|
| Status |
Public on Aug 09, 2023 |
| Title |
ospipt6-KO, root, 3 |
| Sample type |
RNA |
| |
|
| Source name |
Rice seedlings
|
| Organism |
Oryza sativa |
| Characteristics |
tissue: root
genotype: ospipt6-KO
|
| Treatment protocol |
Shoot and root tissues from 28 day-old wild-type and ospipt6-KO seedlings grown under phosphate-sufficient conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the Maxwell RSC RNA kit (Promega) following the manufacturer's recommendations.
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug 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 Agilent Genome Oligo Microarrays (G4112A) 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 (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).
|
| Description |
Gene expression in root tissues
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
|
| |
|
| Submission date |
Aug 09, 2022 |
| Last update date |
Aug 09, 2023 |
| Contact name |
Yasuhito Sakuraba |
| E-mail(s) |
[email protected]
|
| Phone |
81358413076
|
| Organization name |
The University of Tokyo
|
| Department |
Agro-Biotechnology Research Center
|
| Lab |
Plant Functional Biotechnology Lab.
|
| Street address |
Yayoi 1-1-1
|
| City |
Bunkyo-ku |
| State/province |
Tokyo |
| ZIP/Postal code |
113-8657 |
| Country |
Japan |
| |
|
| Platform ID |
GPL6864 |
| Series (1) |
| GSE210819 |
Gene expression in shoot and root tissues (wild-type, ospipt6-KO) |
|
