|
| Status |
Public on Nov 11, 2014 |
| Title |
Rice seedlings roots_V Replicate 2 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Roots of rice seedlings were exposed to 1 mM V
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: TN-67
age: 6 day
treatment: exposed to 1 mM V
|
| Treatment protocol |
Six-dayold rice samples (100 mg) treated with 1 mM V for 1 and 3 h were harvested for total RNA extraction.
|
| Growth protocol |
Seeds of rice (O. sativa L. cv. TN67) were surface-disinfected with 2.5% (v/v) sodium hypochlorite (Katayama, Japan) for 15 min, then thoroughly washed in distilled water, and placed in 9-cm Petri dishes containing 25 ml distilled water at 37 ℃ in darkness for 3 days. Then, uniformly germinated seeds were selected and placed on filter paper discs (Advantec No.1) moistened with 10 ml distilled water in Petri dishes. Each Petri dish contained 15 germinated seeds that were grown for 3 days at 26 ℃ in darkness.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from each plant sample using RNeasy Plant Mini kit (QIAGEN, Hilden, Germany) with some modification [40]. The concentrations of total RNA samples were measured by the use of NanodropND 2000 (Nanodrop Technologies, Wilmington, DE, USA). RNA samples >2 g/ l with high purity (OD260/280 > 2, OD260/230 > 2) underwent microarray analysis and semi-quantitative RT-PCR.
|
| Label |
Cy5
|
| Label protocol |
Microarray RNA pool was prepared by combining a fixed volume of rice root samples collected at the following time points: 1 and 3 h. Briefly, 0.5 mg total RNAwas amplified by use of a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP (control samples) or Cy5-CTP (V-treatment) (CyDye, PerkinElmer, USA) during in vitro transcription. RNA was labeled with Cy3 or Cy5.
|
| |
|
| Channel 2 |
| Source name |
Rice seedlings roots were exposed to water
|
| Organism |
Oryza sativa |
| Characteristics |
cultivar: TN-67
treatment: exposed to water
|
| Treatment protocol |
Six-dayold rice samples (100 mg) treated with 1 mM V for 1 and 3 h were harvested for total RNA extraction.
|
| Growth protocol |
Seeds of rice (O. sativa L. cv. TN67) were surface-disinfected with 2.5% (v/v) sodium hypochlorite (Katayama, Japan) for 15 min, then thoroughly washed in distilled water, and placed in 9-cm Petri dishes containing 25 ml distilled water at 37 ℃ in darkness for 3 days. Then, uniformly germinated seeds were selected and placed on filter paper discs (Advantec No.1) moistened with 10 ml distilled water in Petri dishes. Each Petri dish contained 15 germinated seeds that were grown for 3 days at 26 ℃ in darkness.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from each plant sample using RNeasy Plant Mini kit (QIAGEN, Hilden, Germany) with some modification [40]. The concentrations of total RNA samples were measured by the use of NanodropND 2000 (Nanodrop Technologies, Wilmington, DE, USA). RNA samples >2 g/ l with high purity (OD260/280 > 2, OD260/230 > 2) underwent microarray analysis and semi-quantitative RT-PCR.
|
| Label |
Cy3
|
| Label protocol |
Microarray RNA pool was prepared by combining a fixed volume of rice root samples collected at the following time points: 1 and 3 h. Briefly, 0.5 mg total RNAwas amplified by use of a Fluorescent Linear Amplification Kit (Agilent Technologies, USA) and labeled with Cy3-CTP (control samples) or Cy5-CTP (V-treatment) (CyDye, PerkinElmer, USA) during in vitro transcription. RNA was labeled with Cy3 or Cy5.
|
| |
|
| |
| Hybridization protocol |
The fragmented labeled cRNA was then pooled and hybridized to the Rice Oligo DNA Microarray 44K RAP-DB (G2519F#15241; Agilent Technologies) 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 with or without 1 mM-treated V
|
| 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 |
Nov 10, 2014 |
| Last update date |
Nov 11, 2014 |
| Contact name |
Hao-Jen Huang |
| E-mail(s) |
haojen@mail.ncku.edu.tw
|
| Organization name |
National Cheng Kung University
|
| Department |
Life Sciences
|
| Lab |
Prof. Huang Hao-Jen
|
| Street address |
No.1, University Raod,
|
| City |
Tainan |
| ZIP/Postal code |
701 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE63152 |
Transcriptome response to vanadium stress in rice roots |
|
