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| Status |
Public on Mar 10, 2015 |
| Title |
Whole brain RNA from congenic littermates does not support a general effect of Nxf1 CAST alleles on alternative pre-mRNA processing |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by array
|
| Summary |
Microarray hybridization was used to compare RNA from mouse brains with opposite genotypes at the Mvb1 (Nxf1) modifier locus for known alternative processing events.
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| Overall design |
6 samples of total brain RNA, from 3 littermate pairs, were hybridized to splicing-sensitive microarrays
*Addendum
Depending on the analysis software used, these CEL files may not load correctly using default parameters. This is due to the custom chip type of MJAY not being used during the array scanning step. There are three workarounds known for this problem so far.
1) If using APT, use multiple --chip-type parameters. Specifically, --chip-type mjay --chip-type MJAY --chip-type MoEx-1_0-st-v1.1sq
2) Edit the CEL file by converting to text using the APT command apt-cel-convert, then replacing the MoEx-1_0-st-v1.1sq in the DatHeader line with MJAY (all caps).
3) Edit the .pgf, .clf, and antigenomics.bmp files to use the MoEx-1_0-st-v1.1sq array instead of MJAY for the chip_type and lib_set_name options. (works on AltAnalyze software)
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| |
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| Contributor(s) |
Hamilton BA, Yeo GW |
| Citation(s) |
25835743 |
| |
| Submission date |
Mar 09, 2015 |
| Last update date |
Jun 09, 2015 |
| Contact name |
Gene Yeo |
| E-mail(s) |
[email protected]
|
| Organization name |
UCSD
|
| Street address |
2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92037 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL13185 |
[mjay] Custom Affymetrix Mouse Exon Junction Array |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA277743 |
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