|
| Status |
Public on Oct 24, 2009 |
| Title |
Adult_mouse_heart_infarcted_rep3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Adult_mouse_heart_infarcted
|
| Organism |
Mus musculus |
| Characteristics |
tissue: heart infarcted
strain: C57Bl/6
age: 8-10 weeks
treatment: Ischemic heart failure induced by ligation of the descending branch of the left coronary artery
|
| Biomaterial provider |
Federal University of Rio de Janeiro, Brazil
|
| Treatment protocol |
Permanent myocardial infarcts were produced by ligation of the descending branch of the left coronary artery. Animals were anesthetized by an intraperitoneal injection with ketamine (40mg/kg) and xylazine (80mg/kg), placed in a supine position and intubated. Mice were ventilated with a volume-cycled ventilator (100 cycles/min, Harvard Apparatus; Holliston, MA) with volume sufficient to adequately expand but not overexpand the lungs. After a left anterior thoracotomy, the heart was exposed and the suture (8-0 mononylon) was passed under the artery at a position ~1mm from the tip of the normally positioned left auricle. The chest was then closed and the skin sutured with 5-0 nylon. Sham operations were created by the same method but without tying the suture in LAD.
|
| Growth protocol |
Mice were housed at controlled temperature (23ºC) with 12:12-hour light-dark cycle and received standard mouse chow and water ad libitum.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)
|
| Label |
Alexa Fluor®_647
|
| Label protocol |
30ug total RNA extracted from each heart was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_647–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).
|
| |
|
| Channel 2 |
| Source name |
Universal mouse RNA reference
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
reference: universal mouse RNA reference prepared from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females)
|
| Biomaterial provider |
Spray’s lab, Albert Einstein College of Medicine, Bronx, NY
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was extracted using the TRIzol® protocol (Invitrogen, CA). RNA concentration was determined with a WU-83060-00 Thermo Scientific NanoDrop ND-1000 1-position Spectrophotometer and its quality with a 2100 Bioanalyzer (Agilent, DE)
|
| Label |
Alexa Fluor®_555
|
| Label protocol |
30ug total RNA extracted from each heart was reverse transcribed into cDNA incorporating fluorescent Alexa Fluor®_555–aha-dUTP using SuperScriptTM Plus Direct cDNA Labeling System (Invitrogen, CA).
|
| |
|
| |
| Hybridization protocol |
Alexa Fluor®_647-labeled cDNA was co-hybridized with Alexa Fluor®_555-labeled universal mouse reference prepared in our lab from ten adult mouse tissues (aorta, brain, heart, kidney, liver, lung, ovary/testicles, spleen, and stomach - equal amounts from males and females) overnight at 50°C on a MO3 AECOM mouse oligonucleotide array spotted with 32k Operon 70-mer oligonucleotides V3.0 (GPL5371).
|
| Scan protocol |
After washing (0.1% SDS and 1% SSC) to remove the non-hybridized cDNAs, each array was scanned WITH A 4000B scanner (MDS, Toronto, Canada)) and images were primarily analyzed with GenePixPro 6.0 (Axon Instruments, CA).
|
| Description |
Determine the transcriptomic alteration induced in a murine model of post ischemic heart failure
|
| Data processing |
Data were normalized and analyzed with in-house developed algorithms described in Iacobas et al. Physiol Genomics 2005.
|
| |
|
| Submission date |
Oct 22, 2009 |
| Last update date |
Jun 08, 2011 |
| Contact name |
Dumitru Andrei Iacobas |
| E-mail(s) |
[email protected]
|
| Phone |
936-261-9926
|
| Organization name |
Prairie View A&M University
|
| Department |
Undergraduate Medical Academy
|
| Lab |
Personalized Genomics
|
| Street address |
Ann Preston St
|
| City |
Prairie View |
| State/province |
TX |
| ZIP/Postal code |
77446 |
| Country |
USA |
| |
|
| Platform ID |
GPL5371 |
| Series (2) |
| GSE18703 |
Cardiac gene expression and systemic cytokine profile are complementary in a murine model of post ischemic heart failure |
| GSE29769 |
Functional and Transcriptomic Recovery of Infarcted Mouse Myocardium Treated with Bone Marrow Mononuclear Cells |
|
| Data table header descriptions |
| ID_REF |
|
| X |
X-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image |
| Y |
Y-coordinate of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image |
| Dia. |
diameter of the feature-indicator |
| F635 Median |
median feature pixel intensity for Alexa Fluor®_647 channel |
| F635 Mean |
mean feature pixel intensity for Alexa Fluor®_647 channel |
| F635 SD |
standard deviation of feature pixel intensity for Alexa Fluor®_647 channel |
| B635 Median |
median background pixel intensity for Alexa Fluor®_647 channel |
| B635 Mean |
mean background pixel intensity for Alexa Fluor®_647 channel |
| B635 SD |
standard deviation of background pixel intensity for Alexa Fluor®_647 channel |
| F635 % Sat. |
percent saturated pixels for Alexa Fluor®_647 channel |
| F532 Median |
median feature pixel intensity for Alexa Fluor®_555 channel |
| F532 Mean |
mean feature pixel intensity for Alexa Fluor®_555 channel |
| F532 SD |
standard deviation of feature pixel intensity for Alexa Fluor®_555 channel |
| B532 Median |
median background pixel intensity for Alexa Fluor®_555 channel |
| B532 Mean |
mean background pixel intensity for Alexa Fluor®_555 channel |
| B532 SD |
standard deviation of background pixel intensity for Alexa Fluor®_555 channel |
| F532 % Sat. |
percent saturated pixels for Alexa Fluor®_555 channel |
| FLAG |
A feature was considered as valid (0 value) if there are no local corruption, no saturated pixels and the foreground signal is at least 2x larger than the background signal. Negative values indicate substandard feature. |
| VALUE |
normalized to the green channel log2 ratio of the background subtracted signal of that feature and the median of the background subtracted signals of all valid features of the block (700 features) in the red channel. A NULL indicates that the feature was not valid (negative FLAG) |
