|
| Status |
Public on Nov 01, 2008 |
| Title |
Hippocampus veh 2 |
| Sample type |
RNA |
| |
|
| Source name |
hippocampus 24h after PBS injection
|
| Organism |
Mus musculus |
| Characteristics |
Strain: C57BL/6 and SV129/Ola cross, Age: 12-15 weeks of age
|
| Treatment protocol |
At sacrifice, hippocampus and cerebral cortex were rapidly dissected, flash frozen at -60°C, and stored at -80°C until RNA extraction.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from hippocampus and cerebral cortex samples using Qiagen RNeasy Lipid Tissue Mini and Midi kits, respectively (Qiagen, Valencia, CA, USA).
|
| Label |
Cy3
|
| Label protocol |
A 0.5 ug aliquot of total RNA from each sample was labeled using the Illumina TotalPrep RNA Amplification Kit (Ambion; Austin, TX, USA). RNA was first converted into single-stranded cDNA using reverse transcription with an oligo-dT primer containing the T7 RNA polymerase promoter, and then the single-stranded cDNA was copied to produce double-stranded cDNA molecules. The double-stranded cDNA was used in an overnight in vitro transcription reaction where single-stranded RNA (cRNA) was generated and labeled by incorporating biotin-16-UTP.
|
| |
|
| Hybridization protocol |
A total of 0.75 ug of biotin-labeled cRNA was hybridized for 16 hours to Illumina's Sentrix MouseRef-8 Expression BeadChips (Illumina, San Diego, CA, USA).
|
| Scan protocol |
The arrays were washed and blocked. Biotinylated cRNA was detected with streptavidin-Cy3 and quantitated using Illumina's BeadStation 500X Genetic Analysis Systems scanner. The image data was extracted using BeadStudio software (Illumina).
|
| Description |
none
|
| Data processing |
The expression data were filtered to include only probes with a consistent signal on each chip; the cutoff value was established at P < 0.02. The resulting dataset was next analyzed with DIANE 6.0, a spreadsheet based microarray analysis program. Using DIANE, the background was subtracted from the raw signal intensity of each gene, and the results were normalized with a Z-Score transformation. Only 16 of the 64 total arrays are included in this GEO Archive file.
|
| |
|
| Submission date |
Jul 29, 2008 |
| Last update date |
Nov 01, 2008 |
| Contact name |
Robert H Bonow |
| E-mail(s) |
robert.bonow@tufts.edu
|
| Organization name |
National Institute on Aging / NIH
|
| Department |
Brain Physiology and Metabolism Section
|
| Lab |
Molecular Neuroscience Unit
|
| Street address |
9 Memorial Drive, Building 9
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892-0947 |
| Country |
USA |
| |
|
| Platform ID |
GPL7108 |
| Series (1) |
| GSE12284 |
Gene expression changes in LPS-induced neuroinflammation |
|
