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Sample GSM503337 Query DataSets for GSM503337
Status Public on Oct 01, 2010
Title Liver Mouse02_Sample01
Sample type RNA
 
Source name Liver Mouse02_Sample01
Organism Mus musculus
Characteristics tissue type: Liver
strain: C57BL/6J
gender: male
body weight (g): 23.35
age (days): 70
Treatment protocol At 10 weeks, body weight was recorded and the mice were euthanized by cervical dislocation. Dissection procedures were started at 11:00 a.m. after a 4-hour fasting period and were completed within a one-hour time window.
Growth protocol We obtained twelve C57BL/6J male mice from The Jackson Laboratory. Six pairs of littermates were pair-housed from weaning and put on a 5k52 diet (standard chow containing 6% fat).
Extracted molecule total RNA
Extraction protocol Inguinal fat pad, heart, liver, and both kidneys were extracted, perfused with RNase-free DEPC-treated PBS, cut into pieces not exceeding 0.5 cm in any dimension, and placed in 15 ml conical tubes. The pieces were divided into 2 aliquots and stored in RNAlater (Ambion, Austin TX). Each kidney aliquot consisted of one complete kidney. Tissues were homogenized in TRIzolTM (Invitrogen, Carlsbad, CA). Total RNA was isolated by standard TRIzolTM methods according to the manufacturer’s protocols, and quality was assessed using an Agilent 2100 Bioanalyzer instrument and RNA 6000 Nano LabChip assay (Agilent Technologies, Santa Clara, CA). The RNA was then treated with DNase1 (Qiagen, Valencia, Ca.) according to the manufacturer’s methods. Total RNA was then reverse transcribed followed by second strand cDNA synthesis.
Label biotin
Label protocol Illumina Sentrix ® Mouse-6 v1.1 BeadChip processing. For each sample, an in-vitro transcription (IVT) reaction was carried out incorporating biotinylated nucleotides according to the manufacturer’s protocol for Illumina® Totalprep RNA amplification kit (Ambion).
 
Hybridization protocol 1.5µg biotin-labeled cRNA was then hybridized onto Mouse-6 Expression BeadChips (Illumina, San Diego CA) for 16 hours at 55°C. Post-hybridization staining and washing were performed according to manufacturer’s protocols (Illumina).
Scan protocol Illumina Sentrix ® Mouse-6 v1.1 BeadChips were scanned using Illumina’s BeadStation 500 scanner.
Description We analyzed intensities of 45,905 probes with unique sequences and annotated by Illumina as probes for genomic regions corresponding to protein-coding genes.
Data processing Images were checked for grid alignment and then quantified using the BeadStudio software. Control summary graphs generated by BeadStudio were used as quality assurance tools for hybridization, washing stringency, and background. Integrity of the arrays was investigated using the BeadStudio array images and also using bead level image plots generated using the R/beadarray package. Mean pixel intensities by bead type, were created using BeadStudio v3.1 and processed within the R/beadarray package (Dunning et al. 2006).
The raw data conains the log base 2 transformed intensities. A two-step procedure was used for normalization. Quantile normalization (Bolstad et al. 2003) was applied within each tissue type. Then, a correction for batch effects was applied separately for each gene performed using an MM-regression estimator described in Yohai (1987) and computed using the R/robustbase software package (Rousseeuw et al. 2009). The normalized data is also on a log base 2 scale.
 
Submission date Feb 01, 2010
Last update date Jan 18, 2011
Contact name Peter Thomas Vedell
E-mail(s) vedellpt@gmail.com
Organization name The Jackson Laboratory
Street address 600 Main Street
City Bar Harbor
State/province ME
ZIP/Postal code 04609
Country USA
 
Platform ID GPL6481
Series (1)
GSE20121 Transcript variation in C57BL/6J mice under normal laboratory conditions
Relations
Affiliated with GSM656899

Data table header descriptions
ID_REF
VALUE normalized data (log2 scale)

Data table
ID_REF VALUE
4070563 7.964843465
106860400 7.986079659
4850021 7.405022919
103290400 15.92791992
103120725 7.422936247
103800270 7.761730612
360593 9.088797702
3190390 8.293613856
100730735 7.5455766
105130100 7.429336136
6620148 7.963532819
6220328 7.991151169
105890397 7.378714378
105900039 7.179041386
104920600 7.365667427
105420110 7.618800759
100870452 7.222273718
103610239 7.229639985
106760450 7.351146924
1010368 10.11199587

Total number of rows: 45905

Table truncated, full table size 929 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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