|
| Status |
Public on Jan 01, 2012 |
| Title |
C2C12 untreated day3 rep1 |
| Sample type |
RNA |
| |
|
| Source name |
RNA from untreated, subconfluent C2C12 myoblasts, day 3
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
treatment: untreated
|
| Treatment protocol |
Cells were treated with DMEM 10%NCS with or without 10 micromolar 5-azacytidine for 3 days, after which total RNA was extracted
|
| Growth protocol |
C2C12 myoblasts were plated at 1500 cells/cm2 in DMEM 10% Newborn Calf Serum (NCS) and grown for 24 hrs
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1.5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
10 µg of biotin-labeled cRNA was hybridized to a GeneChip Mouse Genome 430 2.0 array (Affymetrix, Santa Clara, CA, USA). Hybridization signals were amplified using a streptavidin-biotin amplification procedure and scanned with a GeneChip G3000 7G scanner (Affymetrix).
|
| Scan protocol |
GeneChips were scanned with a GeneChip G3000 7G scanner (Affymetrix).
|
| Description |
gene expression from untreated C2C12 myoblasts (day 3)
|
| Data processing |
Data were quantified using GCOS 1.4 software (Affymetrix) and normalization and statistical analysis were performed using the error model developed for Affymetrix GeneChips (35) in Rosetta Resolver Version 7. To identify genes that were significantly upregulated in samples treated for 3 days with 5AC, their expression profiles were compared with untreated day 3 controls, whereby expression ratios (and corresponding p-values) were calculated using the stats package in R 2.4.1. To correct for multiple hypothesis testing, the q-value was calculated for each p-value using Benjamini & Hochberg correction, indicating the significance of the corresponding ratio. Genes were selected as significantly regulated by 5AC if the q-value < 0.01.
|
| |
|
| Submission date |
Jun 24, 2011 |
| Last update date |
Jan 01, 2012 |
| Contact name |
Marlinda Hupkes |
| E-mail(s) |
m.hupkes@science.ru.nl
|
| Phone |
+31(0)243652519
|
| Organization name |
Radboud University Nijmegen
|
| Department |
Cell and Applied Biology
|
| Street address |
Heyendaalseweg 135
|
| City |
Nijmegen |
| ZIP/Postal code |
6525 AJ |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE30192 |
Effect of 5-azacytidine on gene expression in C2C12 myoblasts |
|
