|
| Status |
Public on Jun 10, 2024 |
| Title |
agb1-3_NaCl 4h_rep2 |
| Sample type |
RNA |
| |
|
| Source name |
root
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: root
age: 7d
treatment: NaCl 4h
genotype: agb1-3
|
| Treatment protocol |
The Arabidopsis wild-type and agb1-3 mutant seeds were sown on half-strength MS agar plates and grown under a 16 h/8 h light-dark cycle at 22 °C with a light intensity of 150 µmol m^-2 s^-1 for 7 days. The roots were detached from seedlings that had been immersed in 150 mM NaCl/MS liquid media for 0 or 4 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was prepared using the TRI reagent (Invitrogen AM9738) following the manufacturer's recommendations. The DNase digestion (Qiagen) were used to remove genomic contamination. RNA was quantified using a NanoDrop spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 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 Whole Arabidopsis Genome Oligo Microarrays 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 after 4hr in Arabidopsis agb1-3 root
|
| Data processing |
The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
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| |
|
| Submission date |
Apr 19, 2024 |
| Last update date |
Jun 10, 2024 |
| Contact name |
Yueh Cho |
| E-mail(s) |
choyueh@gate.sinica.edu.tw
|
| Organization name |
Academia Sinica
|
| Department |
Institute of Plant and Microbial Biology
|
| Street address |
128 Sec. 2, Academia Rd, Nankang
|
| City |
Taipei |
| ZIP/Postal code |
115201 |
| Country |
Taiwan |
| |
|
| Platform ID |
GPL12621 |
| Series (1) |
| GSE264404 |
Quantification of salinity-induced gene expression in young AGB1-deficient roots |
|
