|
| Status |
Public on Aug 15, 2023 |
| Title |
aba2_1_50nM_1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole seedling 10 DAG
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
line: T3
genotype: aba2-1
age: 10 DAG
tissue: Whole seedling
treatment: 50nM ABA
|
| Treatment protocol |
Seedlings were then incubated in liquid MS for three hours. The media contained mock for PYLCA, and mock, ABA 10nM or ABA 50nM for Col-0 and aba2-1.
|
| Growth protocol |
T3 lines of expressing PYLCA, Col-0 and aba2-1 were grown for seven days on MS plates.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Following treatment, seedlings were frozen in liquid nitrogen and stored in -80°C. RNA was extracted using RNeasy Plant Mini Kit (QIAGEN, Germany) followed by DNase treatment using an AMBION DNA-free™ Kit (Life Technologies, CA, USA) according to manufacturers' instructions.
Libraries were prepared using KAPA Stranded RNA-Seq Library Preparation Kit and sequenced with Illumina® NextSeq® 500.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
ODED16
mRNA
|
| Data processing |
Trimmed the raw reads using Trimmomatic version 0.38.
Reads were mapped using Salmon version 1.3.0.
Trimmed-mean normalized using edgeR (3.28.0).
Genome_build: TAIR10
Supplementary_files_format_and_content: allOdedRaw.csv: Comma-separated text file includes TMM normalized data for all samples.
|
| |
|
| Submission date |
Jul 31, 2021 |
| Last update date |
Aug 15, 2023 |
| Contact name |
Idan Efroni |
| E-mail(s) |
idan.efroni@mail.huji.ac.il
|
| Organization name |
Hebrew University
|
| Department |
Plant Sciences
|
| Street address |
POB 12
|
| City |
Rehovot |
| ZIP/Postal code |
76100 |
| Country |
Israel |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE181260 |
Regulation of transpiration hinges on spatial differences in abscisic acid perception |
|
| Relations |
| BioSample |
SAMN20512288 |
| SRA |
SRX11617727 |
