|
| Status |
Public on Dec 23, 2013 |
| Title |
root_WT_2 |
| Sample type |
RNA |
| |
|
| Source name |
root, WT, replicate 2
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: root
genotype/variation: wild type
|
| Treatment protocol |
No treatment
|
| Growth protocol |
Plants of Arabidopsis thaliana were grown in a greenhouse under long-day conditions (22°C, 16/8 h photoperiod cycles). Flowers buds were collected from 4-week-old wild-type (Col-0) plants. Root and leaf samples were collected from 30-d-old wild-type plants (Col-0) grown hydroponically in full-strength MGRL medium under long-day conditions.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted and treated with DNase I using RNeasy Plant mini kit (Qiagen).
|
| Label |
Cy3
|
| Label protocol |
We performed RNA labeling, hybridization and scaning using protocols according to the Agilent's instructions. Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent).
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to ATH NAT array for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides.
|
| Data processing |
Raw data of processed signal intensities are obtained by analysis using Feature Extraction Software (Agilent) with default parameters. Standard QC analysis, background normalization and quantile normalization were performed using GeneSpring GX Software (Agilent) with default parameters.
|
| |
|
| Submission date |
Jul 30, 2013 |
| Last update date |
Dec 25, 2013 |
| Contact name |
Huan Wang |
| E-mail(s) |
hwang01@rockefeller.edu
|
| Organization name |
The Rockefeller University
|
| Lab |
Chua Nam-Hai
|
| Street address |
1230 York Avenue
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17515 |
| Series (1) |
| GSE49381 |
Expression of Arabidopsis cis-NAT pairs in inflorescences, leaves and roots |
|
