The landscape of abiotic and biotic stress-responsive splice variants using RNA-seq datasets in hot pepper

Name: The landscape of abiotic and biotic stress-responsive splice variants using RNA-seq datasets in hot pepper
Creator: figshare
Published: 2023-09-06 06:53:28
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DataCite Commons2023-09-06 更新2024-08-18 收录

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https://figshare.com/articles/dataset/The_landscape_of_abiotic_and_biotic_stress-responsive_splice_variants_using_deep_RNA-seq_datasets_in_em_Capsicum_annuum_em_/23671647/3

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1.Supplementary table 1.xlsx: Supplementary Table 1. Overview of the pepper transcriptomes used in this study 2.Supplementary figure.zip: Supplementary Figure 1. Quality assessment of raw read preprocessing on 129 raw RNA-seq datasets from C. annuum infected with P. capsici, TMV-P2, Xag8ra, and Xcv. (a-d) Quality scores of reads for P. capsici, TMV-P2, Xag8ra, and Xcv, respectively. X-axis represents mean sequence quality (Phred score) and y-axis represents read counts.. (e-h) Graphs for quality scores per position. The x-axis represents the position (bp), and the y-axis Phred score.: Supplementary Figure 2. Principal components analysis (PCA) for RNA-seq datasets infected with biotic stressors in hot pepper. PCA plots with normalized data of (a) P. capsici; (b) TMV-P2; (c) Xag8ra; (d) Xcv1; (e) Xcv3.: Supplementary Figure 3. Proportion of alternative splicing events detected in hot pepper under different conditions. The stacked bar plot indicates the number of alternative splicing events in response to biotic and abiotic stressors, developmental stages, and phytohormones. Blue, exon skipping (SE); yellow, intron retention (RI); light grey, mutually exclusive exons (MXE); green, alternative 5’ splice site (A5SS); pink, alternative 3’ splice site (A3SS). 3.Information of AS events results.7z: AS events information under environmental stressors, developmental stages, and phytohormones 4.Supplementary File 1.xlsx: Gene list of shared DAS genes under different conditions.Sheet 1 (Abio&Biotic&Tissue&Phytohormone): Gene list of shard DAS genes under abiotic, biotic stressors, developmental stages, and phytohormonesSheet 2 (Abiotic&Biotic&Tissue): Gene list of shard DAS genes under abiotic, biotic stressors, and developmental stagesSheet3 (Abiotic&Tissue): Gene list of shard DAS genes under abiotic stressors and developmental stagesSheet4 (Biotic&Tissue): Gene list of shard DAS genes under biotic stressors and developmental stages 5.Code availability. zip: 1. Annotated gene_filtering.pl - Filtering code of transcripts containing two or more annotated genes: 2. Stop codon_filtering.pl - Filtering code of transcripts that didn't have a stop codon: 3. AS_counting code.pl - code for counting the number of AS: 4. DAS_gene_counting code.pl - code for counting the DAS genes

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figshare

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2023-09-06