|
| Status |
Public on Mar 22, 2013 |
| Title |
Control sham-operated cortex Replicate 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Control sham-operated cortex Pool
|
| Organism |
Rattus norvegicus |
| Characteristics |
treatment: sham
tissue: Brain - cortex
strain: Sprague Dawley
|
| Growth protocol |
Brain tissues were collected from 4 transient middle cerebral artery occlusion (tMCAO) rats and 4 controls at 24 hr. Selection of optimal time points was primarily based upon the time course of infarct formation (histological data). Brain tissue of 4 mm thick ipsilateral brain section (dissected into cortex and striatum) were collected but only cortex samples were used for expression profiling.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from brain cortex using Qiagen RNeasy Midi kit as described by the manufacturer. Samples were treated with DNaseI on-column (Qiagen) for 30 minutes. RNA concentration was measured using a NanoDrop ND-1000 and RNA integrity was determined with a 2100 Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
100 ng-input two-round RT/IVT RNA amplification protocol
|
| |
|
| Channel 2 |
| Source name |
Stroke_Cortex_Ctrl#60
|
| Organism |
Rattus norvegicus |
| Characteristics |
treatment: sham
strain: Sprague Dawley
tissue: Brain - cortex
|
| Growth protocol |
Brain tissues were collected from 4 transient middle cerebral artery occlusion (tMCAO) rats and 4 controls at 24 hr. Selection of optimal time points was primarily based upon the time course of infarct formation (histological data). Brain tissue of 4 mm thick ipsilateral brain section (dissected into cortex and striatum) were collected but only cortex samples were used for expression profiling.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from brain cortex using Qiagen RNeasy Midi kit as described by the manufacturer. Samples were treated with DNaseI on-column (Qiagen) for 30 minutes. RNA concentration was measured using a NanoDrop ND-1000 and RNA integrity was determined with a 2100 Bioanalyzer.
|
| Label |
Cy5
|
| Label protocol |
100 ng-input two-round RT/IVT RNA amplification protocol
|
| |
|
| |
| Hybridization protocol |
Oligoarray control targets and hybridization buffer (Agilent In Situ Hybridization Kit Plus) were added, and samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential
|
| Scan protocol |
Scanned on an Agilent G2565AA scanner.
Images were quantified using Agilent Feature Extraction Software (version A.8.5.1.1).
|
| Description |
Biological replicate 4 of 4 sham-operated cortex
|
| Data processing |
Agilent Feature Extraction Software (v 8.5.1.1) was used for background subtraction and LOWESS normalization.
|
| |
|
| Submission date |
May 17, 2012 |
| Last update date |
Mar 22, 2013 |
| Contact name |
I-Ming Wang |
| E-mail(s) |
i_ming_wang@merck.com
|
| Phone |
215-652-1287
|
| Organization name |
Merck Research Lab
|
| Department |
Genetics and Pharmacogenomics
|
| Lab |
Discovery Pharmacogenomics
|
| Street address |
770 Sumneytown Pike
|
| City |
West Point |
| State/province |
PA |
| ZIP/Postal code |
19486 |
| Country |
USA |
| |
|
| Platform ID |
GPL3631 |
| Series (2) |
| GSE31559 |
Various mice and rat tissues subjected to various treatments |
| GSE38037 |
Profiling brain cortex from tMCAO rat stroke model |
|
