|
| Status |
Public on Nov 01, 2017 |
| Title |
sog1-1_mock_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
sog1-1, whole plants, mock
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: whole plants
ecotype: Col-0
genotype: sog1-1
treatment: mock
|
| Treatment protocol |
Two-week-old WT and sog1-1 plants were transferred to liquid MS medium with or without 15 µM zeocin and treated for 2 h.
|
| Growth protocol |
Arabidopsis plants were grown in liquid Murashige and Skoog (MS) medium [0.5 x MS salts, 0.5 g/l 2-(N-morpholino)ethanesulfonic acid (MES), 1% sucrose, and 1 x vitamin (pH 6.3)] with gentle shaking (70 rpm) under continuous light at 22 ˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from two biological replicates with Plant Total RNA Mini Kit (FAVORGEN) according to the manufacturer’s instructions.
|
| Label |
Cy3
|
| Label protocol |
200 ng of total RNA was used to prepare for Cy3-labeled cRNA, using Low Input Quick Amp Labeling Kit (Agilent).
|
| |
|
| Hybridization protocol |
600 ng of cRNAs were hybridized to an Arabidopsis Agilent custom microarrays at 65oC for 17 h, using Gene Expression Hybridization kit. After hybridization, the microarrays were washed with Gene Expression Wash Buffer 1 (Agilent) and Gene Expression Wash Buffer (Agilent), then dried immediately by brief centrifugation.
|
| Scan protocol |
The microarrays were scanned by Agilent DNA Microarray Scanner (G2539A ver.C).
|
| Data processing |
When Agilent feature extraction software outputted raw data, the software omitted rows associated with spots where DNA proves were not spotted (8198 negative spots).
RMA normalization was performed for signals of microarray probes using limma package (Ritchie et al., 2015) on R (ver. 3.4.2) (R Core Team, 2013).
|
| |
|
| Submission date |
Oct 25, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Nobuo Ogita |
| E-mail(s) |
[email protected]
|
| Organization name |
Nara Institute of Science and Technology
|
| Department |
Graduate School of Biological Sciences
|
| Street address |
8916-5 Takayama-cho
|
| City |
Ikoma |
| State/province |
Nara |
| ZIP/Postal code |
630-0192 |
| Country |
Japan |
| |
|
| Platform ID |
GPL22706 |
| Series (2) |
| GSE106154 |
Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1-regulated genes in Arabidopsis |
| GSE106418 |
Genome-wide identification of SUPPRESSOR OF GAMMA RESPONSE 1-regulated and 1 (SOG1)-target genes in Arabidopsis |
|
