|
| Status |
Public on Apr 23, 2008 |
| Title |
mdx Biological Replicate 5 |
| Sample type |
RNA |
| |
|
| Source name |
Skeletal muscle tibialis anterior (TA) from mdx line
|
| Organism |
Mus musculus |
| Characteristics |
Male mice from mdx (C57BL/10ScSn-Dmdmdx/J) line were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
| Biomaterial provider |
mdx (C57BL/10ScSn-Dmdmdx/J) breeding pairs originally from Jackson Laboratory, Bar Harbor, ME
|
| Growth protocol |
male mice were acclimatized and caged in groups of six or less at our in house facility. Animals were sacrificed by asphyxiation with carbon dioxide at 56 days old. Skeletal muscle tibialis anterior (TA) were dissected bilaterally and pooled. Tissue samples were flash-frozen in liquid N2 and stored at -80ºC until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Invtrogen) and further purified using the RNeasy mini kit (Qiagen) according to the manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
8 microgram total RNA was used in Affymetrix one cycle target labelling kit cat. no. 900493
|
| |
|
| Hybridization protocol |
Fragmented labelled cRNA (15µg) was used in 300µl hybridization cocktail containing spiked controls (Affymetrix #900299). An aliquot of 200µl of this hybridization cocktail was used on each chip which was incubated at 45°C for 16 h in the hybridization oven, rotating at 60 rpm. Following hybridization, the arrays were processed using a Genechip Fluidics Station 400 according to recommended protocols (EukGE-WS2v4, Affymetrix) of double-staining and post-hybridisations washes.
|
| Scan protocol |
Fluorescent images were captured using gene Array Scanner 2500 and GCOS1.2 software (Affymetrix)
|
| Description |
Here we have addressed important question of changes in the global gene expression profile of mdx mouse muscle compared to normal mouse muscle and compared the data with that obtained from the transgenic line (fiona) expressing high level of utrophin on mdx background.
|
| Data processing |
We have used the GeneChip Robust Multi-array Average expression measurements (GC-RMA) as implemented in BioConductor R statistics (www.bioconductor.org). Cell Intensity files (CEL) were used to obtain expression values for all the 22,690 probe sets (transcripts) on each of these
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| |
|
| Submission date |
Mar 05, 2007 |
| Last update date |
Apr 23, 2008 |
| Contact name |
Dilair Baban |
| E-mail(s) |
[email protected]
|
| Phone |
+44(0)1865287521
|
| Organization name |
University of Oxford
|
| Department |
Wellcome Trust Centre Human Genetics
|
| Lab |
Genomics
|
| Street address |
Roosevelt Drive
|
| City |
Oxford |
| ZIP/Postal code |
OX3 7BN |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL339 |
| Series (1) |
| GSE7187 |
Microarray analysis of mdx mice expressing high levels of utrophin: therapeutic implications for DMD |
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