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Sample GSM674625 Query DataSets for GSM674625
Status Public on May 10, 2011
Title D22-D2 whole brain RNA
Sample type RNA
 
Source name D2 whole brain RNA
Organism Mus musculus
Characteristics tissue: whole brain
strain: DBA/2J (D2)
gender: Male
Extracted molecule total RNA
Extraction protocol Naïve, adult, male C57BL/6J (B6) (n=12) and DBA/2J (D2) (n=12) strain mice were euthanized by cervical dislocation, the whole brain was rapidly removed and flash frozen in liquid nitrogen. Total RNA was isolated using TRIzol® reagent (Invitrogen, Carlsbad, CA) in a one-step guanidine isothiocyanate procedure. For microarray analyses, the extracted RNA was purified using RNeasy (Qiagen, Valencia, CA). RNA samples were evaluated by ultraviolet spectroscopy for purity and concentration.
Label Biotin
Label protocol Samples containing at least 10 μg of total RNA were sent to the Oregon Health & Science University Gene Microarray Shared Resource facility for further quality assessment using an Agilent 2100 BioAnalyzer and for GeneChip array analysis. Because two samples were scanned by a different scanner , the dataset reported here includes whole brain samples from 22 individual mice (10 B6 and 12 D2). After ribosomal RNA reduction, amplification and labeling, whole-brain total RNA samples were each hybridized to AffymetrixGeneChip® Mouse Exon 1.0 ST Array (24 arrays total). The procedures used follow the Affymetrix Whole Transcript Sense Target Labeling Assay, rev3, protocol. Additional details can be found at (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).
 
Hybridization protocol Samples containing at least 10 μg of total RNA were sent to the Oregon Health & Science University Gene Microarray Shared Resource facility for further quality assessment using an Agilent 2100 BioAnalyzer and for GeneChip array analysis. Because two samples were scanned by a different scanner , the dataset reported here includes whole brain samples from 22 individual mice (10 B6 and 12 D2). After ribosomal RNA reduction, amplification and labeling, whole-brain total RNA samples were each hybridized to AffymetrixGeneChip® Mouse Exon 1.0 ST Array (24 arrays total). The procedures used follow the Affymetrix Whole Transcript Sense Target Labeling Assay, rev3, protocol. Additional details can be found at (https://www.affymetrix.com/support/downloads/manuals/wt_sensetarget_label_manual.pdf).
Scan protocol Standard Affymetrix protocol.
Description 23B-11H1A_D22_334RH.CEL
Data processing All CEL files were processed using the Affy package (version 1.12.2) in the statistical programming environment R under the Bioconductor package [R version 2.6.0 (http://www.r-project.org), Bioconductor2.1 (http://www.bioconductor.org)]. All data was RMA [11] background corrected and normalized. Data were summarized at the probeset level using the median polish. The Mouseexonpmcdf package was utilized for summarization at the probeset-level (http://xmap.picr.man.ac.uk/download/). The data were SNP masked at the probe level. Prior to the summarization step at the probeset level described above, individual probes were masked (expression value replaced by 'null') if there was a known SNP within the boundaries of the probe. The SNP mask was built by comparing the Affymetrix design time annotation files (GFF) files (based on NCBI mouse build 36) for each chromosome to known SNP locations in DBSNP. A total of 12,101 probesets were masked to some degree, representing 5.4% of the core probesets.
 
Submission date Feb 14, 2011
Last update date May 10, 2011
Contact name Ted Laderas
Organization name Oregon Health & Science University
Department OHSU Knight Cancer Institute
Street address 3181 SW Sam Jackson Rd CR145
City Portland
State/province OR
ZIP/Postal code 97212
Country USA
 
Platform ID GPL6193
Series (1)
GSE27282 Comparison of B6/D2 Whole Brain Alternative Splicing

Data table header descriptions
ID_REF
VALUE log2 expression (signal intensity)

Data table
ID_REF VALUE
4304920 -0.202560264475777
4304921 -0.117514361573236
4304922 2.98979408755731
4304923 4.86524232392824
4304925 4.25735767427646
4304927 0.324461503417174
4304928 9.9722291513639
4304929 7.7633615387085
4304930 0.530843071029244
4304931 0.163037576900988
4304932 0.467471935452014
4304933 0.8718198618968
4304934 0.477363496270777
4304935 1.30403087654599
4304937 6.66232820434111
4304938 0.383217788027437
4304939 1.01488549633934
4304940 1.01923281190305
4304941 1.58454290386381
4304942 5.23153882635489

Total number of rows: 1201338

Table truncated, full table size 29800 Kbytes.




Supplementary file Size Download File type/resource
GSM674625.CEL.gz 18.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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