|
| Status |
Public on Jun 05, 2013 |
| Title |
Qk rep2 |
| Sample type |
RNA |
| |
|
| Source name |
C2C12 myoblasts
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12 myoblast cells
sirna: Qk siRNA
|
| Treatment protocol |
siRNA targeting Qk , PTB , and mock siRNA were used
|
| Growth protocol |
Mouse C2C12 myoblast cells (ATCC) were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS, Invitrogen).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Ribosomal RNAs were removed from three replicate individual total RNA preparation for each sample using the RiboMinus Transcriptome Isolation Kit (Invitrogen) according to the manufacturers instructions.
|
| Label |
biotin
|
| Label protocol |
Amplified, labeled cDNA was produced using the GeneChip® Whole Transcript Sense Target Labeling and Control Reagents (Affymetrix) according to the manufacturer’s instructions
|
| |
|
| Hybridization protocol |
The labeled, amplified cDNA was hybridized overnight to the MJAY Chip (Affymetrix)
|
| Scan protocol |
Chips were washed and labeled using the Affymetrix Fluidics Station 450, and scanned on an Affymetrix GeneChip scanner.
|
| Description |
C2C12
|
| Data processing |
Intensity was calculated by AffyPowerTools using dabg , gc background correction, iter-plier and quantile normalization
Data was analyzed according to the methods in Sugnet et al. PLoS Comput Biol. 2006 Jan;2(1):e4. PMID: 16424921
probe group file: mjay.clf
meta-probeset file: mjay.pgf
|
| |
|
| Submission date |
Sep 18, 2012 |
| Last update date |
Jun 05, 2013 |
| Contact name |
Manny Ares |
| Organization name |
UCSC
|
| Department |
Molecular and Cellular Biology
|
| Lab |
Ares
|
| Street address |
1125 High St
|
| City |
Santa Cruz |
| State/province |
CA |
| ZIP/Postal code |
95062 |
| Country |
USA |
| |
|
| Platform ID |
GPL13185 |
| Series (2) |
| GSE40961 |
Quaking is a global regulator of muscle-specific alternative splicing in vertebrates [siRNA data] |
| GSE40962 |
Quaking is a global regulator of muscle-specific alternative splicing in vertebrates |
|
