|
| Status |
Public on Feb 25, 2009 |
| Title |
Cortex 48ko |
| Sample type |
RNA |
| |
|
| Source name |
cerebral cortex, knock-out
|
| Organism |
Mus musculus |
| Characteristics |
genotype: Cux2-/-
tissue: brain
gender: male
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cerebral cortex were dissected and total RNA was obtained using Qiagen RNAeasy kit.
|
| Label |
Cy3
|
| Label protocol |
For each sample, we have generated cyanine 3-labeled cRNA from one microgram of total RNA, using the Agilent Low RNA Input Linear Amplification Kit PLUS, One-Color. Briefly, total RNA is reverse-transcribed using T7-oligo (dT) primer; after first and second strand cDNA synthesis, cRNA is synthesized from the double-stranded cDNA using T7 RNA polymerase, which simultaneously incorporates cyanine 3.
|
| |
|
| Hybridization protocol |
1.65 ug of Cy3 labelled aRNA were hybridized for 17 hours at 65ºC in a hybridization oven (G2545A, Agilent) set to 10 rpm in a final concentration of 1X GEx Hybridization Buffer HI-RPM, according to manufacturer's instructions (One-Color Microarray-Based Gene Expression Analysis, Agilent Technologies).
|
| Scan protocol |
Arrays were scanned at 5um resolution on an Agilent DNA Microarray Scanner (G2565BA, Agilent Technologies) using the default settings for 4x44k format one-color arrays. Images provided by the scanner were analyzed using Feature Extraction software (Agilent Technologies).
|
| Description |
Cux2 knock-out
|
| Data processing |
Data files from Feature Extraction were imported into GeneSpring® GX software version 9.0. (Agilent Technologies). Quantile normalization was performed and expression values (log2 transformed) were obtained for each probe.
|
| |
|
| Submission date |
Feb 24, 2009 |
| Last update date |
Feb 24, 2009 |
| Contact name |
Ana Dopazo |
| E-mail(s) |
adopazo@cnic.es
|
| Phone |
34914531217
|
| Organization name |
CNIC
|
| Department |
Genomics Unit
|
| Street address |
Melchor Fdez Almagro
|
| City |
madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL7202 |
| Series (1) |
| GSE14971 |
Comparative gene expression profile of Cux2 knock-out cortex |
|
