|
| Status |
Public on Aug 01, 2012 |
| Title |
Sugarcane transcriptome - ch1: Drought_24h_Exp_2; ch2: control_24h_2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Drought_24h_Exp_2
|
| Organism |
Saccharum hybrid cultivar (mixed) |
| Characteristics |
tissue: Aerial parts of sugarcane
cultivar: hybrid SP90-1638
pool: 6 individuals
time point: 24h
condition: exposure to drought conditions
|
| Treatment protocol |
Sugarcane plantlets with 105 days were maintained without irrigation for 24h and aerial parts of six individuals were collected and immediately frozen in liquid nitrogen.
|
| Growth protocol |
Sugarcane one-eyed seed sets obtained from a variety sensitive to drought conditions (cv. SP90-1638, CTC, Brazil) were cultivated on moist sand for 15 days. The plants were transferred to pots containing moist sand and were irrigated with Hoagland's solution (Hoagland and Arnon, 1950). Plants were maintained under greenhouse conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriZol reagent
|
| Label |
Cy3
|
| Label protocol |
Agilent's Quick Amp Labeling Kit Protocol
|
| |
|
| Channel 2 |
| Source name |
Drought_24h_control_2
|
| Organism |
Saccharum hybrid cultivar (mixed) |
| Characteristics |
tissue: Aerial parts of sugarcane
cultivar: hybrid SP90-1638
pool: 6 control plants
time point: 24h
condition: irrigation
|
| Treatment protocol |
Sugarcane plantlets with 105 days were maintained with irrigation for 24h and aerial parts of six individuals were collected and immediately frozen in liquid nitrogen.
|
| Growth protocol |
Sugarcane one-eyed seed sets obtained from a variety sensitive to drought conditions (cv. SP90-1638, CTC, Brazil) were cultivated on moist sand for 15 days. The plants were transferred to pots containing moist sand and were irrigated with Hoagland's solution (Hoagland and Arnon, 1950). Plants were maintained under greenhouse conditions.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriZol reagent
|
| Label |
Cy5
|
| Label protocol |
Agilent's Quick Amp Labeling Kit Protocol
|
| |
|
| |
| Hybridization protocol |
Two-Color Microarray-Based Gene Expression Analysis (Quick Amp Labeling) Protocol
|
| Scan protocol |
Fluorescent array images were collected for both Cy3 and Cy5 with a GenePix 4000B Scanner using Agilent Settings and image intensity data were extracted with Feature Extraction Software using Agilent Settings
|
| Description |
Plants under drought conditions (24h) x control plants, experiment 2
|
| Data processing |
Raw and background corrected data. The used software was the Feature Extraction version 9.5.3.1 (Agilent Technologies).
|
| |
|
| Submission date |
Nov 09, 2011 |
| Last update date |
Aug 01, 2012 |
| Contact name |
Milton Yutaka Nishiyama Jr |
| E-mail(s) |
yutakajr@gmail.com
|
| URL |
http://sucest-fun.org
|
| Organization name |
Universidade de São Paulo - USP
|
| Department |
Biochemistry
|
| Lab |
Signal Transduction Laboratory
|
| Street address |
Av. Professor Lineu Prestes, 748
|
| City |
São Paulo |
| State/province |
São Paulo |
| ZIP/Postal code |
05508-000 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL14862 |
| Series (1) |
| GSE33574 |
Sugarcane Expression Data from Stress Time Series |
|
| Data table header descriptions |
| ID_REF |
ID column of the reference platform |
| VALUE |
log2(gProcessedSignal/rProcessedSignal) |
| gSignal |
Raw Median Signal of feature in green channel |
| rSignal |
Raw Median Signal of feature in red channel |
| gProcessedSignal |
Dye-normalized signal after surrogate "algorithm,"green "channel,"used for computation of log ratio. |
| rProcessedSignal |
Dye-normalized signal after surrogate "algorithm,"red "channel,"used for computation of log ratio. |
| INV_VALUE |
log2(rProcessedSignal/gProcessedSignal) |
