|
| Status |
Public on Jun 05, 2013 |
| Title |
0h rep3 |
| Sample type |
RNA |
| |
|
| Source name |
C2C12 undifferentiated
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12 myoblast cells
time differentiated: 0 hr
|
| Treatment protocol |
Differentiation was verified visually by myotube formation and via Western blot to visualize myogenic markers. RNA and protein were isolated either immediately prior to (zero time) or up to 72 hours after addition of differentiation medium.
|
| 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). To induce myogenesis, 1.5 x 105 cells were plated in growth medium (DMEM + 10% FBS) per well in 6-well tissue culture-treated plates (Fisher) 12-18 hours prior to the addition of differentiation medium. Cells were washed once with differentiation medium (DMEM supplemented with 2% horse serum [Invitrogen]) prior to maintenance in the same medium. Media was changed every 24 hours, and myotube formation was visible
|
| 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) |
| GSE40956 |
Quaking is a global regulator of muscle-specific alternative splicing in vertebrates [differentiation data] |
| GSE40962 |
Quaking is a global regulator of muscle-specific alternative splicing in vertebrates |
|
