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Sample GSM8256468 Query DataSets for GSM8256468
Status Public on May 08, 2024
Title Cannabis sativa L. Leaf, Drought stress, R2
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 SAMN41256088
SRA SRX24485624

Supplementary file Size Download File type/resource
GSM8256468_RNASTAR_raw_count_file_DRT2.txt.gz 139.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA

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