|
| Status |
Public on Aug 11, 2020 |
| Title |
TT2_1 (Drought-stressed) |
| Sample type |
SRA |
| |
|
| Source name |
Leaf of cultivar Crimson Sweet
|
| Organism |
Citrullus lanatus |
| Characteristics |
protocol: 7 hours after initiation of salt stress
stress: Drought-stressed
|
| Growth protocol |
Seedlings of the cv. Crimson Sweet were grown in a non-nutrient sandy/stone soil (Quick Dry Infield Conditioner, Turface Atheletics™, USA) were used for salt stress study. Six-week-old seedlings with three fully expanded leaves were subjected to salinity stress. The seedlings with four replicates for each treatment were carefully lifted out from the media, washed under running water and were incubated in 50mL Conical-Bottom tubes (1) 300 mM NaCl (2) MilliQ water After 7 hours of exposure to salt stress, leaf tissue samples were collected from seedlings each with 3 replicates for both treatment and flash-frozen by liquid nitrogen before storing at -80℃ for further processing.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The flash-frozen leaf samples from three independent plants along with control (well-irrigated) plants were used for RNA-Seq analysis. Total RNA was extracted using a Quick-RNA™ Miniprep Kit (Zymo Research Corporation, Irvine, CA ) as per the manufacturer’s protocol and treated with DNase1 (Zymo Research Corporation, Irvine, CA ).
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 |
Treatment
|
| Data processing |
Illumina Novaseq 6000 used for sequencing
Sequenced reads were trimmed for adaptor sequence by fastp, and masked for low-complexity or low-quality sequence, then mapped to Citrullus_lanatus whole genome using hisat2-2.1.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated from mapped read by featureCounts
Differeantial expression analysis with DEseq2
Genome_build: Citrullus_lanatus _WCG_V2
Supplementary_files_format_and_content: Tab-delimited text files include RPKM values for each Sample, and differential expressed gene for each comparasion
|
| |
|
| Submission date |
Feb 28, 2020 |
| Last update date |
Aug 11, 2020 |
| Contact name |
Vijay Joshi |
| E-mail(s) |
[email protected]
|
| Phone |
8302789151
|
| Organization name |
Texas A&M AgriLife Research
|
| Department |
Department of Horticultural Sciences
|
| Street address |
1619 Garner Field Road
|
| City |
Uvalde |
| State/province |
Texas |
| ZIP/Postal code |
78801 |
| Country |
USA |
| |
|
| Platform ID |
GPL28123 |
| Series (1) |
| GSE146087 |
RNA-Sequencing of salt-stressed watermelon seedlings |
|
| Relations |
| BioSample |
SAMN14239885 |
| SRA |
SRX7816639 |
