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Next Generation Sequencing Facilitates Quantitative Analysis of ad-control and ad-ube3b cells' Transcriptomes in lymphoma

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of ad-control and ad-ube3b cells' Transcriptomes in lymphoma

PROVIDER: PRJNA523178 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of ad-control and ad-ube3b 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 ad-control and ad-ube3b lymphoma cells by using NGS-derived lymphoma transcriptome profiling (RNA-seq). Methods: Ad-con and Ad-ube3b 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 Ad-con and Ad-ube3b 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.

2020-10-02 | GSE126742 | GEO

Genome-wide maps of chromatin state in Ad-UBE3B and control lymphoma cells

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of RNAPII with promoters in mammalian cells. We performed ChIP sequencing with antibody to total RNAPII in UBE3B overexpression and control group. Inspection of multiple individual traces and global analyses showed that UBE3B overexpression globally reduced association of RNAPII with promoters.

2020-10-10 | GSE143863 | GEO

Genome-wide maps of chromatin state in Ad-ube3b and control lymphoma cells

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of p-RNAPII(ser2) with promoters in mammalian cells. We performed ChIP sequencing with antibody to total p-RNAPII(ser2) in UBE3B overexpression and control group. Inspection of multiple individual traces and global analyses showed that UBE3B overexpression globally reduced association of p-RNAPII(ser2) with promoters.

2020-10-02 | GSE126746 | GEO

Genome-wide maps of chromatin state in ad-ube3b or Pep2-CM4-treated and control lymphoma cells

Project description:We report the application of single-molecule-based sequencing technology for high-throughput profiling of RNAPII with promoters in mammalian cells. We performed ChIP sequencing with antibody to total RNAPII in UBE3B overexpression or Pep2-CM4-treated and control group. Inspection of multiple individual traces and global analyses showed that UBE3B overexpression globally reduced association of RNAPII with promoters.

2020-10-02 | GSE126745 | GEO

Genome-wide maps of chromatin state in Ad-ube3b and control lymphoma cells

Project description:Genome-wide maps of chromatin state in Ad-ube3b and control lymphoma cells

| PRJNA523181 | ENA

Genome-wide maps of chromatin state in Ad-UBE3B and control lymphoma cells

Project description:Genome-wide maps of chromatin state in Ad-UBE3B and control lymphoma cells

| PRJNA601921 | ENA

Genome-wide maps of chromatin state in ad-ube3b or Pep2-CM4-treated and control lymphoma cells

Project description:Genome-wide maps of chromatin state in ad-ube3b or Pep2-CM4-treated and control lymphoma cells

| PRJNA523182 | ENA

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.

2024-04-18 | GSE243346 | GEO

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

| PRJNA481246 | ENA

Next Generation Sequencing Facilitates Quantitative Analysis of control and Pep2-CM4-treated cells' Transcriptomes in lymphoma

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of control and Pep2-CM4-treated cells' Transcriptomes in lymphoma

| PRJNA523179 | ENA

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