|
| Status |
Public on Dec 11, 2009 |
| Title |
IHP rep1 vs ILP rep1 dye swap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Total RNA from Illinois Low Protein labeled with Cyanine-5 (red)
|
| Organism |
Zea mays |
| Characteristics |
genotype: Illinois Low Protein line
age: 8 Days after Pollination
tissue: leaf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using 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 |
Total RNA from Illinois High Protein labeled with Cyanine-3 (green)
|
| Organism |
Zea mays |
| Characteristics |
genotype: Illinois High Protein line
age: 8 Days after Pollination
tissue: leaf
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using 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 |
none
|
| 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 04, 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) |
|
