|
| Status |
Public on Aug 31, 2020 |
| Title |
Col_systemic_8min_3 |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis leaves
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
repeat: 3
time: 8min
treatment: No treatment
genotype: wild type
tissue: Leaves
molecule: total RNA
|
| Growth protocol |
4-week-old plants grown on soil; 10hr/14hr light/dark regime; 21-24C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
leaves were flash frozen in liquid nitrogen; frozen samples were ground and RNA was extracted using Qiagen Plant Rneasy kit (Cat#74904)
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 |
Col systemic
|
| Data processing |
Base calling was done with RTA3 implemeation software in the NovaSeq 6000 system
3' trimming for Illumina adapters was performed using cutadapt v1.18
Quality control of reads were performed using FastQC v0.11.7
RNA-seq reads were aligned to Arabidopsis thaliana genome obtained from TAIR using STAR aligner v2.4.0.1
Differential gene expression analysis was performed using DeSeq2 v1.20.0
Genome_build: TAIR 10
Supplementary_files_format_and_content: tab-deliminated files included mean normalized counts for each sample
|
| |
|
| Submission date |
Dec 12, 2019 |
| Last update date |
Aug 31, 2020 |
| Contact name |
Soham Sengupta |
| Organization name |
St. Jude Children's Research Hospital
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE141916 |
MYB30 orchestras ROS wave-triggered systemic transcriptomic responses and plant acclimation in Arabidopsis |
|
| Relations |
| BioSample |
SAMN13547224 |
| SRA |
SRX7354446 |
