|
| Status |
Public on May 16, 2008 |
| Title |
SMA mouse brain, biological rep 3 |
| 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 |
|
