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The application of second-generation sequencing in congenital pulmonary airway malformations

ABSTRACT: The application of second-generation sequencing in congenital pulmonary airway malformations

PROVIDER: PRJNA787785 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR17194353_1.fastq.gz	Fastqsanger.gz
	SRR17194353_2.fastq.gz	Fastqsanger.gz
	SRR17194354_1.fastq.gz	Fastqsanger.gz
	SRR17194354_2.fastq.gz	Fastqsanger.gz
	SRR17194355_1.fastq.gz	Fastqsanger.gz

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The application of second-generation sequencing in congenital pulmonary airway malformations

Project description:Objective: To investigate the differential expression of genes in whole transcripts of congenital pulmonary airway malformation (CPAM) using second-generation sequencing (also known as next-generation sequencing, NGS) technology. Methods: Children with CPAM were strictly screened after setting the criteria, and grouped by taking CPAM parietal tissue and CPAM lesion tissue respectively, and RNA-Seq libraries were established separately using second-generation sequencing technology, followed by differential expression analysis and GO (gene ontology) functional enrichment analysis, KEGG pathway analysis and GSEA (Gene Set Enrichment Analysis) analysis. Results: Five cases were screened from 36 children with CPAM, and high-throughput sequencing was performed to obtain 10 whole transcripts of samples with acceptable sequence quality and balanced gene coverage. One aberrantly expressed sample was found by analysis of principal components, which was excluded and then subjected to differential expression analysis, and 860 up-regulated genes and 203 down-regulated genes. GO functional enrichment analysis of differentially expressed genes demonstrates the functional class and cellular localization of target genes. Conclusion: The whole transcript of CPAM shows obvious gene up- and down-regulation, differentially expressed genes are located in specific cells and belong to different functional categories, and NGS can provide an effective means to study the transcriptional regulation of CPAM from the overall transcriptional level.

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Project description:To investigate the differential expression of genes in whole transcripts of congenital pulmonary airway malformation (CPAM) using second-generation sequencing (also known as next-generation sequencing, NGS) technology. Children with CPAM were strictly screened after setting the criteria, and grouped by taking CPAM parietal tissue and CPAM lesion tissue respectively, and RNA-Seq libraries were established separately using second-generation sequencing technology, followed by differential expression analysis and GO (gene ontology) functional enrichment analysis, KEGG (Kyoto encyclopedia of genes and genomes, a database) pathway analysis and GSEA (Gene Set Enrichment Analysis) analysis. Five cases were screened from 36 children with CPAM, and high-throughput sequencing was performed to obtain 10 whole transcripts of samples with acceptable sequence quality and balanced gene coverage. One aberrantly expressed sample (3b) was found by analysis of principal components, which was excluded and then subjected to differential expression analysis, and 860 up-regulated genes and 203 down-regulated genes. GO functional enrichment analysis of differentially expressed genes demonstrates the functional class and cellular localization of target genes. The whole transcript of CPAM shows obvious gene up and down-regulation, differentially expressed genes are located in specific cells and belong to different functional categories, and NGS can provide an effective means to study the transcriptional regulation of CPAM from the overall transcriptional level.

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