|
| Status |
Public on Sep 06, 2024 |
| Title |
WT_05_1 |
| Sample type |
SRA |
| |
|
| Source name |
Wildtype (Col-0)_~95% air humidity
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
genotype: Wildtype (Col-0)
treatment: ~95% air humidity
time point: 0.5h
age: Four-week-old
tissue: leaf
|
| Treatment protocol |
Four-week-old Arabidopsis plant leaves were treated in growth chambers, with relative humidity about 95% and temperature at 22℃ with 12/12h day/night photoperiod.
|
| Growth protocol |
Plants were grown in soil in environmentally-controlled growth chambers, with relative humidity at 60% and temperature at 22℃ with 12/12h day/night photoperiod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total mRNA was extracted from leaves using Trizol reagent. Total RNA was treated with DNase I to remove DNA, and purified RNA was recovered with RNeasy® MinElute™ Cleanup kit. A total amount of 1 μg RNA per sample was used as input material for library preparation and Illumina sequencing.
Sequencing libraries were generated using TruSeq™ RNA Library Prep Kit for Illumina® following manufacturer’s recommendations and sequenced on Illumina Hiseq platform and 150 bp paired-end reads were generated.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing reads were cleaned with Trim Galore v0.4.4, Trimmomatic v0.36 and sickle, including removing bases with low quality score (<25) and irregular GC content, and cutting sequencing adaptors followed by filtering short reads.
The cleaned reads were mapped to TAIR RefSeq v10 using HISAT2 2.1.020 for RNA-seq data, all with default settings.
Genome_build: TAIR 10
Supplementary_files_format_and_content: Read counts for genes (TAIR 10) were provided.
|
| |
|
| Submission date |
Sep 07, 2021 |
| Last update date |
Sep 06, 2024 |
| Contact name |
Minhang Yuan |
| E-mail(s) |
mhyuan@sibs.ac.cn
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Shanghai Institute of Plant Physiology and Ecology
|
| Lab |
Plant-microbe Interactions
|
| Street address |
Fenglin
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (2) |
| GSE183558 |
Genome-wide expression analysis of Arabidopsis Col-0 plant and clf mutant plant under high humidity [RNA-seq] |
| GSE183559 |
Genome-wide histone 3 lysine 27 trimethylation patterns and expression analysis of WT and CLF-deficient Arabidopsis plants after high humidity treatment |
|
| Relations |
| BioSample |
SAMN21250549 |
| SRA |
SRX12030117 |
