|
| Status |
Public on Mar 24, 2010 |
| Title |
W4 vs W8 Rep3 (18Kb) |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Pooled the 3 leaflets of the primary trifoliate leaf
|
| Organism |
Glycine max |
| Characteristics |
tissue: leaflet
genotype: Cultivar Williams 82
development stage: V1 stage (about 2 weeks old)
|
| Biomaterial provider |
Clough Lab
|
| Treatment protocol |
Water control with adjuvant
1% v/v Herbimax, Loveland Industries
4 hr post application
|
| Growth protocol |
Greenhouse (25C)
16h daylength
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Phase-Lock Gel RNA Extraction
|
| Label |
Cy3
|
| Label protocol |
Indirect incorporation using aa-dUTP
|
| |
|
| Channel 2 |
| Source name |
Pooled the 3 leaflets of the primary trifoliate leaf
|
| Organism |
Glycine max |
| Characteristics |
tissue: leaflet
genotype: Cultivar Williams 82
development stage: V1 stage (about 2 weeks old)
|
| Biomaterial provider |
Clough Lab
|
| Treatment protocol |
Water control with adjuvant
1% v/v Herbimax, Loveland Industries
8 hr post application
|
| Growth protocol |
Greenhouse (25C)
16h daylength
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol Phase-Lock Gel RNA Extraction
|
| Label |
Cy5
|
| Label protocol |
Indirect incorporation using aa-dUTP
|
| |
|
| |
| Hybridization protocol |
Hegde P. et al. Biotechniques 2000 29:548-56
|
| Scan protocol |
Scanner: Perkin-Elmer ScanArray Express
Software: ScanArray Express v2.1
|
| Description |
Replicate 3
|
| Data processing |
Spot raw data from GenePix v5.0
in-house PERL programs to format data and remove spots weaker than negative control
log2 transformation and GLowess in R/MAANOVA
|
| |
|
| Submission date |
Mar 24, 2009 |
| Last update date |
Mar 24, 2009 |
| Contact name |
min li |
| Organization name |
University of Illinois at Urbana-Champaign
|
| Lab |
Dr. Steve Clough
|
| Street address |
Rm230 1101 W peabody Dr
|
| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
| |
|
| Platform ID |
GPL6009 |
| Series (2) |
| GSE15375 |
Effects of Photosystem II Interfering Herbicides Atrazine and Bentazon on the Soybean Transcriptome 2 |
| GSE15377 |
Effects of Photosystem II Interfering Herbicides Atrazine and Bentazon on the Soybean Transcriptome |
|
| Data table header descriptions |
| ID_REF |
spot ID |
| F_Pixels |
number of pixels in the spot |
| F635Median |
channel 2 median spot intensity |
| F635SD |
standard deviation around channel 2 mean spot intensity |
| F532Median |
channel 1 median spot intensity |
| F532SD |
standard deviation around channel 1 mean spot intensity |
| Flags |
user defined flags (default = 0) |
| S532N |
channel 1 normalized spot signal |
| S635N |
channel 2 normalized spot signal |
| PRE_VALUE |
S532N/S635N |
| VALUE |
log2 ratio of PRE_VALUE: normalized S532N/S635N |
