|
| Status |
Public on Dec 07, 2007 |
| Title |
D2_SleepDep_ZT 6_1 |
| Sample type |
RNA |
| |
|
| Source name |
DBA/2J, sleep deprived, time of sacrifice ZT 6, replicat 1
|
| Organism |
Mus musculus |
| Characteristics |
Strain: DBA/2J, Gender: male, Age: 12-13 weeks of age, Tissue: whole brain
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were sacrificed by cervical dislocation. RNA from whole brain was isolated and purified with Rneasy Lipid tissue Midi kit (Qiagen) and Dnase treated. Equal amount of total RNA was pooled from 3 mice within each of the 24 experimental groups (3 strains, 2 conditions, 4 ZT = 24 ; in triplicate : 24 * 3 = 72 chips).
|
| Label |
biotin
|
| Label protocol |
Target preparations were performed as described by the Affymetrix GeneChip Expression Analysis Technical Manual (http://www.affymetrix.com), and were conducted at the DNA array facility of the University of Lausanne (Switzerland). 3 ug of each pool was used to perform the chiparray experiment according to the Affymetrix Gene Expression procedure.
|
| |
|
| Hybridization protocol |
Twelve micrograms of biotinylated cRNA from each sample were fragmented and hybridized to GeneChip Mouse 430 2.0 arrays, according to standard procedures. Washing and staining was performed using the EuGE-WS2v5 protocol.
|
| Scan protocol |
Scanning was done on an Affymetrix GeneChip Scanner 7G and hybridization quality control were assessed using RACE (Psarros et al., 2005), a web service based on Bioconductor “affy” and “affyPLM” packages (Gautier et al., 2004).
|
| Description |
none
|
| Data processing |
Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).
|
| |
|
| Submission date |
Oct 26, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Mehdi Tafti |
| E-mail(s) |
mehdi.tafti@unil.ch
|
| Phone |
+41216923971
|
| Organization name |
University of Lausanne
|
| Department |
CIG
|
| Street address |
Genopode
|
| City |
Lausanne |
| ZIP/Postal code |
1015 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL1261 |
| Series (2) |
| GSE9442 |
Molecular correlates of sleep deprivation in the brain of three inbred mouse strains in an around-the-clock experiment |
| GSE9444 |
Sleep deprivation and the brain |
|
| Relations |
| Reanalyzed by |
GSE119085 |
