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Next-generation sequencing facilitates quantitative analysis of CON and PMB treatment HepG2 cells transcriptomes

ABSTRACT: Next-generation sequencing facilitates quantitative analysis of CON and PMB treatment HepG2 cells transcriptomes

PROVIDER: PRJNA856662 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR20020465_1.fastq.gz	Fastqsanger.gz
	SRR20020465_2.fastq.gz	Fastqsanger.gz
	SRR20020466_1.fastq.gz	Fastqsanger.gz
	SRR20020466_2.fastq.gz	Fastqsanger.gz
	SRR20020467_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of CON and PMB treatment HepG2 cells Transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analysis the differiational genes and pathways in CON and PMB treatment cells by using RNA-seq Methods: CON and PMB treatment cells mRNA profiles were generated by deep sequencing, using Illumina Novaseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 , IGV was used to to view the mapping result by the Heatmap, histogram, scatter plot or other stytle, FPKM was then calculated to estimate the expression level of genes in each sample, EdgeR software was used for differential gene expression analysis and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents detailed analysis of CON and PMB cells transcriptomes, with biologic replicates, 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 or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2023-08-11 | GSE185840 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of CON and PMB treatment HepG2 cells Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of CON and PMB treatment HepG2 cells Transcriptomes

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Next-generation sequencing facilitates quantitative analysis of CON and PMB treatment HepG2 cells transcriptomes

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to analyse the differential genes and pathways in CTRL and PMB treatment cells by using RNA-seq. Methods: CTRL and PMB treatment cells mRNA profiles were generated by deep sequencing, using Illumina Novaseq. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2, IGV was used to view the mapping result by the Heatmap, histogram, scatter plot or other style, FPKM was then calculated to estimate the expression level of genes in each sample, EdgeR software was used for differential gene expression analysis and Function Enrichment Analysis including GO enrichment analysis and KEGG. Conclusions: Our study represents detailed analysis of CTRL and PMB cells transcriptomes, with biologic replicates, 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 or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.

2023-08-11 | GSE207670 | GEO

Next-generation sequencing facilitates quantitative analysis of CON and PMB treated HepG2 cells and CreAlbMYC and CreAlbScarb2F/FMYC mice liver transcriptomes, and CUT&Tag analysis genome-wide maps of chromatin state in CTRLcas9 and SCARB2cas9 HepG2 cells

Project description:Next-generation sequencing facilitates quantitative analysis of CON and PMB treated HepG2 cells and CreAlbMYC and CreAlbScarb2F/FMYC mice liver transcriptomes, and CUT&Tag analysis genome-wide maps of chromatin state in CTRLcas9 and SCARB2cas9 HepG2 cells

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Project description:Purpose: Using RNA-seq to analyze the different expressions induced by IFNα among the SETD2-KO HepG2 cells, STAT1-KO HepG2 cells and STAT1-K525A-Re HepG2 cells and HepG2 control cells Methods: mRNA profiles of HepG2 control cells and SETD2-KO cells, STAT1-KO cells, STAT1-K525A-Re cells were generated by deep sequencing, using BGISEQ-500RS. The sequence reads that passed quality filters were analyzed at the transcriptional level with RSEM (RNA-seq by Expectation Maximization).

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p53-dependent transcription program in HepG2 cells

Project description:In order to obtain a global picture regarding regulation of p53 in liver cells we used HepG2 hepatoma cells.We created two isogenic sub-cultures of HepG2 cells with altered expression of p53. HepG2 cells were infected with a retroviral vector harboring either small-hairpin RNA targeting p53 (termed HepG2sh-p53) or a non relevant small-hairpin RNA (termed HepG2sh-con). Cells were treated with two different p53 stimulators - Nutlin and AICAR

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