GSE66696
GSE GEOWhole brain RNA from congenic littermates does not support a general effect of Nxf1 CAST alleles on alternative pre-mRNA processing
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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.
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)
Analysis (6 steps)
View Data Processing- Data processed using Affymetrix package (Affy Power Tools) apt-probeset-summarize.
- Iter-plier algorithm used to quantify probesets.
- probe group file: GPL13185_mjay.pgf
- Data were analyzed with Omniviewer software: http://exon.ucsc.edu/omniviewer/.
- The Omniviewer output is available on the series record.
- The "A" set represents the Nxf1-CAST mutants and the "B" set represents the Nxf1-B6 mutants.