|
| Status |
Public on Jan 22, 2016 |
| Title |
Rice seedlings roots Cu Replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Roots of rice seedlings were exposed to 5μM Cu
|
| Organism |
Oryza sativa |
| Characteristics |
treatment: copper
age: 6 day
cultivar: TN-67
tissue: root
|
| Treatment protocol |
Rice roots exposed to 5μM Cu and 25μM Cd
|
| 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. Sample 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 60℃ for 30 minutes.
|
| |
|
| Channel 2 |
| Source name |
Rice seedlings roots were exposed to water
|
| Organism |
Oryza sativa |
| Characteristics |
treatment: water
cultivar: TN-67
age: 6 day
tissue: root
|
| Treatment protocol |
Rice roots exposed to 5μM Cu and 25μM Cd
|
| 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. Sample 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 60℃ 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 2 of 3. Rice seedling roots treated with 5 μM Cu
|
| 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 05, 2012 |
| Last update date |
Jan 22, 2016 |
| Contact name |
Chung-Yi Lin |
| E-mail(s) |
L5895101@mail.ncku.edu.tw
|
| Organization name |
National Cheng Kung University
|
| Street address |
No.1, University Road
|
| City |
Tainan City |
| ZIP/Postal code |
701 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE34895 |
Comparative early transcriptomic responses to copper and cadmium exposure in rice roots |
|
