|
| Status |
Public on Sep 09, 2010 |
| Title |
Prdm16 VZ KO2 Rep2 |
| Sample type |
RNA |
| |
|
| Source name |
Brain ventricular zone cells of newborn Prdm16LacZ/LacZ mice
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/Ka strain
genotype/variation: Prdm16LacZ/LacZ
tissue: Newborn mouse Brain ventricular zone
|
| Treatment protocol |
The ventricular zone cells were processed without treatment. The gene expression comparison is between the different genotypes.
|
| Growth protocol |
The uncultured ventricular zone cells from newborn Prdm16LacZ/LacZ, Prdm16LacZ/+, and Prdm16+/+ mice were dissected from the brains and placed into the Trizol reagent.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions followed by additional purification with RNA Clean & Concentrator™-5 (R1015, Zymo research). Purified RNA was reverse transcribed and amplified using the WT-Ovation™ Applause WT/Amp RNA amplification system (NuGEN Technologies,) following the manufacturer’s instructions.
|
| Label |
Biotin
|
| Label protocol |
cDNA was fragmented and labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN). 2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.
|
| |
|
| Hybridization protocol |
2.5µg of labeled cDNA were hybridized to Affymetrix Mouse Gene ST 1.0 microarrays.
|
| Scan protocol |
The chips were scanned using the Affymetrix 3000 7G GeneChip Scanner with Autoloader.
|
| Description |
Gene expression data from ventricular zone cells of newborn Prdm16LacZ/LacZ mice
|
| Data processing |
Data was analyzed using the limma and affy Bioconductor packages implemented in the R-statistical language. RMA was used to normalize the data and fit log2 transformed expression values.
|
| |
|
| Submission date |
Aug 04, 2010 |
| Last update date |
Sep 09, 2010 |
| Contact name |
Sean J Morrison |
| E-mail(s) |
[email protected]
|
| Phone |
734-647-6261
|
| Organization name |
Center for Stem Cell Biology, 5435 Life Sciences Institute University of Michigan
|
| Department |
HHMI/Department of Internal Medicine
|
| Street address |
210 Washtenaw Ave
|
| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109-2216 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE23406 |
Prdm16 newborn mouse (ventricular zone) VZ cells microarray |
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