|
| Status |
Public on Mar 24, 2010 |
| Title |
PAL7 |
| Sample type |
RNA |
| |
|
| Source name |
Cardiomyocytes, palmitic acid
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Wistar
gender: male
developmental stage: adult
genotype: wildtype
cell type: cardiomyocytes
treatment: exposed to 1%BSA + palmitic acid
|
| Treatment protocol |
Isolated, cultured adult rat cardiomyocytes were challenged with 1% BSA (control) or 0.4 mM octanoate, palmitate, stearate, oleate, or linoleate conjugated to 1% BSA for 24 h, after which RNA was isolated and utilized for gene expression analysis.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted from all tissues using a standard protocol and Tri-reagent.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was converted to cDNA by reverse transcription using Superscript II reverse transcriptase and T7-(dT)24 primers, followed by second-strand synthesis to generate double-stranded cDNA.
|
| |
|
| Hybridization protocol |
A total of 0.75 micrograms of biotin-labeled cRNA was applied to a BeadChip and allowed to hybridize overnight at 55°C for approximately 18 hours, followed by washing and staining with streptavidin-Cy3 prior to visualization.
|
| Scan protocol |
BeadChips were visualized using the BeadStation scanner, which uses a dual-laser confocal scanner with 0.8 µm resolution to determine fluorescence values for each bead on the chip.
|
| Description |
Approximately 22,000 RefSeq and EST transcripts are present on the arrays in the form of oligo-coated (50mer) beads.
PAL7
|
| Data processing |
After scanning the probe arrays, the resulting images were analyzed using the BeadStudio software (V3, Illumina, Inc., San Diego, CA), which calculates the mean fluorescence signal across all replicates of each gene/transcript, along with a probability that the mean signal for each gene/transcript on the chip is greater than background (i.e., detection p-value). Both non-normalized and normalized (qspline) data were generated for each tissue type.
|
| |
|
| Submission date |
Mar 23, 2010 |
| Last update date |
Mar 31, 2010 |
| Contact name |
Molly Bray Bray |
| E-mail(s) |
mbray@uab.edu
|
| Phone |
205-975-7651
|
| Fax |
205-934-8665
|
| Organization name |
Univ of Alabama at Birmingham
|
| Department |
Genetics
|
| Lab |
KAUL-406
|
| Street address |
720 20th Street S
|
| City |
Birmingham |
| State/province |
AL |
| ZIP/Postal code |
35294 |
| Country |
USA |
| |
|
| Platform ID |
GPL10239 |
| Series (1) |
| GSE21023 |
Bioinformatic profiling of the transcriptional response of adult rat cardiomyocytes to distinct fatty acids |
|
