|
| Status |
Public on Aug 06, 2013 |
| Title |
Sham_vehicle_d3_r3 |
| Sample type |
RNA |
| |
|
| Source name |
3 day - sham - vehicle
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6J
tissue: heart
|
| Treatment protocol |
All mice were C57Bl/6J littermate males aged 10-12 weeks. For TAC, mice were anesthetized with ketamine/xylazine, mechanically ventilated (Harvard apparatus), and subject to thoracotomy. The aortic arch was constricted between the left and right carotid arteries using a 7.0 silk suture and a 27-guage needle as previously described (Hu et al., 2003). In our hands, this protocol created a consistent peak pressure gradient of approximately 50 mmHg across the constricted portion of the aorta. Injections of JQ1 or vehicle were begun 1.5 days postoperatively.
|
| Growth protocol |
All models were conducted in C57Bl/6J mice (Jackson Laboratories), which were maintained in a pathogen-free facility with standard light/dark cycling and access to food and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For tissue RNA, a 10-20 mg piece of mouse heart tissue was preserved in RNA Later stabilization reagent (Qiagen) followed by mechanical disruption/homogenization in PureZOL (BioRad) on a TissueLyser (Qiagen) using stainless steel beads (Qiagen). The aqueous phase was extracted with chloroform. RNA was purified from the aqueous phase using the Aurum purification kit (BioRad #732-6830) following manufacturer’s instructions.
|
| Label |
biotin allonamide triphosphate
|
| Label protocol |
cDNA was generated using the Ambion WT Expression Kit. The samples were labeled using the Affymetrix GeneChip WT Terminal Labeling and Hybridization protocol.
|
| |
|
| Hybridization protocol |
The labeled, fragmented DNA was hybridized to the Mouse Gene 1.0 ST Array (Affymetrix, Santa Clara, CA) for 16-18 hours in a GeneChip Hybridization oven 645 at 45C with rotation (60 rpm). The hybridized samples were washed and stained using an Affymetrix fluidics station 450.
|
| Scan protocol |
After staining, the genechip arrays were immediately scanned using an Affymetrix GeneArray Scanner 3000 7G Plus (Affymetrix, Santa Clara, CA).
|
| Description |
gene expression of sham surgery mouse heart followed by dmso treatment
|
| Data processing |
Bioconductor (http://bioconductor.org) packages affyQCReport, rma, and limma were used to perform quality control, normalization and differential expression analysis, respectively.
|
| |
|
| Submission date |
Jun 19, 2013 |
| Last update date |
Aug 06, 2013 |
| Contact name |
James Bradner |
| E-mail(s) |
bradner_computation@dfci.harvard.edu
|
| Organization name |
Dana-Farber Cancer Institute
|
| Department |
Medical Oncology
|
| Lab |
Bradner Lab
|
| Street address |
450 Brookline
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (2) |
| GSE48110 |
BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure [Mouse Heart Expression] |
| GSE48112 |
BET Bromodomains Mediate Transcriptional Pause Release in Heart Failure |
|
