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RNA-seq identifies a distinct response in macrophages stimulated from phagosome with early secreted antigenic target 6-KDa from Mycobacterium tuberculosis

ABSTRACT: RNA-seq identifies a distinct response in macrophages stimulated from phagosome with early secreted antigenic target 6-KDa from Mycobacterium tuberculosis

PROVIDER: PRJNA427122 | ENA |

REPOSITORIES: ENA

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RNA-seq identifies a distinct response in macrophages stimulated from phagosome with early secreted antigenic target 6-KDa from Mycobacterium tuberculosis

Project description:Purpose: The goals of this study are to obtain the NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages, which were stimulated from phagosome with early secreted antigenic target 6-KDa (ESAT6) Methods: First we fabricated a nanocapsule enclosing ESAT6 (nESAT6) and a nanocapsule enclosing BSA (nBSA) as control. mRNA profiles of THP-1 macrophages treated with nESAT6 were generated by deep sequencing, using Illumina Hiseq3000. The sequence reads that passed quality filters were first mapped to the latest UCSC transcript set using Bowtie2 (version 2.1.0). Then the gene expression level was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.15), and normalized with TMM (trimmed mean of M-values) to identify differentially expressed genes (DEGs) using the edgeR package edgeR. qRT–PCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 23 million sequence reads per sample to the human genome (GRCh38/hg38) and identified 25,343 transcripts. Conclusions: Our study represents the first detailed analysis of transcriptomes for macrophages response to ESAT6 stimulation in phagosome, generated by RNA-seq technology.

2020-12-21 | GSE108393 | GEO

RNA-seq identifies a distinct response in macrophages stimulated with early secreted antigenic target 6-KDa from Mycobacterium tuberculosis

Project description:RNA-seq identifies a distinct response in macrophages stimulated with early secreted antigenic target 6-KDa from Mycobacterium tuberculosis

| PRJNA419953 | ENA

RNA-seq identifies a distinct response in macrophages stimulated with early secreted antigenic target 6-KDa from Mycobacterium tuberculosis

Project description:Purpose: The goals of this study are to obtain the NGS-derived transcriptome profiling (RNA-seq) for THP-1 macrophages response to early secreted antigenic target 6-KDa (ESAT6) from Mycobacterium tuberculosis Methods: mRNA profiles of THP-1 macrophages treated with ESAT6 were generated by deep sequencing, using Illumina Hiseq3000. The sequence reads that passed quality filters were first mapped to the latest UCSC transcript set using Bowtie2 (version 2.1.0). Then the gene expression level was estimated using RSEM (RNA-Seq by Expectation Maximization, v1.2.15), and normalized with TMM (trimmed mean of M-values) to identify differentially expressed genes (DEGs) using the edgeR package edgeR. qRT–PCR validation was performed using SYBR Green assays. Results: Using an optimized data analysis workflow, we mapped about 23 million sequence reads per sample to the human genome (GRCh38/hg38) and identified 25,343 transcripts. Conclusions: Our study represents the first detailed analysis of transcriptomes for macrophages response to ESAT6, generated by RNA-seq technology.

2019-03-10 | GSE107387 | GEO

Response of peripheral blood mononuclear cells from patients with allergy to cat and silver birch wood derived antigenic peptide stimulation.

Project description:CD4 T cell responses are characterized based on a limited number of molecular markers selected from exisiting knowledge. The goal of the experiment was to assess antigenic-peptide specific T-cell responses in vitro without bias using microarrays. PBMCs were isolated from 2 donors with allergy. The cells were stimulated with antigenic peptides derived from silver birch wood and cat for 24 hours. Unstimulated cells were cultured without the peptides for 24 hours.

