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Next Generation Sequencing Facilitates Quantitative Analysis of EL4+Ctrl and EL4+RGFP966 cells' Transcriptomes in T cells lymphoma

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of EL4+Ctrl and EL4+RGFP966 cells' Transcriptomes in T cells lymphoma

PROVIDER: PRJNA1017862 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR26071833_1.fastq.gz	Fastqsanger.gz
	SRR26071833_2.fastq.gz	Fastqsanger.gz
	SRR26071834_1.fastq.gz	Fastqsanger.gz
	SRR26071834_2.fastq.gz	Fastqsanger.gz
	SRR26071835_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Facilitates Quantitative Analysis of EL4+Ctrl and EL4+RGFP966 cells' Transcriptomes in T cells lymphoma

Project description:We here reported that HDAC3 inhibition induces the infiltration of NK cells in lymphoma and enhances their cytotoxicity by promoting the secretion of CXCL12 from lymphoma cells. RNA-seq analysis of EL4 cells treated with or without RGFP966 showed that chemokine signaling was significantly enriched in the HDAC3 inhibitor-treated group. And the expression of CXCL12 in mRNA and protein level were increased. ATF3 overexpression decreased the mRNA level of CXCL12 in lymphoma cells and reduced CXCL12 transcription can be reversed by HDAC3 inhibition in H9 cells. To sum up, targeting HDAC3 promoted the secretion of CXCL12 by inhibiting ATF3’s transcriptional activity.

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Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' Transcriptomes in lymphoma

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' Transcriptomes in lymphoma

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Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-Cas9 and TRIB3-Cas9 cells' Transcriptomes in lymphoma

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 Ctrl-Cas9 and TRIB3-Cas9 lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: Ctrl-Cas9 and TRIB3-Cas9 cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, 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, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of Ctrl-Cas9 and TRIB3-Cas9 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.

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Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

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 Ctrl-siRNA and c-Myc-siRNA lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: Ctrl-siRNA and c-Myc-siRNA cells' mRNA profiles were generated by deep sequencing, in triplicate, using Illumina HiSeq 4000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with following methods: Alignment by using HISAT2 v2.1, 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, DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates and Function Enrichment Analysis including GO enrichment analysis and KEGG . Conclusions: Our study represents the first detailed analysis of Ctrl-siRNA and c-Myc-siRNA 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.

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Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Ctrl-siRNA and c-Myc-siRNA cells' Transcriptomes in lymphoma

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Gene expression changes following demethylation by 5-aza-2'-deoxycytidine（decitabine, DAC）in mouse T cell lymphoma EL4 cells

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