|
| Status |
Public on Jul 01, 2018 |
| Title |
cerebellum (WT) on P16, biological rep2 |
| Sample type |
RNA |
| |
|
| Source name |
wild-type (WT), cerebellum
|
| Organism |
Mus musculus |
| Characteristics |
age: P16
tissue: cerebellum
genotype: wild-type (WT)
|
| Growth protocol |
Cerebellums were dissected from P16 mice.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA from the entire cerebellum of P16 mice was isolated using Trizol Reagent (Life Technologies), treated with DNase I, and further purified using the RNeasy Mini Kit (Qiagen). RNA samples for microarray analysis were processed using the NuGEN WT-Ovation Pico RNA Amplification System, NuGEN WT-Ovation Exon Module, and NuGEN FL-Ovation cDNA Biotin Module.
|
| Label |
biotin
|
| Label protocol |
Sense-strand cDNA targets were generated using the NuGEN WT-Ovation Exon Module and biotinylated using the NuGEN FL-Ovation cDNA Biotin Module.
|
| |
|
| Hybridization protocol |
Standard Affymetrix protocol.
|
| Scan protocol |
Affymetrix Model 7G upgraded scanner
|
| Description |
cerebellum total RNA from one (WT) mouse
|
| Data processing |
Raw microarray CEL files were imported into Partek Genomics Suite 6.6. Signal intensities for the probe-sets were quantile normalized and median polished using Robust Multichip Average background correction. The signal intensities of exon probe-sets were used to calculate the overall expression level of each gene represented in MJAY. Normalized intensity of each exon probe-set was calculated by adjusting the exon probe-set signals of gt/gt samples with the gene expression difference (between gt/gt and WT) that was measured for the exon-containing gene. The normalized probe-set signals of gt/gt samples were compared with the probe-set signals of WT samples using two-tailed Student t-test. Probe-sets with significantly different signals (P <0.01) were queried against the Affymetrix annotation map file (which contains alternative/constitutive annotations for each measured splicing event), and probe-sets that measure constitutive events or are not annotated to RefSeq transcripts were filtered out. The remaining probe-sets were queried against the “SIB Alt-Splicing track” in the UCSC Genome Browser to identify and remove probe-sets that 1) show more than 50% identity with more than one transcript, 2) measure alternative promoter activity, or 3) measure splicing only in the non-coding regions of mRNAs. The sequences of the remaining probe-sets were queried against the mouse genome to identify those that measure the same splicing events. We required that probe-sets targeting competing isoforms have opposite trends in probe-set signal differences.
MJAY_r2.pgf
MJAY_r2.full.mps
|
| |
|
| Submission date |
Jul 29, 2015 |
| Last update date |
Jul 01, 2018 |
| Contact name |
Botond Banfi |
| E-mail(s) |
botond-banfi@uiowa.edu
|
| Phone |
1-319-335-4228
|
| Organization name |
University of Iowa
|
| Department |
Anatomy and Cell Biology
|
| Lab |
Banfi Lab
|
| Street address |
2501 Crosspark Road
|
| City |
Coralville |
| State/province |
Iowa |
| ZIP/Postal code |
52241 |
| Country |
USA |
| |
|
| Platform ID |
GPL14865 |
| Series (2) |
| GSE71479 |
MJAY analysis of cerebellar RNA obtained from Srrm3 gene-trapped mice and wild-type mice |
| GSE71481 |
Overlapping activities of SRRM3 and SRRM4 regulate vital pre-mRNA splicing events for neuromuscular synaptogenesis and neuron-specific gene expression |
|
