|
| Status |
Public on Dec 31, 2018 |
| Title |
dal2_GMSUC1 |
| Sample type |
SRA |
| |
|
| Source name |
dal2_GMSUC_seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Col-0
genotype: dal-2
age: 20 days post germination
tissue: seedlings with 4 open true leaves
|
| Treatment protocol |
Seedlings were treated with either 0.1% ethanol (control) or 0.1% ethanol with 10 μM Dex (treatment) directly added into the GM-Suc media.
|
| Growth protocol |
Seeds harvested from plants subjected to the same growth conditions were vapor-phase surface sterilized for 3-5 hr with 50 ml NaOCl (bleach) supplemented with 3 ml HCl. Seeds were germinated and grown on 0.6% (w/v) agar plates containing Gamborg’s B-5 basal medium (GM, Sigma-Aldrich), 1% (w/v) sucrose (Suc), 0.05% N-morpholinoethansulphonic acid (MES; pH 5.7) supplemented with or without 10 μM Dex under a long-day (LD) photoperiod (16-hr light [100 μmol white light m-2 s-1]/8-hr dark at 21°C/19°C, respectively).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Seedlings with 4 open true leaves were harvested, immediately frozen in liquid nitrogen, and kept at -80°C until RNA extraction. RNA was extracted and purified using the RNeasy plant mini kit (Qiagen) as according to the manufacturer’s protocol. The Illumina TruSeq RNA Sample Prep Kit was used with 1 µg of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were processed for quality control by Trimmomatic to remove adapter and low quality sequences (phred=33, minimum length=36). Processed sequences were aligned to the A. thaliana Col-0 genomic sequence (TAIR10) via TOPHAT2 to identify accepted hits, which were then used to generate an absolute expression level (counts) of each locus by HTSeq.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include CPKM values for each Sample.
|
| |
|
| Submission date |
Jul 20, 2016 |
| Last update date |
May 15, 2019 |
| 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 |
GPL17639 |
| Series (1) |
| GSE84607 |
Cytoplasmic Control of Plastid Retrograde Signaling by SCFDIF-Mediated Degradation of DIFFERENTIATION AND GREENING-LIKE |
|
| Relations |
| BioSample |
SAMN05417931 |
| SRA |
SRX1961748 |
