|
| Status |
Public on Jul 01, 2015 |
| Title |
heart-KO.Control.937 |
| Sample type |
RNA |
| |
|
| Source name |
heart, KO, sham, replicate 1
|
| Organism |
Mus musculus |
| Characteristics |
genotype: MHC-cre-klf4
strain: C57BL6
tissue: heart, apex
gender: male
age: 10wk
|
| Treatment protocol |
young adult male mice, Cre and KO, on C57BL6 background, were subjected to TAC or sham operation for 3 days. Hearts then were removed, washed in cold PBS, weighted and apex was stored in liquid nitrogen for RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total ventricular RNA was extracted from A-Cre and A-cKO mice with Sham or TAC at 3 days post surgery (n = 4 in each group) using TRIzol reagent and purified using Qiagen RNA purification kit. Total RNA quality was assessed using a Pico Chip on an Agilent 2100 Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
RNA was amplified and labeled with Cy3-CTP using the Agilent low RNA input fluorescent linear amplification kits following the manufacturers protocol (Agilent).
|
| |
|
| Hybridization protocol |
Labeled cRNA was assessed using the Nandrop ND-100 (Nanodrop Technologies, Inc., Wilmington DE), and equal amounts of Cy3 labeled target were hybridized to Agilent whole mouse genome 4x44K Ink-jet arrays (Agilent). Hybridizations were performed for 14 h, according to the manufacturers protocol (Agilent).
|
| Scan protocol |
Arrays were scanned using the Agilent microarray scanner (Agilent) and raw signal intensities were extracted with Feature Extraction v10.1 software (Agilent).
|
| Description |
Gene expression after 3 days of sham operation
|
| Data processing |
Microarray data were log-transformed before differential expression analysis using the limma package. The 4th replicate in Cre-TAC group did not pass quality control, thus was removed from final data analysis.
Probes with a p value of less than 0.05 after adjusting for false discovery rate using Benjamini and Hochberg method were considered significant in differential expression. Enrichment in biological processes was analyzed using the DAVID bioinformatics suite.
|
| |
|
| Submission date |
Sep 05, 2014 |
| Last update date |
Jul 01, 2015 |
| Contact name |
Mukesh Jain |
| Organization name |
Case Western Reserve University
|
| Street address |
2103 Cornell Rd
|
| City |
Cleveland |
| State/province |
OH |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE61177 |
Myocardial gene expression in response to pressure overload |
|
