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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ZNFX1-overexpresed A549 Cells Transcriptomes

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ZNFX1-overexpresed A549 Cells Transcriptomes

PROVIDER: PRJNA549405 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR9317855_1.fastq.gz	Fastqsanger.gz
	SRR9317855_2.fastq.gz	Fastqsanger.gz
	SRR9317856_1.fastq.gz	Fastqsanger.gz
	SRR9317856_2.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and ZNFX1-overexpresed A549 Cells Transcriptomes

Project description:Analysis of the pathways among genes significantly up-regulated or down-regulated between ZNFX1 overexpressed cells and wild-type A549 cells.

2019-08-30 | GSE132890 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Genes expression profiles in ZNFX1 overexpression in Rig-I-/- cells with or without poly I:C stimulation

Project description:Genes expression profiles in ZNFX1 overexpression in Rig-I-/- cells with or without poly I:C stimulation in A549 cells.

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Next Generation Sequencing Facilitates Quantitative Analysis of A549 Control and A549 infected with Zika virus Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of A549 Control and A549 infected with Zika virus Transcriptomes

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Next Generation Sequencing Facilitates Quantitative Analysis of A549 Control and A549 infected with Zika virus Transcriptomes

Project description:Purpose:The goals of this study to compare NGS-derived transcriptome profiling (RNA-seq) to examine differentially expressed genes berween A549 infected with Zika virus and A549 Control . Methods: A549 cells mRNA profiles of A549 cells-infected with Zika virus and aun-infected A549 cells were generated by deep sequencing, in triplicate, using Illumina Hiseq4000. The mapped reads of each sample were assembled by StringTie (v1.3.1) (Mihaela Pertea.et al. 2016) in a reference-based approach. StringTie uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Results: Using an optimized data analysis workflow, we mapped about identified 11124 transcripts in the A549 cells of control and Zika virus with Cuffcompare workflow. RNA-seq data confirmed stable expression of 20 known housekeeping genes, and 10 of these were validated with qRT–PCR. Approximately 10% of the transcripts showed differential expression between the control and DV, with a fold change >1 and p value <0.05. Altered expression of 25 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 A549 cells transcriptomes, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2020-03-06 | GSE146423 | GEO

UV-RIP experiments of ZNFX1 in VSV infected A549 cells

Project description:UV-RIP experiments of ZNFX1 in VSV infected A549 cells

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Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum bud and flower Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum bud and flower Transcriptomes

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UV-RIP experiments of ZNFX1 in VSV infected A549 cells

Project description:UV-RIP-seq was used to identify VSV-RNA associated with endogenous ZNFX1 in VSV infected A459 cells.

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