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Characterization of three CpG ODN classes in B cells

ABSTRACT: Characterization of three CpG ODN classes in B cells

PROVIDER: PRJNA597990 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10799686.fastq.gz	Fastqsanger.gz
	SRR10799687.fastq.gz	Fastqsanger.gz
	SRR10799688.fastq.gz	Fastqsanger.gz
	SRR10799689.fastq.gz	Fastqsanger.gz
	SRR10799690.fastq.gz	Fastqsanger.gz

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Characterization of three CpG ODN classes in plasmacytoid dendritic cells (pDCs)

Project description:Characterization of three CpG ODN classes in plasmacytoid dendritic cells (pDCs)

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Characterization of three CpG ODN classes in plasmacytoid dendritic cells and B cells

Project description:Characterization of three CpG ODN classes in plasmacytoid dendritic cells and B cells

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Characterization of three CpG ODN classes in B cells

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare distinct immunostimulatory activities of three classes of CpG ODNs in B cells using RNA-seq. mRNA profiles of murine B cells induced by three classes of CpG ODNs were generated by RNA-Seq studies. Methods: mRNA profiles of murine B cells induced by three classes of CpG ODNs were generated by deep sequencing, in triplicate, using BGISEQ. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: HISAT based on Burrows-Wheeler transform and Ferragina-Manzini and Bowtie2 followed by RSEM. Results: Using an optimized data analysis workflow, we mapped > 60 million total clean reads per sample to the mouse genome (build mm10), with a clean reads Q20 score >97% and a mapping rate to the reference genome of each sample varying from 89.33% to 93.29%. The Pearson correlation coefficient between each sample revealed that the all samples had a high correlation. In particular, CpG-B and CpG-C have the highest correlation. A total of 28,020 genes were detected as being expressed. More than 10,000 genes were downregulated and 1,000 genes were upregulated in CpG ODNs stimulated groups relative to control group, with a fold change ≥ 2 and Q value <0.001. In addition, only 91 genes were upregulated and 99 genes were downregulated in CpG-C group relative to CpG-B group. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes uncovered several genes that may contribute to characterize the features of three classes of CpG ODNs in B cells. Conclusions: Our study represents the first detailed analysis of B-cell transcriptomes stimulated with three classes of CpG ODNs, with biological replicates, generated by RNA-seq technology.

2022-12-24 | GSE142689 | GEO

Characterization of three CpG ODN classes in plasmacytoid dendritic cells (pDCs)

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare distinct immunostimulatory activities of three classes of CpG ODNs in pDCs using RNA-seq. mRNA profiles of murine pDCs induced by three classes of CpG ODNs were generated by RNA-Seq studies. Methods: mRNA profiles of murine pDCs induced by three classes of CpG ODNs were generated by deep sequencing, in triplicate, using Illumina Hiseq Xten. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: HISAT based on Burrows-Wheeler transform and Ferragina-Manzini and Bowtie2 followed by RSEM. Results: Using an optimized data analysis workflow, we mapped > 60 million total clean reads per sample to the mouse genome (build mm10), with a clean reads Q20 score > 98.58% and a mapping rate to the reference genome of each sample varying from 92.3% to 96.56%. The Pearson correlation coefficient between each sample revealed that CpG-A and CpG-C have the highest correlation. A total of 21,573 genes were detected as being expressed. More than 5,000 genes were downregulated and 2,000 genes were upregulated in CpG ODNs stimulated groups relative to control group, with a fold change ≥ 2 and Q value <0.001. Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of differentially expressed genes uncovered several genes that may contribute to characterize the features of three classes of CpG ODNs in pDCs. Conclusions: Our study represents the first detailed analysis of pDC transcriptomes stimulated with three classes of CpG ODNs, with biological replicates, generated by RNA-seq technology.

