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Next Generation Sequencing Facilitates Quantitative Analysis of cmtR-deleted mutant and wild-type strains Transcriptomes in Mycobacterium tuberculosis H37Ra

ABSTRACT: Next Generation Sequencing Facilitates Quantitative Analysis of cmtR-deleted mutant and wild-type strains Transcriptomes in Mycobacterium tuberculosis H37Ra

PROVIDER: PRJNA588288 | ENA |

REPOSITORIES: ENA

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Next Generation Sequencing Facilitates Quantitative Analysis of cmtR-deleted mutant and wild-type strains Transcriptomes in Mycobacterium tuberculosis H37Ra

Project description:Compare the gene expression difference between MRA_2010 knockout strains and wild-type strains by RNA sequencing in Mycobacterium tuberculosis H37Ra. The goal of this study is that detection cmtR acts as a transcriptional factor and regulates the target genes expression.

2020-10-05 | GSE140113 | GEO

Genome-wide maps of gene transcription level in wild-type and mpbR-deleted Mycobacterium tuberculosis H37Ra strains

Project description:We report the application of RNA-seq technology for high-throughput profiling of gene transcription in M. tuberculosis H37Ra strains. By obtaining over four billion bases of sequence from mRNA, we generated genome-wide gene transcription maps of wild-type and mpbR-deleted Mycobacterium tuberculosis H37Ra strains. We find that a group of genes is significantly up-regulated in the mpbR-deleted mutant strain. This finding indicates that MpbR negatively regulates gene expression.

2022-08-26 | GSE136322 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Zinc treated Wild-Type or CmtR-deleted strains of Mycobacterium bovis BCG Transcriptomes

Project description:The goal of this study aims to quantitatively compare the gene expression difference in wild-type or cmtR-deleted strains of Mycobacterium bovis BCG with and without excess zinc treatment at the transcriptome level and find the underlying mechanism how could excess zinc inhibit mycobacterial growth and its relation with transcription factor CmtR.

2021-09-22 | GSE179966 | GEO

Quantitative proteomic and phosphoproteomic analysis of H37Ra and H37Rv strains of Mycobacterium tuberculosis

Project description:Mycobacterium tuberculosis, the causative agent of tuberculosis accounts for 1.5 million annual deaths worldwide. The two well-characterized strains of the parental H37 strain namely, H37Ra and H37Rv show different pathogenic phenotypes. In order to identify factors that are responsible for virulence, we compared the proteome and the phosphoproteome profiles of virulent (H37Rv) and virulence attenuated (H37Ra) strains of M. tuberculosis. Quantitative proteomic analysis resulted in the identification and quantitation of 2,709 proteins and 505 phosphosites. Comparative analysis revealed over 5-fold overexpression of several proteins associated with virulence. Our data indicates that there are definable molecular differences between H37Rv and H37Ra strains at both the proteome and phosphoproteome levels which may explain the virulence and phenotypic differences.

2017-05-08 | PXD004161 | Pride

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and POT1a deleted MSPCs Transcriptomes.

Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to evaluate POT1a deleted MSPCs functions by using NGS-derived MSPCs transcriptome profiling (RNA-seq) in vitro and vivo. Methods: In vitro, bone marrow cells flushed out from mouse femurs and tibiae were cultured, and adherent cells were collected. CD51+/PDGFRɑ+ cells were sorted and further cultured, and Cre Recombinase Gesicles were applied. After 48 hours culture, tdTomato fluorescently colored cells were re-sorted, cultured for about 4 weeks, and used for gene analyses. In vivo, bone marrow cells weer flushed out from mouse femurs and tibiae, and the flow-through fraction with tdTomato signals was sorted as an MSPC-enriched population. Results: Gene set enrichment analysis of the differentially expressed genes revealed that several pathways related to bone development were significantly affected. Conclusions: POT1a is essential for bone marrow MSPCs to maintain osteo- differentiation potential.

2023-09-13 | GSE197720 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Zinc treated Wild-Type or CmtR-deleted strains of Mycobacterium bovis BCG Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Zinc treated Wild-Type or CmtR-deleted strains of Mycobacterium bovis BCG Transcriptomes

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PBMCs exposed to the Mycobacterium tuberculosis H37Ra strain

Project description:Human peripheral blood mononuclear cells were cultured in presence of H37Ra strain at 37oC, 5%CO2. Cellular aggregates were collected at 24h, and RNA extracted and hybridized to Affymetrix microarrays (HG-U133). Raw data from microarray experiments was analyzed with dCHIP and SAM programs to determine the significance of changes at the biological context. PBMCs were exposed in triplicate to H37Ra strain. PBMCs from the same donor were cultured in triplicate at the same conditions than treated samples. RNA was extracted from each sample and hybridized to Affymetrix Human arrays.

2014-05-28 | E-GEOD-16250 | biostudies-arrayexpress

Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum bud and flower Transcriptomes

Project description:Next Generation Sequencing Facilitates Quantitative Analysis of Solanum lycopersicum bud and flower Transcriptomes

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Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes.

Project description: Not available

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Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Kansl1-/- MEFs Transcriptomes

Project description:We report the application of RNA-sequence in WT and Kansl1-deleted MEF cells with 3 biological replicates. We mapped over 42 million sequence reads per sample to the mouse genome (build mm10).

2021-06-10 | GSE176424 | GEO

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