|
| Status |
Public on Oct 17, 2023 |
| Title |
Mh, 1h, biol rep2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaf
age: Four-week-old
cell type: WT
genotype: Col-0
treatment: Mh, 1h
|
| Treatment protocol |
The 3.5-4 weeks old plants were placed in three chambers, in which humidity was set to 40-45% RH (for low humidity treatment) , 55-60% RH (for moderate humidity treatment) and 95% RH (for high humidity treatment). Temperature was set at 22℃ and photoperiod at 12 h light/12 h dark in all chambers. The plants were treated with different humidity for 1 h.
|
| 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 |
Illumina Casava1.8 software used for basecalling.
The raw paired end reads were trimmed and quality controlled by Fastp (https://github.com/OpenGene/fastp )with default settings.
Then clean reads were separately aligned to reference genome with orientation mode using HISAT2(http://ccb.jhu.edu/software/hisat2/index.shtml) software.
the expression level of each transcript was calculated according to the fragments per Transcripts Per Million reads (TPM) method.RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances.
Assembly: TAIR 10
Supplementary files format and content: Read counts for genes (TAIR 10) were provided.
|
| |
|
| Submission date |
Jul 05, 2023 |
| Last update date |
Oct 17, 2023 |
| Contact name |
xiufang xin |
| E-mail(s) |
[email protected]
|
| Organization name |
Chinese Academy of Sciences
|
| Street address |
Xuhui
|
| City |
Shanghai |
| ZIP/Postal code |
200000 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE236463 |
Genome-wide expression analysis of Arabidopsis Col-0 plants under different air humidity |
|
| Relations |
| BioSample |
SAMN36293151 |
| SRA |
SRX20885079 |