2022-12-24 | GSE142688 | GEO

Gene expression profile of IGROV1 cells after in vitro treatment with CpG-ODN

2011-04-01 | GSE23442 | GEO

Transcription profiling of Bos taurus CD14+ purified bovine monoctye stimulation with CpG ODN 2007 vs. GpC ODN 2007, CpG 2007 vs. Control, GpC 2007 vs. Control and Media vs Control (

Project description:CD14+ purified bovine monoctye stimulation with CpG ODN 2007 vs. GpC ODN 2007, CpG 2007 vs. Control, GpC 2007 vs. Control and Media vs Control (Control is unstimluated CD14+ purified bovine monocytes at time zero). Before stimulation, the CD14+ purified bovine monocytes were rested for 20 h. Then the cells were stimulated for 4hrs.

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Gene expression profile of IGROV1 cells after treatment of saline or CpG-ODN

Project description:This SuperSeries is composed of the following subset Series: GSE23440: Gene expression profiling of IGROV1 cells after in vitro treatment with ascitic fluid from human ovarian cancer bearing mice GSE23441: IGROV1 gene expression analysis after in vivo locoregional treatment with CpG-ODN GSE23442: Gene expression profile of IGROV1 cells after in vitro treatment with CpG-ODN Refer to individual Series

2011-04-01 | E-GEOD-23491 | biostudies-arrayexpress

An integrated transcriptomics and metabolomics study of the immune response of newly hatched chicks to the CpG-ODN stimulation

Project description:This study aims at identifying a dual transcriptomics and metabolomics blood signature following administration of CpG-ODN (cytosine-phosphate-guanine oligodeoxynucleotides), a reference immune-stimulatory molecule. A clinical study was conducted with chicks and transcriptomics and metabolomics analyses were performed on whole-blood and plasma samples respectively. Statistical analyses resulting in lists of differentially expressed genes and metabolites with different abundance were identified in chicks treated with CpG-ODN. The results showed that CpG-ODN activates the innate immune systems within hours following administration and its effect lasts over time, as metabolomic and transcriptomic profiles are still varying at 6 days after administration.

2019-10-17 | GSE138956 | GEO

Gene expression profile of IGROV1 cells after in vitro treatment with CpG-ODN

Project description:CpG-ODN is a potent immuno-stimulatory molecule. In order to exclude a direct effect of murine CpG-ODN on IGROV1 human ovarian cancer cell line a gene expression experiment was performed. The ovarian cancer cell line IGROV-1 was obtained from the ATCC (Rockville, MD). Cells were routinely maintained in RPMI medium 1640 (Sigma, St. Louis, MO) supplemented with 10% FCS (Sigma) and 2 mM glutamine (Cambrex, East Rutherford, NJ). Cells were maintained at 37°C in a water-saturated atmosphere of 5% CO2 in air. 1x106 IGROV-1 cells were seeded in 6-well plates and, after seeding, cells were treated with 10uM of CpG-ODN in culture medium [phosphorothioated ODN1826 (5’-TCCATGACGTTCCTGACGTT-3’), TriLink Biotechnologies (San Diego, CA, USA)] for 24 hours. At the end of treatment, cells were collected and RNA extracted.

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Identification of differentially expressed lncRNAs in CpG ODN-activated macrophage

Project description:The innate immune system is the first line of defense against microbial pathogens. The activated innate immune system plays important roles in eliciting antimicrobial defenses. Despite the benefits of innate immune responses, excessive inflammation will cause host damage. Thus, tight regulation of these processes is required for the maintenance of immune homeostasis. Recently, a new class of long non-coding RNAs (lncRNAs) has emerged as important regulators in many physiological and pathological processes. Dysregulated lncRNAs have been found to be associated with excessive or uncontrolled inflammation. In this study, we employed a lncRNA microarray-based profiling assay to detect changes of lncRNAs at different stages of CpG ODN-induced macrophage activation. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were performed based on the function of mRNAs. Co-expression and network potential targeting relationship were constructed according to the microarray results and bioinformatics predictions. Our findings revealed the involvement of lncRNAs in the process of CpG ODN-induced macrophage activation.

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