|
| Status |
Public on Jul 12, 2012 |
| Title |
Balb/cJ 12-week-old, Control antisense oligo, biological replicate 3 |
| Sample type |
RNA |
| |
|
| Source name |
BALB/c, 12-week-old control mouse
|
| Organism |
Mus musculus |
| Characteristics |
original sample name: DW_59_4wk ctrl no NAC
strain: BALB/c
gender: Female
phenotype: asymptomatic
genotype/variation: Npc1+/+
treatment: injected with control antisense oligo
age: 12-week-old
tissue: Liver
replicate: 3
|
| 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
Female Balb/cJ mice were obtained from JAX mice and subsequently had free access to water and normal mouse chow as they were acclimated to our animal facility. Antisense oligo-treated mice were injected with control or antisense oligos for 4 weeks from 8 to 12 weeks of age. A subset of mice simultaneously received treatment with the antioxidant N-acetyl-cysteine (NAC) during the same 4 weeks as antisense oligo treatment. At 12 weeks of age, livers were collected from animals and immediately frozen on dry ice or preserved in RNAlater solution. Livers were collected from 5 biological replicates for each treatment group.
|
| 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 |
Apr 18, 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 |
|
