|
| Status |
Public on May 08, 2024 |
| Title |
Cannabis sativa L. Leaf, Drought stress, R3 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Cannabis sativa |
| Characteristics |
tissue: Leaf
genotype: Cannabis sativa L. Pink pepper
treatment: Drought stress
|
| Treatment protocol |
Drought stress groups were treated by stopping irrigation for 10 days before sampling.
Trichoderma hamatum HSKNU treatment group was treated directly in the soil rhizosphere with 5×10^7 onidia/kg (spore count/soil weight) 13 days before sampling.
Drought stress with Trichoderma hamatum The HSKNU treatment group consisted of a mixture of protocol 1 and protocol 2.
|
| Growth protocol |
The Cannabis sativa L. seeds were soaked in a 1% hydrogen peroxide soution for 12 hours. Then, they were planted in a 105-well seedling tray (42 mL per well) and grown for 14 days under controlled conditions of 25±2°C temperature and 43±7% relative humidity. After this period, the plants were transferred to large pots (8.5 L) and allowed to grow and adapt for an additional 30 days.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy Micro Kit. (Qiagen, Hilden, Germany)
Libraries were prepared using the TruSeq standard mRNA. (Illumina Inc., San Diego, CA, USA)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The transcriptome analysis was conducted in the computational and server-sharing platform, Galaxy.
The generated reads were trimmed to remove adapter sequences and abnormally short reads using Cutadapt (version 4.4) with a minimum length setting of 20 and a quality cutoff of 20.
The trimmed reads were mapped using RNASTAR. (version 2.7.10b; length of the genomic sequence around annotated junctions: read length -1)
DEG analysis was conducted using DESeq2. (version 2.11.40.8)
Assembly: Cannabis sativa L. RefSeq genome (RefSeq: GCF_029168945.1)
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.
Supplementary files format and content: tab-delimited text files include DESeq2 Normalized Count for each Sample. (Input: All samples, header=T)
|
| |
|
| Submission date |
May 07, 2024 |
| Last update date |
May 08, 2024 |
| Contact name |
Byeong-Ryeol Ryu |
| E-mail(s) |
byeongryeol.ryu@csupueblo.edu
|
| Phone |
001-719-557-2463
|
| Organization name |
Kangwon National Univsersity
|
| Department |
Department of Bio-Health Convergence
|
| Street address |
1, Kangwondaehak-gil
|
| City |
Chuncheon-si |
| State/province |
Gangwon-state |
| ZIP/Postal code |
24341 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL34455 |
| Series (1) |
| GSE266916 |
Transcriptomic Responses of Cannabis sativa L. to Trichoderma hamatum Treated under Drought Conditions |
|
| Relations |
| BioSample |
SAMN41256087 |
| SRA |
SRX24485625 |
