|
| Status |
Public on Aug 28, 2013 |
| Title |
714_WT.rep3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Universal mouse reference (UMR) from Stratagene
|
| Organism |
Mus musculus |
| Characteristics |
reference: Universal mouse reference (UMR) from Stratagene
|
| Treatment protocol |
DLK knockdown was induced by placing mice on a tamoxifen diet for 3 weeks. All wild type animals were on the tamoxifen diet as well. Animals were taken down and hippocampus was dissected out and processed for RNA extraction.
|
| Growth protocol |
Mice were bread to give the specific genotypes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNAesy mini kit following the manufacturer's instructions and including on column DNAse digestion. RNA quality was verified by running samples on Agilent Bioanalyzer 2100.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).
|
| |
|
| Channel 2 |
| Source name |
WT.rep3
|
| Organism |
Mus musculus |
| Characteristics |
tissue: adult hippocampus
genotype: DLK wild-type
|
| Treatment protocol |
DLK knockdown was induced by placing mice on a tamoxifen diet for 3 weeks. All wild type animals were on the tamoxifen diet as well. Animals were taken down and hippocampus was dissected out and processed for RNA extraction.
|
| Growth protocol |
Mice were bread to give the specific genotypes.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using RNAesy mini kit following the manufacturer's instructions and including on column DNAse digestion. RNA quality was verified by running samples on Agilent Bioanalyzer 2100.
|
| Label |
Cy5
|
| Label protocol |
Total RNA was converted to double-stranded cDNA and then into Cy-dye labeled cRNA using Agilent’s Quick Amp Labeling Kit. For all samples, 750 ng of the labeled cRNA was fragmented and hybridized against Cy3-labeled Universal mouse reference (Stratagene, La Jolla, CA).
|
| |
|
| |
| Hybridization protocol |
Agilent In Situ Hybridization Kit Plus was used where Cy-dye labeled control and test samples were applied to microarrays enclosed in Agilent SureHyb-enabled hybridization chambers. After hybridization, the arrays were washed twice, dried and then scanned.
|
| Scan protocol |
Scanned on an Agilent scanner, images were processed using Agilent Feature Extraction software version 11.
|
| Data processing |
Agilent Feature Extraction software version 11 was used to create feature extraction files. The normal exponential convolution model was applied for the background correction, Loess and quantile were applied for within array and cross-array normalization. Gene differential expression was analyzed by the package of limma.
|
| |
|
| Submission date |
Aug 27, 2013 |
| Last update date |
Aug 28, 2013 |
| Contact name |
Jessica Lynn Larson |
| E-mail(s) |
[email protected]
|
| Phone |
6502251802
|
| Organization name |
Genentech
|
| Department |
Bioinformatics and Computational Biology
|
| Lab |
Larson
|
| Street address |
1 DNA Way
|
| City |
South San Francisco |
| State/province |
California |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL11202 |
| Series (1) |
| GSE50245 |
Dual leucine zipper kinase is required for excitotoxicity induced neuronal degeneration |
|
