|
| Status |
Public on Apr 19, 2011 |
| Title |
5758 |
| Sample type |
RNA |
| |
|
| Source name |
Cardiac progenitor cells
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: Knockout (beta-sarcoglycan null)
cell type: Cardiac progenitor cells
tissue: aorta
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA, RNeasy Mini Ki, Qiagen
|
| Label |
Cy3
|
| Label protocol |
1µg of sample was spiked with a set of 10 positive control transcripts (Agilent Technologies), converted to double stranded cDNA in a reverse transcription reaction, amplified and labeled with Cy3 in an in vitro transcription reaction according to the manufacturer’s protocol (Agilent Technologies).
|
| |
|
| Hybridization protocol |
For Cy3 28 pmol incorporated dye was fragmented and resuspended in 55ul hybridization buffer HI-RPM (Agilent Technologies). The arrays were hybridized in microarray hybridization chambers (Agilent Technologies) overnight at 65ºC, rpm=10 for 17 hours.
|
| Scan protocol |
After washing the slides were scanned with a DNA microarray scanner (Agilent Technologies) and images were processed with the Feature Extraction Software version 9.5 (Agilent Technologies).
|
| Description |
Cardiac progenitor cells: derived from aorta, atrium and ventricle biopsies of wild-type (WT) mice and dystrophic mice (beta-sarcoglycan null). WT cardiac progenitors differentiate into beating cardiomyocytes, Beta sarcoglycan O progenitor cells differentiate into skeletal muscle fibers.
|
| Data processing |
The Agilent processed signal values (i.e., feature gProcessedSignal from Agilent Feature Extraction v9.5.3.1) were used for the data analysis. Intensities were base 2 log-transformed and in case of multiple probes for the same Agilent ID, log-intensities were averaged. Control probes were removed prior to analysis.
|
| |
|
| Submission date |
Aug 24, 2009 |
| Last update date |
Apr 20, 2011 |
| Contact name |
Rekin's Janky |
| E-mail(s) |
Nucleomics.Bioinformatics@vib.be
|
| Organization name |
VIB
|
| Department |
Nucleomics Core
|
| Street address |
Herestraat 49 Box 816
|
| City |
Leuven |
| ZIP/Postal code |
B-3000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE17774 |
Gene profile of dystrophic cardiac progenitor cells |
|
