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Next Generation Sequencing Analysis of the Transcriptomes of Wild Type and ALKBH5-/- Peritoneal Macrophages

ABSTRACT: Next Generation Sequencing Analysis of the Transcriptomes of Wild Type and ALKBH5-/- Peritoneal Macrophages

PROVIDER: PRJNA525150 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8655520_1.fastq.gz	Fastqsanger.gz
	SRR8655520_2.fastq.gz	Fastqsanger.gz
	SRR8655521_1.fastq.gz	Fastqsanger.gz
	SRR8655521_2.fastq.gz	Fastqsanger.gz
	SRR8655522_1.fastq.gz	Fastqsanger.gz

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Next Generation Sequencing Analysis of the Transcriptomes of Wild Type and ALKBH5-/- Peritoneal Macrophages

Project description:By performing RNA sequencing (RNA-seq) analysis on the peritoneal macrophages that derived from ALKBH5-/- mice and littermate mice infected with or without vesicular stomatitis virus (VSV), we want to investigate whether deficiency of ALKBH5 controls viral replication through a more general mechanism such as enhancing innate response, and if not, what's the critical downstream target(s) of ALKBH5. RNA-seq analysis showed that mRNA expression of innate genes remained unchanged or not increased in ALKBH5-deficient cells. While thourgh KEGG pathway enrichment analysis of the RNA-seq data, we found that metabolic pathways were the ones most significantly affected in ALKBH5-deficient macrophages upon VSV infection. These results demonstrated that deficiency of ALKBH5 controls viral replication by significantly changing the metabolism-related genes expression.

2019-08-22 | GSE127739 | GEO

Transcriptome-wide m6A Methylation Profiling of Wild Type and ALKBH5-/- Peritoneal Macrophages by m6A-seq

Project description:By performing m6A-seq analysis on the peritoneal macrophages that derived from ALKBH5-/- mice and littermate mice infected with or without vesicular stomatitis virus (VSV), we want to investigate whether ALKBH5 deficiency-mediated m6A RNA methylation contributes to the regulation of its target genes expression. m6A-seq analysis revealed enriched and specific m6A peaks on the transcript of ALKBH5-targeted gene, which were substantially increased in ALKBH5-deficient peritoneal macrophages than that in wild-type cells whatever infected with or without VSV. Meanwhile we didn’t observe up-regulation of m6A signal on VSV in ALKBH5-deficient cells; and also didn't find significant difference of m6A signals on IFN-β mRNA between ALKBH5-deficient and wild type cells whatever infected with or without VSV. These demonstrated that deficiency of ALKBH5 controls viral replication by increasing the m6A modification of ALKBH5 target gene to regulate its expression.

2019-08-22 | GSE127732 | GEO

Next Generation Sequencing and Analysis of the Transcriptomes of Wild-type and Alkbh5-/- Neutrophils

Project description:By performing transcriptome-wide RNA sequencing (RNA-seq) analysis on the peritoneal neutrophils from Alkbh5-deficient mice (Alkbh5-/-) and Wild-type littermates (Alkbh5+/+) at 12h or 36h after mild cecal ligation and puncture (CLP), respectively, we want to identify potential targets of ALKBH5 and characterize the transcriptional landscape in neutrophils during antibacterial innate defense. Gene Ontology biological processes enrichment analysis of the significantly differentially expressed genes (DEGs) showed that neutrophil migration made up the most significantly enriched biological processes with annotations of neutrophil association upon loss of ALKBH5 in neutrophils, at both 12h and 36h after CLP. Many significantly DEGs also encompassed transcriptional signatures related to neutrophils, specifically to neutrophil influx into the infection site, including chemotaxis, response to chemokine, extravasation, ERK1 and ERK2 cascade, homeostasis of neutrophils. ALKBH5 deletion led to significantly decreased transcript expression of neutrophil migration-promoting Cxcr2 and Nlrp12; while increased transcript expression of neutrophil migration-suppressive Ptger4, Tnc, and Wnk1. These results demonstrated that ALKBH5 imprints migration-promoting transcriptional landscape in neutrophils to enable their migration into the site of infection for antibacterial innate defense.

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Next Generation Sequencing of Wild Type and RXRa-/- peritoneal cavity macrophages

Project description:Next Generation Sequencing of Wild Type and RXRa-/- peritoneal cavity macrophages

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Next Generation Sequencing of Wild Type and RXRa-/- peritoneal cavity macrophages

Project description:The goal of this study is to compare the transcriptome profile (RNA-seq) of peritoneal cavity macrophages of RXRa-deficient and WT mice to identify genes which are controlled by the expression of the TF RXRa

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Next Generation Sequencing Facilitates Quantitative Analysis of Peritoneal Macrophage Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Peritoneal Macrophage Transcriptomes

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Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kdm2b-/- Peritoneal Macrophage Transcriptomes

Project description:Purpose: The purpose of this study is to detect activated or silenced genes during Kdm2b-deficient peritoneal macrophages and the control cells. Gene expression differences between two samples could be found using transcriptome profiling (RNA-seq) analysis. Methods: Mouse peritoneal macrophages were harvested from mice 4 days after thioglycollate (BD, Sparks, MD) injection. Macrophages RNA profiles were generated by deep sequencing, using Illumina. Results: We mapped about 10 million sequence reads per sample to the mouse genome, identified hundreds of genes with significant mRNA variation between Kdm2b-deficient macrophages and the control cells.

2019-12-31 | GSE120651 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Vehicle or R-2-HG Treating Mouse Peritoneal Macrophages Transcriptomes

Project description:Purpose: The goals of this study are to screen differentially expressed genes in mouse peritoneal macrophages treated by vehicle or R-2-HG and to explore potential mechanisms of how R-2-HG regulating the process of macrophage activation. Methods: After RNA extraction, purification, and library construction, the samples were paired-end (PE) sequenced by Next-Generation Sequencing using an Illumina sequencing platform (Illumina HiSeq 2500). After sequencing, the filtered high-quality sequences (Clean Data) filtered from the original raw data were mapped to the Mus_musculus GRCm38.p4 (mm10) genome. Based on the mapped results, the expression level of each gene was calculated, and the samples of the different groups were subjected to further analysis for differences in expression, enrichment, and cluster analysis. Results: The mRNA expression levels of only a few genes were changed after R-2-HG treatment in mouse peritoneal macrophages, but HIF1A was not included. Conclusions:Regulating the macrophage activation by R-2-HG may not be due to its effect on gene transcription, and R-2-HG doses not affect the mRNA expression of HIF1A.

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Next Generation Sequencing and Analysis of the Transcriptomes of Wild-type and Alkbh5-/- Neutrophils

Project description:Next Generation Sequencing and Analysis of the Transcriptomes of Wild-type and Alkbh5-/- Neutrophils

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Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kdm2b-/- Peritoneal Macrophage Transcriptomes

Project description:Next-Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kdm2b-/- Peritoneal Macrophage Transcriptomes

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