|
| Status |
Public on Mar 10, 2015 |
| Title |
total_RNA_genotypeC_pair1 |
| Sample type |
RNA |
| |
|
| Source name |
Brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
strain: B6.CAST congenic line
animal_id: N37.033
generation: N37F1
genotype_mvb1: C
age_days: 46
Sex: F
|
| Treatment protocol |
Same-sex pairs of mice, homozygous with respect to alternative alleles at Nxf1 (B6 or CAST).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Each brain was homogenized in Trizol reagent on a Polytron PT2100. RNA was extracted from Trizol (LifeTechnologies) according to the manufacturer’s instructions, then further purified using an RNeasy Plus Mini Kit (Qiagen).
|
| Label |
biotin
|
| Label protocol |
WT Terminal Labeling Kit, Affymetrix
|
| |
|
| Hybridization protocol |
Hybridization cocktails containing ~5.5 ug of fragmented and labeled DNA target were prepared and applied to GeneChip Human Splice Junction arrays. Hybridization was performed for 16 hours using the Fluidics 450 station.
|
| Scan protocol |
Arrays were scanned using the Affymetrix 3000 7G scanner and GeneChip Operating Software version 1.4 to produce .CEL intensity files.
|
| 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.
|
| |
|
| Submission date |
Mar 09, 2015 |
| Last update date |
Mar 10, 2015 |
| Contact name |
Gene Yeo |
| E-mail(s) |
geneyeo@ucsd.edu
|
| 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 |
| |
|
| Platform ID |
GPL13185 |
| Series (1) |
| GSE66696 |
Whole brain RNA from congenic littermates does not support a general effect of Nxf1 CAST alleles on alternative pre-mRNA processing |
|
