|
| Status |
Public on Oct 20, 2014 |
| Title |
Gtf2i(+/Δex2) vs. WT(+/+) Cortex replicate 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Gtf2i(+/Δex2) Cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed background (98.4% C57BL/6J , 1.6% 129Sv/CD1)
genotype/variation: Gtf2i(+/Δex2)
age: 16 weeks old
tissue: Cortex
|
| Growth protocol |
Cortex were fresh dissected from adult, 16 weeks old animals. Dissected tissues were directly frozen in liquid Nitrogen until RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions. RNA quantification was performed through a Nanodrop spectrophotometer.
Starting material: 500 ng of Total RNA
Quality Control: The quality of every RNA sample were tested by nanochip analysis on the Agilent Bioanalyzer and by measuring the A260/A280 and A260/A230 ratios. All samples have a minimum RIN score of at least 7.0 , an OD (A260/A280) ratio value >1.8 and an OD (A260/A230) ratio>1.5.
|
| Label |
Cy3
|
| Label protocol |
500 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004).
|
| |
|
| Channel 2 |
| Source name |
WT (+/+) Cortex
|
| Organism |
Mus musculus |
| Characteristics |
strain background: mixed background (98.4% C57BL/6J , 1.6% 129Sv/CD1)
genotype/variation: WT (+/+)
age: 16 weeks old
tissue: Cortex
|
| Growth protocol |
Cortex were fresh dissected from adult, 16 weeks old animals. Dissected tissues were directly frozen in liquid Nitrogen until RNA extraction
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extracted using Trizol following manufacturer's instructions. RNA quantification was performed through a Nanodrop spectrophotometer.
Starting material: 500 ng of Total RNA
Quality Control: The quality of every RNA sample were tested by nanochip analysis on the Agilent Bioanalyzer and by measuring the A260/A280 and A260/A230 ratios. All samples have a minimum RIN score of at least 7.0 , an OD (A260/A280) ratio value >1.8 and an OD (A260/A230) ratio>1.5.
|
| Label |
Cy5
|
| Label protocol |
500 ng of total RNA were reverse transcribed, amplified, labelled by in vitro transcription using the Low Input Linear Amplification Kit (Agilent 5184-3523), and hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004).
|
| |
|
| |
| Hybridization protocol |
Three biological replicate experiments were hybridized following the manufacturer’s instructions (SSC wash Agilent 60-mer oligo microarray processing protocol, Version 4.1, April 2004), each comparing Gtf2i+/Δex2 verus wild type cortex tissues. Thus, three microarray hybridizations were processed.
|
| Scan protocol |
Fluorescent images were obtained with the Agilent G2565BA Microarray Scanner System (Agilent Technologies) and TIFF images were quantified with the use of the Spot program (http://experimental.act.cmis.csiro.au/Spot/index.php) under the R environment (http://www.r-project.org).
|
| Description |
Cortex Replicate 3
|
| Data processing |
The original raw data file (i.e. Agilent feature extraction files) are not available. The modified raw data files are provided along with the file contents description (raw_data_readme.txt available on Series records).
The resulting raw values were filtered and an intensity cut-off was applied, selecting those points with a foreground median/background median >3 in at least one channel. A series of programs, collectively packaged as Array File Maker 4.0 (AFM), were use to manipulate and manage DNA microarray data (Breitkreutz, Jorgensen et al. 2001). AFM 4.0, Quantarray Data Handler 3.0, and Array Database 1.0 can be downloaded at the Tyers Lab Home Page [http://www.mshri.on.ca/tyers/] and are copyrighted against commercial gain.
|
| |
|
| Submission date |
Oct 01, 2012 |
| Last update date |
Oct 20, 2014 |
| Contact name |
Victoria Campuzano |
| E-mail(s) |
[email protected]
|
| Organization name |
Universitat Pompeu Fabra
|
| Department |
CEXS
|
| Lab |
Genetic
|
| Street address |
Dr Aiguader, 88
|
| City |
Barcelona |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL2872 |
| Series (1) |
| GSE41251 |
Murine Adult Cortex: Gtf2i (+/Δex2 ) VS WT (+/+) |
|
