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RNA-Seq analysis of Arabidopsis thaliana splicing factor AtU2AF65a and AtU2AF65b against the wild type (Col).

ABSTRACT: RNA-Seq analysis of Arabidopsis thaliana splicing factor AtU2AF65a and AtU2AF65b against the wild type (Col).

PROVIDER: PRJEB60004 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR10903220.fastq.gz	Fastqsanger.gz
	ERR10903220_1.fastq.gz	Fastqsanger.gz
	ERR10903220_2.fastq.gz	Fastqsanger.gz
	ERR10903221.fastq.gz	Fastqsanger.gz
	ERR10903221_1.fastq.gz	Fastqsanger.gz

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RNA-Seq analysis of Arabidopsis splicing factor U2AF65 against the wild type (Col).

Project description:RNA-Seq analysis of Arabidopsis splicing factor U2AF65 against the wild type (Col).

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RNA-Seq analysis of Arabidopsis thaliana splicing factor AtU2AF65a and AtU2AF65b against the wild type (Col).

Project description:Two Arabidopsis thaliana splicing factor [AtU2AF65 isoforms (AtU2AF65a and AtU2AF65b)] mutants displayed the opposite flowering phenotypes. To assay the RNA processing including alternative splicing and pre-mRNA splicing of target genes of this protein in Arabidopsis, the 7-day seedlings (shoot apices) of wild type atu2af65a and atu2af65b mutants were used for RNA-Seq.

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RNA-Seq analysis of Arabidopsis splicing factor U2AF65 against the wild type (Col).

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Project description:RNA-Seq analysis of Arabidopsis splicing factor U2AF65 against the wild type (Col).

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SPLICING FACTOR FOR PHYTOCHROME SIGNALING promotes photomorphogenesis by regulating alternative splicing in Arabidopsis

Project description:Purpose: The goals of this study are to compare the transcriptome profiling and alternative splicing (AS) profiling between Col-0 wild type and SFPS knockout mutant (sfps-2) through RNA-seq to determine the molecular mechanisms of how splicing factor SFPS regulates photomorphogenesis in Arabidopsis. Results: Using an optimized data analysis workflow, we mapped about 100 million sequence reads per sample to the Arabidopsis genome (TAIR10) and identified 1495 differentially expressed genes between Col-0 and mutant dark samples; 1361 differentially expressed genes between Col-0 and mutant red light treated samples; 4291 differentially expressed genes between Col-0 dark and red light treated samples; and 4479 differentially expressed genes between mutant dark and red light treated samples. Except for gene expression, we also discovered 788 differentially spliced bins between Col-0 and mutant dark samples; 827 differentially spliced bins between Col-0 and mutant red light treated samples; 610 differentially spliced bins between Col-0 dark and red light treated samples; and 405 differentially spliced bins between mutant dark and red light treated samples. Altered splicing of 9 genes was confirmed with qRT-PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Conclusions: Our study represents the first detailed analysis of SFPS mutant transcriptomes, with biologic replicates, generated by RNA-seq technology. Our results show that SFPS regulates photomorphogenesis in Arabidopisis through regulating the splicing activity of light signaling genes, which helps us.

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