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PBMCs exposed to the Mycobacterium tuberculosis H37Ra strain

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE16250 | GEO | 2014/05/28

SECONDARY ACCESSION(S): PRJNA115191

REPOSITORIES: GEO

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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

Mycobacterium tuberculosis H37Ra

Project description:Mycobacterium tuberculosis H37Ra genome sequencing and assembly

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Transcription profile of intracellular H37Ra of bEnd.3 and Raw 264.7 cells

Project description:Transcription profile of intracellular H37Ra of bEnd.3 and Raw 264.7 cells 3 d.p.i

2021-07-28 | GSE162200 | GEO

MtrA is involved in progression of Mycobacterium tuberculosis cell cycle

Project description:Synchronised cultures of Mycobacterium tuberculosis (M. tb H37Ra DnaAcos115) were used to determine the cell cycle dependent gene expression. Mycobacterium tuberculosis H37Ra DnaAcos115 strain was grown in Middlebrook 7H9 broth at 30C for 30h which arrests replication and later cultures were allowed to grow at 37oC for 30h. Samples were collected at 0, 2, 6, 12,18, 24 and 30 hours. Samples at 30oC for 30h were considered as '0' time point. A total of 18 samples, consisting of triplicates for 6 time-points were analyzed using microarray.

2015-12-31 | E-GEOD-53640 | biostudies-arrayexpress

Integrated multi-omic analysis of M. tuberculosis H37Ra redefines virulence attributes

Project description:M. tuberculosis H37Ra, an avirulent tubercle bacillus, is a commonly used model to investigate virulence attenuation in M. tuberculosis. Comparative high-throughput studies have earlier correlated its avirulence to the presence of specific mutations or absence of certain proteins. However, a recent sequencing study of H37Ra has disproved several genomic differences earlier reported to be associated with virulence. This warrants further investigations on the H37Ra proteome as well. In this study, we carried out an integrated analysis of the genome, transcriptome and proteome of H37Ra. In addition to confirming single nucleotide variations and insertion-deletions that were reported earlier, our study provides novel insights into the mutation spectrum in the promoter regions of 7 genes. In all, we provide protein coding evidence for 3,199 proteins representing ~79% of the total predicted gene count. Transcriptome analysis revealed the expression of 3,945 high-confidence transcripts including several transcripts mapping to the genome that were previously thought to be non-coding. We identified 9 genes whose coding potential was hitherto reported to be absent in H37Ra . These include 2 putative virulence factors belonging to ESAT-6 like family of proteins. Furthermore, proteogenomic analysis enabled us to identify 63 novel proteins coding genes and correct 25 existing gene models in H37Ra genome. A majority of these were found to be conserved in the virulent strain H37Rv as well as in other mycobacterial sp. suggesting that that the differences in the virulent and avirulent strains of M. tuberculosis are not entirely dependent on the expression of certain proteins or their absence but may possibly be ascertained to functional changes.

2018-10-22 | PXD008555 | Pride

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

Genome-wide maps of gene transcription levels in RAW264.7 infected with CdhM-related Mycobacterium tuberculosis H37Ra strain.

Project description:We report the application of RNA-seq technology for high-throughput profiling of gene transcription in RAW264.7 infected with Mycobacterium tuberculosis H37Ra. By obtaining over six billion bases of sequence from mRNA, we generated genome-wide gene transcription maps of RAW264.7 infected with CdhM-related Mycobacterium tuberculosis H37Ra. We find that numerous genes involved in ER stress are significantly affected by CdhM. This finding indicates that CdhM may induce ER stress during Mtb infection of host cells.

2022-02-24 | GSE196961 | 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

LIX48 (H37Ra-devR overexpression) versus LIX47 (control strain) and LIX50 (H37Rv-devR overexpression) versus LIX49 (control strain)

Project description:Transcription analysis of M. tuberculosis H37Ra devR overexpressing strain (LIX48) versus empty vector control strain (LIX47); H37Rv devR overexpressing strain t (LIX50) versus empty vector control strain (LIX49) to study the effect of DevR overexpression

2018-08-31 | GSE103551 | GEO

A PhoP point mutation discriminates between the virulent H37Rv and avirulent H37Ra strains of Mycobacterium tuberculosis

Project description:To uncover mutations underlying the attentuation of H37Ra, we embarked on sequencing its genome using a novel massive parallel pyrosequencing technology. Comparison with the virulent H37Rv parental strain revealed only few polymorphisms, one of which was located in the DNA binding domain of the transcriptional regulator PhoP. Keywords: Expresion profiling

2007-07-05 | GSE7539 | GEO

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