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Sample GSM267177 Query DataSets for GSM267177
Status Public on May 16, 2008
Title SMA mouse spinal cord, biological rep 2
Sample type RNA
 
Source name SMA mouse spinal cord, postnatal day 11
Organism Mus musculus
Characteristics Phenotype: SMA, Tissue: spinal cord
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 spinal cord
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 2.69014
4304928 12.1774
4304938 2.57704
4304943 2.58229
4304945 10.3104
4304949 7.84344
4304956 5.63368
4304972 4.53445
4304978 7.18865
4304981 5.7115
4304986 2.63305
4304997 3.78663
4305011 3.25858
4305019 2.74601
4305028 6.7034
4305036 4.11671
4305039 3.11508
4305048 9.19229
4305053 4.34216
4305054 6.15227

Total number of rows: 193380

Table truncated, full table size 3000 Kbytes.




Supplementary file Size Download File type/resource
GSM267177.CEL.gz 23.2 Mb (ftp)(http) CEL
GSM267177.EXP.gz 507 b (ftp)(http) EXP
Processed data included within Sample table

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