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Series GSE240234 Query DataSets for GSE240234
Status Public on Aug 07, 2023
Title The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper
Organism Capsicum annuum
Experiment type Expression profiling by high throughput sequencing
Summary Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA-seq datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. We report RNA-seq datasets (350.7 Gb) from Capsicum annuum inoculated with one of three bacteria, one virus, or one oomycete and obtained additional existing transcriptome datasets. In this study, we investigated the landscape of AS in response to environmental stressors, signaling molecules, and tissues from 425 total samples comprising 841.49 Gb. In addition, we identified genes that undergo AS under specific and shared stress conditions to obtain potential genes that may be involved in enhancing tolerance to stressors. We uncovered 1,642,007 AS events and identified 4,354 differential alternative splicing (DAS) genes related to environmental stressors, tissues, and signaling molecules. This information and approach provide useful data for basic-research focused on enhancing tolerance to environmental stressors in hot pepper or establishing breeding programs.
 
Overall design The normalization criteria of RNA-seq sets for different pathogens were performed identically to study the resistance response of pepper and to minimize bias in the analysis.
 
Contributor(s) Kim N, Lee J, Yeom S
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BioProject PRJNA223222
Submission date Aug 07, 2023
Last update date Feb 06, 2024
Contact name Seon-In Yeom
E-mail(s) sunin78@gnu.ac.kr
Organization name Gyeongsang National University
Street address 501, Jinjou-daero
City Jinju
ZIP/Postal code 52828
Country South Korea
 
Platforms (3)
GPL16195 Illumina HiSeq 2000 (Capsicum annuum)
GPL26789 Illumina HiSeq 2500 (Capsicum annuum)
GPL33654 HiSeq X Ten (Capsicum annuum)
Samples (219)
GSM7688547 Bukang0-1
GSM7688548 Bukang0-3
GSM7688549 Xag8ra_Mock_1h-1

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE240234_Response_of_peppers_to_abiotic_stress_by_treatment_with_8_pathogens.txt.gz 26.7 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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