|
| Status |
Public on Dec 11, 2009 |
| Title |
Reference vs Genotype1 rep2 dye swap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Oba super 1
|
| Organism |
Zea mays |
| Characteristics |
genotype: Oba super 1
age: at Anthesis
tissue: Earshoot
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using LS TRIzol (Invitrogen, Carlsbad, CA), digested by DNAse, then Rneasy purification kit (Qiagen, Valencia, CA).
|
| Label |
Cy5
|
| Label protocol |
The Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion, Austin, TX) with Cyanine-3 and -5 (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) dyes were used to amplify and label samples.
|
| |
|
| Channel 2 |
| Source name |
4001/4008
|
| Organism |
Zea mays |
| Characteristics |
genotype: 4001/4008
age: at Anthesis
tissue: Earshoot
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using LS TRIzol (Invitrogen, Carlsbad, CA), digested by DNAse, then Rneasy purification kit (Qiagen, Valencia, CA).
|
| Label |
Cy3
|
| Label protocol |
The Amino Allyl MessageAmp™ II aRNA Amplification kit (Ambion, Austin, TX) with Cyanine-3 and -5 (GE Healthcare Bio-Sciences Corp., Piscataway, NJ) dyes were used to amplify and label samples.
|
| |
|
| |
| Hybridization protocol |
Hybridizations were performed overnight in custom designed cassettes in 42 degree water bath, followed by 3 washes.
|
| Scan protocol |
Scanned on a Genepix 4000B scanner (Molecular Devices Corporation, Sunnyvale, CA). Used GenePix Pro 6.0 (Molecular Devices Corporation) for spotfinding.
|
| Description |
Reference vs Genotype1 rep2 dye swap
|
| Data processing |
A Lowess curve was fit to the log-intensity versus log-ratio plot. 20.0% of the data was used to calculate the Lowess fit at each point. This curve was used to adjust the control value for each measurement. If the control channel was lower than 10 then 10 was used instead.
|
| |
|
| Submission date |
Sep 08, 2009 |
| Last update date |
Dec 10, 2009 |
| Contact name |
Stephen Patrick Moose |
| E-mail(s) |
smoose@illinois.edu
|
| Phone |
2172446146
|
| Fax |
2173339817
|
| URL |
http://www.cropsci.illinois.edu/faculty/moose/
|
| Organization name |
University of Illinois at Urbana-Champaign
|
| Department |
Crop Sciences
|
| Lab |
Corn Functional Genomics Laboratory
|
| Street address |
1201 W Gregory
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL5439 |
| Series (1) |
| GSE18008 |
Transcriptomic analysis of maize developing earshoot from tropical maize hybrid genotypes native to Nigeria |
|
