Characterization of three CpG ODN classes in plasmacytoid dendritic cells (pDCs)
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ABSTRACT:
PROVIDER: PRJNA597989 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR10799700_1.fastq.gz | Fastqsanger.gz | |||
| SRR10799700_2.fastq.gz | Fastqsanger.gz | |||
| SRR10799701_1.fastq.gz | Fastqsanger.gz | |||
| SRR10799701_2.fastq.gz | Fastqsanger.gz | |||
| SRR10799702_1.fastq.gz | Fastqsanger.gz |
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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
Project description:Characterization of three CpG ODN classes in plasmacytoid dendritic cells and B cells
| PRJNA597991 | ENA
Project description:Characterization of three CpG ODN classes in B cells
| PRJNA597990 | ENA
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
Project description:The purpose of this experiment was to assess the genes upregulated when pDCs were stimulated with TLR7 agonist imiquimod and TLR9 agonist CpG C. pDCs were isolated from six healthy donors by FACS sorting, and were stimulated with CpG and imiquimod for 18 hours, after which RNA was extracted for next generation sequencing on the Illumina HiSeq platform. Unstimulated samples were included as controls.
2016-03-17 | E-GEOD-79272 | biostudies-arrayexpress
Project description:Synthetic oligonucleotides (ODNs) containing CpG motifs stimulate human plasmacytoid dendritic cells (pDCs) to produce type-1 interferons (IFN) and pro-inflammatory cytokines. Previous studies demonstrated that interferon regulatory factors (IRFs) played a central role in mediating CpG-induced pDC activation. This work explores the inverse effects of IRF-5 and IRF-8 on CpG dependent gene expression. Results from RNA interference and microarray studies indicate that IRF-5 up-regulates TLR9-driven gene expression whereas IRF-8 down-regulates the same genes. Several findings support the conclusion that IRF-8 inhibits TLR9 dependent gene expression by directly blocking the activity of IRF-5. First, the inhibitory activity of IRF-8 is only observed when IRF-5 is present. Second, proximity ligation analysis shows that IRF-8 and IRF-5 co-localize within the cytoplasm of resting human pDC and co-translocate to the nucleus after CpG stimulation. Taken together, these findings suggest that two transcription factors with opposing functions control TLR9 signaling in human pDCs. CAL-1 cells were transfected with siRNA targeting IRF-5 (IRF-5si) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats). CAL-1 cells were transfected with siRNA targeting IRF-8 (IRF-8si) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats). CAL-1 cells were transfected with control siRNA (Contsi) and left unstimulated (n=4, technical repeats) or stimulated with K-type CpG ODN (n=4, technical repeats).
2016-06-01 | E-GEOD-70429 | biostudies-arrayexpress
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.
2011-04-01 | GSE23442 | GEO
Project description:The purpose of this experiment was to assess the genes upregulated when pDCs were stimulated with TLR7 agonist imiquimod and TLR9 agonist CpG C.
2016-03-17 | GSE79272 | GEO
Project description:Plasmacytoid dendritic cells (pDCs) can be activated by the endosomal TLRs, and contribute to the pathogenesis of systemic lupus erythematosus (SLE) by producing type I IFNs. Thus, blocking TLR-mediated pDC activation may represent a useful approach for the treatment of SLE. In an attempt to identify a therapeutic target for blocking TLR signaling in pDCs, we investigated the contribution of Bruton's tyrosine kinase (Btk) to the activation of pDCs by TLR7 and TLR9 stimulation by using a selective Btk inhibitor RN486. Stimulation of TLR7 and 9 with their respective agonist, namely, gardiquimod and type A CpG ODN2216, resulted in the activation of human pDCs, as demonstrated by the expression of activation markers (CD69, CD40, and CD86), elevated production of IFN-alpha and other inflammatory cytokines, as well as up-regulation of numerous genes including IFN-alpha-inducible genes and activation of interferon regulatory factor 7 (IRF7) and NF-kB. RN486 inhibited all of these events induced by TLR9, but not TLR7 stimulation, with a nanomolar potency for inhibiting type A CpG ODN2216-mediated production of cytokines (e.g., IC50=386 nM for inhibiting IFN-alpha). Our data reveal Btk as an important regulatory enzyme in the TLR9 pathway, and a potential therapeutic target for SLE and other TLR-driven diseases. pDCs from healthy donors (n=4) were treated with gardiquimod (TLR7 agonist) or ODN 2216 (TLR9 agonist) with or without BTK inhibitor for 3 hours.
2015-10-24 | E-GEOD-41825 | biostudies-arrayexpress
Project description:To investigate the effect of IVIG and desialylated IVIG on the activation of plasmacytoid dendritic cells (pDCs). Human primary plasmacytoid dendritic cells were treated with TLR stimulation together with or without IVIG or desialylated IVIG, and the change of genes were analyzed. Primary human pDCs were preincubated with or without 10mg/ml IVIG or desialylated IVIG followed by stimulation with CpG overnight. The different genes between IVIG+CpG and desialylated IVIG+CpG were analyzed.
2022-07-04 | GSE207028 | GEO