|
| Status |
Public on Aug 31, 2010 |
| Title |
Cerebellum_NPC_ILM_rep4 |
| Sample type |
RNA |
| |
|
| Source name |
cerebellum from Npc1 (BALB/cNctr-Npc1m1N/J) mice
|
| Organism |
Mus musculus |
| Characteristics |
strain: Npc1 (BALB/cNctr-Npc1m1N/J)
genotype/variation: Npc1-/-
tissue: cerebellum
|
| Treatment protocol |
Mice were genotyped using tail DNA with PCR methods described by Baudray (Baudray et al., 2003). Cerebelli were collected from 8 mice (4 Npc1+/+mice, and 4 Npc1-/- mice) at 3 weeks postnatal and were snap-frozen in liquid nitrogen.
|
| Growth protocol |
Npc1(BALB/cNctr-Npc1m1N/J) heterozygous male and female mice on BALB/c background were purchased from Jackson Laboratory (Bar Harbor, MN) and housed in the vivarium under protocols approved by the local IACUC. Mice had free access to water and food; Npc1-/- mice were produced by in-house breeding.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRIzol reagent (Invitrogen, Carlsbad, CA) and purified with RNeasy Mini Kit according to the manufacturer instructions (Qiagen, Valencia, CA).
|
| Label |
Biotin
|
| Label protocol |
200 ng of total RNA was labeled using a MessageAmp II-biotin enhanced kit (Applied Biosystems, Foster City, CA). Double stranded cDNA was synthesized using T7-oligo (dT) primers followed by an in vitro transcription (IVT) reaction to amplify antisense-RNA (aRNA), while biotin was incorporated into the synthesized aRNA target.
|
| |
|
| Hybridization protocol |
The biotinylated cRNA target was hybridized to the MouseWG-6 BeadChip according to the manufacturer’s instructions with the addition of a 10-min washing in high-temp wash buffer (Illumina) at 55 ºC in a Hybex Microarray Incubation System (SciGene Corportaion, Sunnyvale, CA) following the overnight hybridization.
|
| Scan protocol |
The chips were scanned using a BeadScan 2.3.0.10 (Illumina) at a multiplier setting of “2”.
|
| Description |
Gene expression profiling data from cerebellum
|
| Data processing |
The microarray images were registered and gene expression data were extracted automatically according to the manufacturer’s default settings. After background subtraction, raw microarray intensity data were normalized using the cubic spline normalization method (Illumina). Intensity data were then adjusted to set the minimum intensity of an array equal to 1.
|
| |
|
| Submission date |
Aug 30, 2010 |
| Last update date |
Aug 30, 2010 |
| Contact name |
Leming Shi |
| E-mail(s) |
lemingshi@fudan.edu.cn
|
| Phone |
+86-18616827008
|
| Organization name |
Fudan University
|
| Department |
School of Life Sciences
|
| Lab |
Center for Pharmacogenomics
|
| Street address |
2005 Songhu Road
|
| City |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL6481 |
| Series (1) |
| GSE20450 |
Microarray analysis in Npc1-/- mouse cerebellum |
|
