|
| Status |
Public on Dec 31, 2020 |
| Title |
WD54_Ch_Water deficit (WD) |
| Sample type |
SRA |
| |
|
| Source name |
Glycine max leaves
|
| Organism |
Glycine max |
| Characteristics |
treatment: Water deficit
genotype: Wild type
tissue: Leaves
cultivar: Magellan, PI595362
|
| Treatment protocol |
Soybean plants were subjected to drought, heat or a combination of drought and heat stress
|
| Growth protocol |
Soybean plants were grown under control conditions and watered 3 times a week in growth chambers
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Plant RNeasy kit (Qiagen, Hilden, Germany) according to the manufacturer's instructions.
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 |
sample name in processed data file:
WD54_Ch
|
| 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: Glycine_max_v2.1
Supplementary_files_format_and_content: tab-deliminated files included mean normalized counts for each sample
|
| |
|
| Submission date |
Jul 07, 2020 |
| Last update date |
Dec 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 |
GPL28801 |
| Series (1) |
| GSE153951 |
Combination of drought and heat in soybean plants |
|
| Relations |
| BioSample |
SAMN15464737 |
| SRA |
SRX8680411 |
