|
| Status |
Public on Sep 10, 2012 |
| Title |
8-day Cux2-siRNA-treated female CD-1 mouse liver Replicate #2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
non-specific siRNA treated 8 week CD-1 female mouse liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: CD-1
Sex: Female
age: 8 wk
treatment: non-specific siRNA
tissue: liver
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of RNA
|
| Label |
Alexa 647
|
| Label protocol |
RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI). Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.
|
| |
|
| Channel 2 |
| Source name |
Cux2 siRNA 8 day treated 8 week CD-1 female mouse liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
strain: CD-1
Sex: Female
age: 8 wk
treatment: Cux2 siRNA
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of RNA
|
| Label |
Alexa 555
|
| Label protocol |
RNA samples were amplified as antisense-RNA (aRNA) while incorporating aminoallyl modified bases using the TargetAMP 1-Round Aminoallyl-aRNA Amplification Kit 101 per the vendor’s protocol (Epicentre, Madison, WI). Five µg of each aminoallyl-aRNA sample was fluorescent labeled using Alexa 555 or Alexa 647 by incubating with an amine-reactive dye conjugate for 1 hr at room temperature. Unincorporated dye was removed using an RNeasy column (Qiagen, Valencia, CA). Dye incorporation efficiency was determined using a Nanodrop spectrophotometer.
|
| |
|
| |
| Hybridization protocol |
Hybridization was performed using 0.825 µg of Alexa 555-labeled aRNA and 0.825 µg of Alexa 647-labeled aRNA. Agilent’s SureHyb hybridization chambers were used in a hybridization oven and rotation rack for 17 hr at 65° C at 10 rpm. After hybridization, the slides were washed per Agilent’s SSPE wash protocol.
|
| Scan protocol |
Slides were scanned using an Agilent dual laser scanner using the extended dynamic range option, which utilizes two 5 m scans of each slide at settings of PMT 100% and PMT 10% to increase signal dynamic range and avoid feature saturation. TIFF images were analyzed using Agilent’s feature extraction software (version 9.5.3, protocol GE2-v5_91_0806).
|
| Description |
8 wk CD-1 non-specific siRNA treated female mouse liver/8 wk CD-1 Cux2 siRNA 8 day treated female mouse liver/Replicate#2
The expression profile for a pool of RNAs isolated from n=6 8 wk old female mouse livers treated with non-specific siRNA vs. a pool of RNAs isolated from n=2 8 wk old female mouse livers treated with Cux2 siRNA for 8 days is given as a normalized ratio. The purpose of this comparison is to identify differences in gene expression due to knockdown of Cux2 expression in female mouse liver.
|
| Data processing |
Linear and LOWESS normalization and analysis using Rosetta Resolver pipeline (version 5.1)
|
| |
|
| Submission date |
Apr 06, 2012 |
| Last update date |
Dec 20, 2012 |
| Contact name |
David J. Waxman |
| E-mail(s) |
djw@bu.edu
|
| Organization name |
Boston University
|
| Department |
Department of Biology and Bioinformatics Program
|
| Street address |
5 Cummington Mall
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL4134 |
| Series (1) |
| GSE37078 |
Impact of Cux2 knockdown on gene expression in female mouse liver (Mus musculus) |
|
