|
| Status |
Public on Dec 01, 2023 |
| Title |
e122e22_ethylene_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedling
genotype: e1-2-2 e2-2 #17
treatment: ethylene
|
| Treatment protocol |
After stratification and light exposure, plated seeds on MS medium were treated with a flow of hydrocarbon free air at 22°C in air-tight containers. After three days in the dark, those etiolated seedlings were subsequently treated with ethylene gas (10 ppm) or hydrocarbon-free air for indicated hours prior to sampling.
|
| Growth protocol |
Arabidopsis seeds were first surface-sterilized with solution containing 50% bleach and 0.01% Triton X-100 for 10 minutes, washed with sterile distilled water for four times, sown on Murashige and Skoog (MS) medium plates containing 1% sucrose and 1% phytoblend agar and stratified for three days at 4°C in the dark.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction was conducted following the manufacturer’s recommendation using the RNeasy Plant Kit (Qiagen) with DNase I digestion and clean up (Qiagen, RNeasy Mini Kit (250)).
Libraries were generated using the NEBNext® Poly(A) mRNA Magnetic Isolation Module (E7490) and the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (E7770), with 1μg RNA as input, following the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Paired-end raw fastq data were evaluated with FastQC and low-quality reads were removed with Trim Galore (Babraham Institute).
The trimmed and filtered reads were then mapped to the Arabidopsis reference genome (TAIR10) with STAR.
Mapped reads were counted by featureCounts (Subread 2.0.1) and differentially regulated genes were identified using R package DESeq2.
Assembly: TAIR10
|
| |
|
| Submission date |
Sep 01, 2022 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Zhengyao Shao |
| E-mail(s) |
zyshao11@utexas.edu
|
| Organization name |
University of Texas at Austin
|
| Department |
MBS
|
| Lab |
Hong Qiao
|
| Street address |
2506 Speedway, NMS 5.324
|
| City |
Austin |
| State/province |
TX |
| ZIP/Postal code |
78712 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (2) |
| GSE212530 |
Nuclear Pyruvate Dehydrogenase Complex regulates EIN2-directed Histone Acetylation and Transcriptional Regulation in the Ethylene Response. [RNA-Seq] |
| GSE212540 |
Nuclear Pyruvate Dehydrogenase Complex regulates EIN2-directed Histone Acetylation and Transcriptional Regulation in the Ethylene Response. |
|
| Relations |
| BioSample |
SAMN30631925 |
| SRA |
SRX17395305 |
