|
| Status |
Public on Jul 12, 2012 |
| Title |
3-week-old Npc1-/-, biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
BALB/cNctr-Npc1m1N/J, 3-week-old mutant mouse
|
| Organism |
Mus musculus |
| Characteristics |
original sample name: DW_05_NPC--3wk
strain: BALB/c
gender: Female
phenotype: pre-symptomatic age
genotype/variation: Npc1-/-
age: 3-week-old
tissue: Liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the liver tissue using TRIzol reagent (Invitrogen), followed by purification with Qiagen RNeasy Mini columns (Qiagen). RNA quality and quantity was assessed using both a Bioanalyzer (Agilent Inc.) and NanoDrop (Thermo Scientiļ¬c Inc.).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
|
| |
|
| Hybridization protocol |
200 ng of total RNA was reverse transcribed to obtain labeled cDNA. Labeled cDNAs was hybridized to the chips. Chips were washed and stained using standard protocols for the Affymetrix Fluidics Station.
|
| Scan protocol |
Arrays were scanned using the Affymetrix Gene Chip Scanner 3000 and gene expression intensities were calculated using the Affymetrix GeneChip Command Console software
|
| Description |
Gene expression data
Heterozygous Npc1+/- mice were intercrossed to obtain control (Npc1+/+) and mutant (Npc1-/-) littermates. Pups were weaned 3 weeks after birth and subsequently had free access to water and normal mouse chow. PCR genotyping was performed using tail DNA. Considering that the phenotypic presentation is slightly different between males and females, we chose to work with only females to avoid any gender-specific variations in gene expression [74]. Female pups were sacrificed at 1, 3, 5, 7, 9, and 11 weeks of age. Livers were collected from both mutant and control animals, and immediately frozen on dry ice. Four livers were collected corresponding to each age and genotype, for a total of 48 samples.
|
| Data processing |
Affymetrix .CEL files were normalized using the RMA (Robust Multi-Array Analysis) algorithm within Partek Genomics Suite software, version 6.5 (Partek Inc.)
|
| |
|
| Submission date |
Nov 03, 2011 |
| Last update date |
Mar 21, 2013 |
| Contact name |
Celine Cluzeau |
| E-mail(s) |
cluzeauc@mail.nih.gov
|
| Organization name |
NICHD/NIH
|
| Department |
PDEGEN
|
| Lab |
Porter Lab
|
| Street address |
10 Center Drive - room 9D41
|
| City |
BETHESDA |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE33467 |
Expression data from liver tissue from Npc1 mouse model |
|
