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Sample GSM267183 Query DataSets for GSM267183
Status Public on May 16, 2008
Title SMA mouse brain, biological rep 2
Sample type RNA
 
Source name SMA mouse brain, postnatal day 11
Organism Mus musculus
Characteristics Phenotype: SMA, Tissue: brain
Growth protocol Littermates of control and SMA mice were provided by Dr. Gordon Lutz (Drexel University, Philadelphia, Pennsylvania,USA). The mice were anesthetized with isoflurane and then sacrificed by cervical dislocation. Tissues were collected by manual dissection.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated using the Ambion mirVana miRNA isolation kit according to the manufacturer's directions.
Label biotin
Label protocol Biotinylated sense-strand DNA targets were prepared using the Affymetrix GeneChip Whole Transcript (WT) Sense Target Labeling Assay according to the manufacturer’s directions. 1 μg of total RNA from normal (n=3) and SMA (n=3) mouse spinal cord, brain and kidney was used as input for the first round of amplification. 10 μg of the resulting cRNA was used to proceed to the second round of amplification.
 
Hybridization protocol A hybridization cocktail including 5.5 μg of fragmented, end-labeled ssDNA was applied to GeneChip Mouse Exon 1.0 ST arrays. Hybridization was performed using F450-001 fluidics wash and stain script on the Affymetrix GeneChip Fluidics Station 450.
Scan protocol Arrays were scanned using the Affymetrix GCS 3000 7G and GeneChip Operating Software (GCOS) to produce .CEL intensity files.
Description Exon array data from SMA mouse brain
Data processing Probeset intensities were calculated from the CEL files of the 18 samples using the RMA algorithm with default settings at both the gene level and the probeset level in Partek Genomic Suite 6.3, using the core probe sets as defined by Affymetrix. Probesets with maximum RMA intensity of 3 across all samples were excluded to eliminate probesets with low expression levels. Alternative splicing multi-way ANOVA was applied using Partek defaults.
 
Submission date Feb 21, 2008
Last update date May 16, 2008
Contact name Gideon Dreyfuss
Organization name HHMI/ University of Pennsylvania
Street address 415 Curie Blvd
City Philadelphia
State/province PA
ZIP/Postal code 19104
Country USA
 
Platform ID GPL6193
Series (1)
GSE10599 SMA mouse tissue exon array analysis

Data table header descriptions
ID_REF
VALUE RMA Probeset signal intensity

Data table
ID_REF VALUE
4304927 3.40276
4304928 13.1146
4304938 2.94367
4304943 5.4331
4304945 11.1831
4304949 8.69547
4304956 4.95817
4304972 7.10805
4304978 10.4576
4304981 8.30643
4304986 3.11084
4304997 6.80228
4305011 2.46667
4305019 5.91079
4305028 8.85413
4305036 5.96683
4305039 5.82777
4305048 9.58864
4305053 7.73931
4305054 7.23714

Total number of rows: 193380

Table truncated, full table size 3000 Kbytes.




Supplementary file Size Download File type/resource
GSM267183.CEL.gz 23.8 Mb (ftp)(http) CEL
GSM267183.EXP.gz 494 b (ftp)(http) EXP
Processed data included within Sample table

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