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Next generation sequencing analysis of ginseng transcriptomes in response to Botrytis cinerea infection

ABSTRACT: Next generation sequencing analysis of ginseng transcriptomes in response to Botrytis cinerea infection

PROVIDER: PRJNA745147 | ENA |

REPOSITORIES: ENA

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Dataset's files

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			Action	DRS
	SRR15084006_1.fastq.gz	Fastqsanger.gz
	SRR15084006_2.fastq.gz	Fastqsanger.gz
	SRR15084007_1.fastq.gz	Fastqsanger.gz
	SRR15084007_2.fastq.gz	Fastqsanger.gz
	SRR15084008_1.fastq.gz	Fastqsanger.gz

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Next generation sequencing analysis of ginseng transcriptomes in response to Botrytis cinerea △BcSpd1 treatment

Project description:Next generation sequencing (NGS) was performed to identify genes changed in ginseng upon Botrytis cinerea △BcSpd1 treatment. The goal of the work is to find interesting genes involved in ginseng in response to fungi induction. The object is to reveal the molecular mechanism of ginseng defense induced by Botrytis cinerea △BcSpd1 .

2023-12-20 | GSE221931 | GEO

Next generation sequencing analysis of ginseng transcriptomes in response to Botrytis cinerea infection

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Next generation sequencing analysis of ginseng transcriptomes in response to Botrytis cinerea △BcSpd1 treatment

Project description:Next generation sequencing analysis of ginseng transcriptomes in response to Botrytis cinerea △BcSpd1 treatment

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Next Generation Sequencing Facilitates Quantitative Analysis of Cucumber and Botrytis cinerea Transcriptome Changes During Infection

Project description:Purpose: The goals of this study are using RNA-seq to obtain cucumber and Botrytis cinerea transcriptome changes during infection Methods: mRNA profiles of anti-infection samples and interaction sample were generate by deep sequencing,using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: BurrowsâWheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRTâPCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow,In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber (differential expression genes) DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. Conclusions:To the best of our knowledge, this is the first analysis of large-scale transcriptome changes of cucumber during the infection of Botrytis cinerea. These results will increase our understanding of the molecular mechanisms of the cucumber defense Botrytis cinerea and may be used to protect plants against disasters caused by necrotrophic fungal pathogens. mRNA profiles of infection and anti-infection cucumber were generated by deep sequencing, using Illumina Hiseq 2500 .

2016-08-01 | E-GEOD-72191 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Cucumber and Botrytis cinerea Transcriptome Changes During Infection

Project description:Purpose: The goals of this study are using RNA-seq to obtain cucumber and Botrytis cinerea transcriptome changes during infection Methods: mRNA profiles of anti-infection samples and interaction sample were generate by deep sequencing,using Illumina Hiseq 2500. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays Results: Using an optimized data analysis workflow,In total, 248,908,688 raw reads were generated; after removing low-quality reads and those containing adapter and poly-N, 238,341,648 clean reads remained to map the reference genome. There were 3,512 cucumber (differential expression genes) DEGs and 1,735 B. cinerea DEGs. GO enrichment and KEGG enrichment analysis were performed on these DEGs to study the interaction between cucumber and B. cinerea. To verify the reliability and accuracy of our transcriptome data, 5 cucumber DEGs and 5 B. cinerea DEGs were chosen for RT-PCR verification. Conclusions:To the best of our knowledge, this is the first analysis of large-scale transcriptome changes of cucumber during the infection of Botrytis cinerea. These results will increase our understanding of the molecular mechanisms of the cucumber defense Botrytis cinerea and may be used to protect plants against disasters caused by necrotrophic fungal pathogens.

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Whole Genome Bisulfite Sequencing of Botrytis cinerea

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Next-generation sequencing analysis of ginseng transcriptomes in response to Colletotrichum panacicola infection

Project description:Next-generation sequencing (NGS) was performed to identify genes changed in ginseng upon Colletotrichum panacicola infection. The goal of the work is to find interesting genes involved in ginseng in response to fungi induction. The object is to reveal the molecular mechanism of ginseng disease development caused by Colletotrichum panacicola.

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