|
| Status |
Public on Feb 10, 2022 |
| Title |
coi1_2h_2 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis thaliana seedings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: the entire tissues of leaf explants
genotype: coi1
Stage: 2 h after detachment
|
| Treatment protocol |
The first pair of rosette leaves were cut at the junction of the blade and petiole, and the detached blades were cultured on sucrose-free B5 medium at 22°C under 24-h light conditions for 0 (t0), 10 min, 30 min, 1 h, 2 h, 4 h, 8 h and 12 h .
|
| Growth protocol |
Arabidopsis seeds (Col-0 and the coi1-2 mutant) were germinated and grown on 1/2 MS medium with 1% sucrose at 22°C under a 16-h light/8-h dark photoperiod for 12 d.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The whole leaf explants were harvested and frozen in liquid nitrogen. RNA was extracted using TRIzol.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
rsemv2.all.genes.tpm_coi1.results.txt
|
| Data processing |
Sequencing reads were cleaned with Trim Galore v0.5.0, including removing bases with low quality score (<20) and cutting sequencing adaptors followed by filtering short reads.
For bulk RNA-seq, the paired-end reads of RNA-seq data were mapped to Arabidopsis thaliana genome (TAIR10) using STAR v2.7.2b. Gene abundance was determined using RSEM v1.3.2 . Differentially expressed genes were detected by EBSeq
Supplementary_files_format_and_content: tab-delimited text files include TPM for each gene
|
| |
|
| Submission date |
Mar 20, 2020 |
| Last update date |
Feb 10, 2022 |
| Contact name |
Lin XU |
| E-mail(s) |
xulin01@sibs.ac.cn
|
| Phone |
86-21-54924101
|
| Organization name |
Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences
|
| Department |
Chinese Academy of Sciences
|
| Street address |
300 Fenglin Road
|
| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE147301 |
Time-lapse RNA-seq analysis to study transcriptional regulation by early signals in De Novo Root Regeneration in Arabidopsis |
|
| Relations |
| BioSample |
SAMN14416694 |
| SRA |
SRX7961254 |
