the British Columbia Cancer Agency, Vancouver, BC, Canada.
Scan protocol Array scanning was performed according to the manufacturer's instructions (Affymetrix).
Description RMA expression value derived from ArrayAssist version 5.0 software; core+extended gene level analysis
Data processing CEL files were processed using ArrayAssist 5.0. Raw intensity calls were normalized using quantile normalization (Bolstad, 2003) and probeset summarization undertaken with gc-rma (Wu, 2004). In this analysis we considered only transcript level summarization for the core plus extended set of probes on the array (about 800,000 probesets). Outliers with greater than 2.0 fold change between genotypes and level of significance, p < 0.05 were selected for further analysis by quantitative PCR (Q-PCR).
ArrayAssist results (Gene and Exon) are available on the series record. Affynetrix Command Console normalized data are presented in the sample tables.
 
Submission date Dec 24, 2009
Last update date Dec 24, 2009
Contact name Steven McKinney
E-mail(s) smckinney@bccrc.ca
Phone 604-675-8000
Organization name British Columbia Cancer Agency
Department Molecular Oncology
Lab Samuel Aparicio
Street address 675 West 10th Ave
City Vancouver
State/province BC
ZIP/Postal code V5Z 1L3
Country Canada
 
Platform ID GPL6193
Series (1)
GSE19648 Murine Histone Methyltransferase Mll5, is involved in Male Gametogenesis

Data table header descriptions
ID_REF
VALUE RMA (Affy Command Console) normalized signal intensity
DETECTION P-VALUE

Data table
ID_REF VALUE DETECTION P-VALUE
4304922 4.73391 0.0885414
4304925 6.38802 0.000832039
4304927 5.76327 0.0503314
4304928 13.939 4.68706e-09
4304929 11.0366 9.33003e-07
4304930 7.00634 0.000753752
4304937 4.12453 0.210905
4304938 7.04843 5.03674e-05
4304941 7.33587 0.00712922
4304943 4.45757 0.0150272
4304945 13.3965 4.55766e-09
4304949 8.62865 0.00728907
4304956 10.88 2.863e-08
4304961 5.74297 0.00996398
4304967 7.85537 0.00452503
4304969 8.29911 3.68065e-05
4304970 4.97181 0.0974955
4304971 5.85854 0.00821022
4304972 6.80907 4.29937e-07
4304973 8.38592 3.53108e-08

Total number of rows: 631748

Table truncated, full table size 16393 Kbytes.




Supplementary file Size Download File type/resource
GSM490127.CEL.gz 25.0 Mb (ftp)(http) CEL
GSM490127.chp.gz 6.0 Mb (ftp)(http) CHP
Processed data included within Sample table
Processed data are available on Series record
Processed data provided as supplementary file

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