|
| Status |
Public on Jul 22, 2013 |
| Title |
Rice seedlings roots_FA short exposures Replicate 3 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Roots of rice seedlings were exposed to 50 ppm ferulic acid during short (pooled from 1- and 3-h treatments) exposures
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: cv. TN-67
agent: 50 ppm ferulic acid
time point: short (pooled from 1- and 3-h treatments)
age: 6 day
|
| Treatment protocol |
Control and rice seedlings were exposed to to 50 ppm ferulic acid during short (pooled from 1- and 3-h treatments) exposures or long (24 h) exposures
|
| Growth protocol |
6-day-old seedlings
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.
|
| Label |
Cy5
|
| Label protocol |
0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process rice roots after ferulic acid treatment RNA was labeled by Cy5 and RNA from control RNA was labeled by Cy3. 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60oC for 30 minutes.
|
| |
|
| Channel 2 |
| Source name |
Rice seedlings roots were exposed to water
|
| Organism |
Oryza sativa |
| Characteristics |
agent: water
cultivar: cv. TN-67
age: 6 day
|
| Growth protocol |
6-day-old seedlings
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were extracted using QIAGEN RNeasy kit follwed by DNAse treatment. The RNA samples were further purified and concentrated by RNeasy MinElute Cleanup.
|
| Label |
Cy3
|
| Label protocol |
0.5 μg of total RNA was amplified by a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP or Cy5-CTP (CyDye, PerkinElmer, USA) during the in vitro transcription process rice roots after ferulic acid treatment RNA was labeled by Cy5 and RNA from control RNA was labeled by Cy3. 0.825 μg of Cy-labled cRNA was fragmented to an average size of about 50-100 nucleotides by incubation with fragmentation buffer (Agilent Technologies, USA) at 60oC for 30 minutes.
|
| |
|
| |
| Hybridization protocol |
Correspondingly fragmented labeled cRNA is then pooled and hybridized to Agilent Rice Oligo 4×44K Microarray (Agilent Technologies, USA) at 60°C for 17 h.
|
| Scan protocol |
After washing and drying by nitrogen gun blowing, microarrays are scanned with an Agilent microarray scanner (Agilent Technologies, USA) at 535 nm for Cy3 and 625 nm for Cy5. Scanned images are analyzed by Feature extraction software 9.5.3 (Agilent Technologies, USA),
|
| Description |
Biological replicate 3 of 3. Rice seedling roots with or without 50 ppm ferulic acid short (pooled from 1- and 3-h treatments) exposures
|
| Data processing |
An image analysis and normalization software is used to quantify signal and background intensity for each feature, substantially normalized the data by rank-consistency-filtering LOWESS method.
|
| |
|
| Submission date |
Jan 06, 2012 |
| Last update date |
Jul 22, 2013 |
| Contact name |
Wen-Chang Chi |
| E-mail(s) |
wenji0918177774@yahoo.com.tw
|
| Phone |
+886918177774
|
| Organization name |
National Cheng Kung University
|
| Department |
Life Science
|
| Lab |
Prof. Huang Hao-Jen
|
| Street address |
No.1, University Road, Tainan City
|
| City |
Tainan |
| State/province |
Taiwan |
| ZIP/Postal code |
701 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE34899 |
Autotoxicity mechanism of Oryza Sativa: Microarray analysis of rice plants in response to allelochemical ferulic acid |
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