|
| Status |
Public on Aug 31, 2015 |
| Title |
lacZ knockdown |
| Sample type |
RNA |
| |
|
| Source name |
NRVM
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell type: Neonatal rat ventricular myocytes
age: 1 to 2 day old rat pups
target: lacZ
|
| Treatment protocol |
One day after cells were switched to recovery media, cells were transduced with a single adenovirus containing an shRNA targeting MEF2D, or the negative control lacZ shRNA.
|
| Growth protocol |
NRVMs were recovered in DMEM with 10% FBS + pen/strep/L-glut. After a 24 hour recovery period, NRVMs were switched to a low serum DMEM with 0.5x Nutridoma + 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 Rat 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 neonatal rat ventricular myocytes (NRVMs) treated with shRNA targeting lacZ.
|
| 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 14.0.0) from the Molecular and Behavioral Neuroscience Institute (Brainarray) at the University of Michigan.
|
| |
|
| Submission date |
Aug 18, 2015 |
| Last update date |
Jun 25, 2019 |
| Contact name |
Boston University Microarray and Sequencing Resource |
| E-mail(s) |
[email protected]
|
| 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 |
GPL17896 |
| Series (1) |
| GSE72157 |
Expression data from pooled biological replicates (n=6) from MEF2D knockdown in neonatal rat ventricular myocytes (NRVMs) |
|