2016-08-15 | E-GEOD-72373 | biostudies-arrayexpress

Global Gene Networks in Porcine Alveolar Macrophage Cells, 3D4/31, Stimulated with Antigenic Epitopes of Actinobacillus pleuropneumoniae ApxIA, IIA and IVA

Project description:Purpose: The goals of this study are to examine the host response with porcine alveolar macrophages (PAMs) cells, 3D4/31 by stimulation of four antigenic epitopes of App exotoxins, ApxIA, IIA and IVA. Methods: total RNA profiles of porcine alveolar macrophage cells stimulated with ApxIA Ct, ApxIIA Nt, ApxIVA C1, ApxIVA C2 and DPBS were generated by transcriptome sequencing, in duplicate, using HiSeq4000 platform.The sequence reads that passed quality filters were analyzed at the transcript isoform level with TopHat followed by Cufflinks. qRT–PCR validation was performed using SYBR Green assays Results: RNA sequencing yielded 617 million 101 bp paired-end clean reads, varying from 28 to 32 million for each sample. Among the clean reads, approximately 95.24% clean reads were uniquely mapped onto the version 11.1 of the sus scrofa. Gene expression was quantified through FPKM conversion of raw reads. The 15,269 genes (mean FPKM of the 10 samples > 0) were considered as expressed in PAMs over the 30,511 gene annotations. RNA-seq data confirmed stable expression of 1 known housekeeping genes, and 5 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.906. Conclusions: Transcriptional responses of the porcine alveolar macrophages (PAMs) stimulated with the antigenic epitopes of ApxIA, ApxIIA, and ApxIVA were analyzed to identify the precious mechanism of Apx toxins in the host. This study will be foundational to understanding the host response by Apx toxins.

2018-06-27 | GSE116263 | GEO

antigenic KPC model_bulk pancreas RNASeq

Project description:antigenic KPC model_bulk pancreas RNASeq

| PRJNA544120 | ENA

Antibodies to protozoan variable surface antigens induce antigenic variation

Project description:The genomes of most protozoa encode families of variant surface antigens, whose mutually exclusive changes in expression allow parasitic microorganisms to evade the host immune response1. It is widely assumed that antigenic variation in protozoan parasites is accomplished by the spontaneous appearance within the population of cells expressing antigenic variants that escape antibody-mediated cytotoxicity1,2. Here we show, both in vitro and in animal infections, that antibodies to Variant-specific Surface Proteins (VSPs) of the intestinal parasite Giardia lamblia are not cytotoxic; instead, anti-VSP antibodies induce VSP clustering into microdomains, triggering a massive release of microvesicles carrying the original VSP and switching in expression to different VSPs by a calcium-dependent process. Surface microvesiculization and antigenic switching are also stimulated when Trypanosoma brucei and Tetrahymena thermophila are confronted to antibodies directed to their GPI-anchored variable surface glycoproteins. This novel mechanism of antigen clearance throughout its release into microvesicles coupled to the stochastic induction of new phenotypic variants not only changes the current paradigm of spontaneous antigenic switching but also provides a new framework for understanding the course of infections as a host/parasite adaptive process.

2023-05-10 | PXD031141 | Pride

BAFF engages distinct NFkappaB effectors in maturing and proliferating B cells

Project description:Identify genes which are induced in wild type B cells under antigenic stimuli, anti-IgM vs pro-survival stimuli, BAFF. Also find the differential expressed genes which are distinct from in co-stimulated conditions. RNAseq analysis of wild type primary B cells stimulated with anti-IgM alone, BAFF alone, or co-stimulated with both anti-IgM and BAFF for 8 and 30 hours

2015-02-01 | E-GEOD-54588 | biostudies-arrayexpress

BAFF engages distinct NFkappaB effectors in maturing and proliferating B cells

2015-02-01 | GSE54588 | GEO

Mature IgM+ plasma cells sense antigen and develop competence for cytokine production upon antigenic challenge

Project description:Dogma holds that plasma cells (PC), as opposed to B cells, cannot bind antigen (Ag) because they have switched from expression of membrane-bound immunoglobulins that constitute the B cell Ag receptor (BCR) to production of the secreted form of immunoglobulins. We have compared the phenotypical and functional attributes of PC generated by the T-cell-dependent and T-cell-independent forms of the hapten NP. We unexpectedly found that the nature of the secreted Ig isotype rather than the chemical structure of the immunizing Ag defines two functionally distinct populations of PC. Fully mature IgM-expressing bone marrow PC retain expression of a functional BCR while their IgG+ counterparts do not. We show that Ag boost modifies the gene expression profile of IgM+ PC and initiates a cytokine production program, characterized by upregulation of CCL5 and IL-10. Our results demonstrate that IgM-expressing PC can sense Ag and acquire competence for cytokine production upon antigenic challenge.

2016-11-01 | GSE80216 | GEO

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