|
| Status |
Public on Dec 21, 2014 |
| Title |
Rice seedlings roots_short Cr(VI) exposures Replicate 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
Roots of rice seedlings were exposed to 50 μM Cr(VI) during short (pooled from 1- and 3-h treatments) exposures
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: Roots of rice seedlings
cultivar: Oryza sativa L. cv. TN-67
age: 6 day
|
| Treatment protocol |
Control and rice seedlings were exposed to to 50 μM Cr(VI) 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 Cr(VI) 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 |
tissue: Roots of rice seedlings
cultivar: Oryza sativa L. cv. TN-67
age: 6 day
|
| Treatment protocol |
Control and rice seedlings were exposed to to 50 μM Cr(VI) 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 |
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 Cr(VI) 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
|
| 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 1 of 3. Rice seedling roots with or without 50 μM Cr(VI) 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 |
Oct 21, 2012 |
| Last update date |
Dec 22, 2014 |
| Contact name |
Tsai-Lien Huang |
| E-mail(s) |
l5893106@gmail.com
|
| Phone |
+886933375382
|
| Fax |
+88662742583
|
| Organization name |
National Cheng Kung University
|
| Department |
Life Sciences
|
| Lab |
Prof. Huang Hao-Jen
|
| Street address |
No.1, University Raod,
|
| City |
Tainan |
| State/province |
Taiwan |
| ZIP/Postal code |
701 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL8852 |
| Series (1) |
| GSE41733 |
Chromium stress response in rice roots: effects on transcriptome profiles and signalling pathways responsive |
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