|
| Status |
Public on Dec 03, 2014 |
| Title |
Mef2d knockdown, replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
C2C12 cells
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
RNAi target: Mef2d
|
| Treatment protocol |
One day prior to induction of differentiation (transition to low serum media), cells are transduced with a single, or a combination of adenoviruses containing an shRNA targeting a single MEF2 factor, or the negative control lacz shRNA.
|
| Growth protocol |
C2C12 myoblasts were maintained in DMEM with 10% FBS + pen/strep/L-glut. Differentiation was induced by switching to a low serum DMEM containing 2% horse serum + pen/strep/L-glut.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from myotubes was preparted by TRIzol© isolation (Invitrogen). Samples were pooled in sets, for a total of 3 biological replicates per condition.
|
| Label |
biotin
|
| Label protocol |
Biotin labeling was performed using the Ambion WT Expression Kit (Life Technologies, Grand Island, NY) according to the manufacturer's protocol, followed by the GeneChip WT Terminal Labeling and Controls Kit (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the GeneChip Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 18 hours in a GeneChip Hybridization oven 640 at 45oC with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450 with streptavidin-R-phycoerythrin (SAPE) and the signal was amplified using a biotinylated goat anti-streptavidin antibody followed by another SAPE staining (Hybridization, Washing and Staining Kit, Affymetrix, Santa Clara, CA).
|
| Scan protocol |
After staining, microarrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).
|
| Description |
Gene expression data from C2C12 cells treated with shRNA targeting Mef2d.
|
| Data processing |
Raw Affymetrix CEL files were normalized to produce gene-level expression values using the implementation of the Robust Multiarray Average (RMA) in the affy Bioconductor package (version 1.36.1) and an Entrez Gene-specific probeset mapping (version 16.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan.
|
| |
|
| Submission date |
Dec 02, 2014 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
msrdata@bu.edu
|
| Organization name |
Boston University
|
| Department |
Microarray and Sequencing Resource
|
| Street address |
72 East Concord Street, E631
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02118 |
| Country |
USA |
| |
|
| Platform ID |
GPL19485 |
| Series (1) |
| GSE63798 |
Expression data from individual MEF2A isoform knockdown in C2C12 myotubes |
|
