|
| Status |
Public on May 26, 2012 |
| Title |
Blood C57Bl/10 mouse recovery sample 4 |
| Sample type |
RNA |
| |
|
| Source name |
blood recovery C57Bl/10 mouse sample 4
|
| Organism |
Mus musculus |
| Characteristics |
sample id: recovery sample n#4
strain: C57Bl/10
age: 3 month old
protocol: exposed to chronic hypoxia during two weeks followed by two weeks under normoxia
|
| Treatment protocol |
To study the effects of chronic hypoxia of blood samples, three different groups of normal mice C57Bl/10 were exposed to normoxia (PO2 21%), CH (from 21% to 8%) or recovery (two weeks under CH protocol followed by two weeks to normoxia).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA was isolated and purified from each blood sample by RNeasy micro kit (Qiagen, Valencia, CA) as described by manufacturer.
|
| Label |
Biotin
|
| Label protocol |
100 ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by poly (T) oligomer that incorporated synthetic RNA sequence. Second-strand cDNA synthesis was followed by ribo-SIPA (Single Primer Isothermal Amplification, NuGen Technologies Inc., San Carlo, CA) for linear amplification of each transcript, and the resulting cDNA was fragmented, assessed by Bioanalyzer and biotinnylated.
|
| |
|
| Hybridization protocol |
cDNA yields ranged from 5000-6000ug, and 3.75ug were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to MOE V2.0 GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain. A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
|
| Scan protocol |
The chip was scanned at 6um resolution with Agilent model G2500A GeneArray scanner. A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.
|
| Description |
each sample came from blood of one mouse.
|
| Data processing |
Quality control parameters such as scaling factors used to normalize the chips, average background, and noise were also evaluated. Signal intensities for each probe set were stored in electronic formats by the GeneChip Operating System version 1.1 (GCOS1.1, Affymetrix Inc.).
|
| |
|
| Submission date |
Aug 19, 2009 |
| Last update date |
May 26, 2012 |
| Contact name |
Matias Mosqueira |
| E-mail(s) |
matias@physiologie.uni-heidelberg.de
|
| Phone |
+496221544143
|
| Organization name |
Heidelberg University Hospital
|
| Department |
Institute of Physiology and Pathop
|
| Lab |
Cardio-Ventilatory Muscle Physiology
|
| Street address |
Im Neuenheimer Feld, 326 R414
|
| City |
Heidelberg |
| State/province |
Baden-Wuttenberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE17728 |
Blood gene expression profile from mouse C57Bl/10 exposed to chronic hypoxia |
|
