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Status |
Public on Nov 01, 2008 |
Title |
Hippocampus lps 2 |
Sample type |
RNA |
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|
Source name |
hippocampus 24h after LPS 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.
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|
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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).
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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.
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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 |
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