|
| Status |
Public on Aug 20, 2020 |
| Title |
ask1 Ds open flower RNA-Seq_S_311 |
| Sample type |
SRA |
| |
|
| Source name |
Open flower
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
strain: Col-0
|
| Growth protocol |
The plants were grown under long-day photoperiod with 16-h light (150 μmol/m2/s)/ 8-h darkness at 21°C and 19°C, respectively.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 10-50 mg of floral buds or open flowers from both WT and ask1 primary inflorescences five hours after dawn using the NucleoSpin® RNA kit (Macherey-Nagel).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Pair end 150-mer RNA-Seq
|
| Data processing |
Adapter and low-quality sequences in the raw FASTQ sequencing data were removed to produce valid sequences using Trimmomatic (phred=33, minimum length=36; (Bolger et al., 2014)), which were further aligned to the A. thaliana Col-0 reference genome (TAIR10; www.arabidopsis.org) via TOPHAT2 (Kim et al., 2013a) to identify accepted hits of each locus. HTSeq was then used to calculate an absolute expression level (counts) of each locus based on the accepted hits (Anders et al., 2015).
|
| |
|
| Submission date |
Jun 17, 2019 |
| Last update date |
Aug 21, 2020 |
| Contact name |
Zhihua Hua |
| E-mail(s) |
hua@ohio.edu
|
| Phone |
7405931123
|
| Organization name |
Ohio University
|
| Department |
Department of Environmental and Plant Biology
|
| Lab |
Hua Lab
|
| Street address |
22 Richland Ave
|
| City |
Athens |
| State/province |
Ohio |
| ZIP/Postal code |
45701 |
| Country |
USA |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE132841 |
Generation of a fertile ask1 mutant uncovers a comprehensive set of SCF‐mediated intracellular functions |
|
| Relations |
| BioSample |
SAMN12078915 |
| SRA |
SRX6078337 |
