|
| Status |
Public on Sep 28, 2022 |
| Title |
Col_Control_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
7-day-old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 7-day-old seedlings
genotype: Col
treatment: Control (no salt)
|
| Treatment protocol |
7-day-old seedlings were transferred into liquid 1/2 MS medium (Control) or liquid 1/2 MS medium containing 200mM NaCl (Salt). Plants were collected after four hours of treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from seedlings with Trizol (Thermo Fisher Scientific) and treated with Turbo DNase (Thermo Fisher Scientific) to remove any remaining genomic DNA
Sequencing libraries were prepared with the NEBNext Ultra RNA library prep kit for Illumina (NEB, 7530L) according to manufacture’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Adapter trimming was performed and low quality reads were filtered with fastp version 0.20.1 (Chen et al., 2018).
Reads were aligned to the Arabidopsis genome (TAIR10) using Hisat2 version 2.1.10 (Kim et al., 2019).
Reads per gene were counted by HTseq version 0.11.2 (Anders et al., 2015).
The coverage track(bigwig) for each sample was computed by DeepTools bamCoverage with RPKM normalization
Transcripts per million (TPM) values were generated using R.
Differential gene expression analysis was performed using DESeq2 version 1.26.0 (Love et al., 2014).Genes were considered as differentially expressed in RNA-seq if they exhibited a more than two-fold change in expression and had a P-adjust value<0.05.
Assembly: tair10
Supplementary files format and content: *.bw, normlized transcripts coverage files
|
| |
|
| Submission date |
May 08, 2022 |
| Last update date |
Sep 28, 2022 |
| Contact name |
Zhang Huairen |
| E-mail(s) |
[email protected]
|
| Phone |
8618911398324
|
| Organization name |
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
|
| Street address |
No. 1 West Beichen Road
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE202487 |
Cap-binding complex assists RNA Polymerase II transcription in plant salt stress response |
|
| Relations |
| BioSample |
SAMN28156882 |
| SRA |
SRX15206789 |
