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High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis

ABSTRACT: High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis

OTHER RELATED OMICS DATASETS IN: GSE40862

PROVIDER: PRJNA175136 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR568027.fastq.gz	Fastqsanger.gz
	SRR568028.fastq.gz	Fastqsanger.gz
	SRR568029.fastq.gz	Fastqsanger.gz
	SRR568030.fastq.gz	Fastqsanger.gz
	SRR568031.fastq.gz	Fastqsanger.gz

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Similar Datasets

High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis (RNA-seq)

Project description:To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches, strand-specific RNA-seq and ChIP-seq, to survey the global transcriptome and monitor genome-wide dynamics of RNA polymerase (RNAP) and NusA. ChIP-seq revealed that RNAP and the antiterminator, NusA, occurred ubiquitously with the NusA profile mirroring RNAP distribution in both the exponential and stationary phases of growth. Generally, promoter-proximal peaks for RNAP and NusA were observed, followed by a decrease in signal strength reflecting transcriptional polarity. Differential binding of RNAP and NusA in the two growth conditions correlated with transcriptional activity as reflected by RNA abundance. Indeed, a significant association between expression levels and the presence of NusA throughout the gene body was detected, confirming the peculiar transcription-promoting role of NusA. Integration of the datasets pinpointed transcriptional units, mapped promoters and uncovered new anti-sense and non-coding transcripts. Highly expressed transcriptional units were situated mainly on the leading strand, despite the relatively unbiased distribution of genes throughout the genome, thus helping the replicative and transcriptional complexes to align. RNA-Seq in exponential and stationary phase cultures

2012-12-01 | E-GEOD-40846 | biostudies-arrayexpress

High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis (ChIP-seq)

Project description:To construct a regulatory map of the genome of the human pathogen, Mycobacterium tuberculosis, we applied two complementary high-resolution approaches, strand-specific RNA-seq and ChIP-seq, to survey the global transcriptome and monitor genome-wide dynamics of RNA polymerase (RNAP) and NusA. ChIP-seq revealed that RNAP and the antiterminator, NusA, occurred ubiquitously with the NusA profile mirroring RNAP distribution in both the exponential and stationary phases of growth. Generally, promoter-proximal peaks for RNAP and NusA were observed, followed by a decrease in signal strength reflecting transcriptional polarity. Differential binding of RNAP and NusA in the two growth conditions correlated with transcriptional activity as reflected by RNA abundance. Indeed, a significant association between expression levels and the presence of NusA throughout the gene body was detected, confirming the peculiar transcription-promoting role of NusA. Integration of the datasets pinpointed transcriptional units, mapped promoters and uncovered new anti-sense and non-coding transcripts. Highly expressed transcriptional units were situated mainly on the leading strand, despite the relatively unbiased distribution of genes throughout the genome, thus helping the replicative and transcriptional complexes to align. ChIP-Seq of RNAP and NusA in Mtb H37Rv at exponential and stationary phase cultures. Each experiment was performed in duplicate. Input DNA (No IP) was used as a control.

2012-12-01 | E-GEOD-40845 | biostudies-arrayexpress

High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis (RNA-seq)

2012-12-01 | GSE40846 | GEO

High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis (ChIP-seq)

2012-12-01 | GSE40845 | GEO

Mycobacterium tuberculosis

Project description:High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis (RNA-seq)

| PRJNA175135 | ENA

Mycobacterium tuberculosis

Project description:High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis (ChIP-seq)

| PRJNA175134 | ENA

Genome-wide profiling of miRNA expression dynamics in monocyte-derived dendritic cells following infection with a panel of intra-cellular bacteria

Project description:We report the application of RNA sequencing to assess the expression dynamics of miRNAs and their isoforms over time upon infection with a panel of six intracellular bacteria (Mycobacterium tuberculosis H37Rv, Mycobacterium tuberculosis Beijing strain GC1237, Mycobacterium bovis BCG, Salmonella typhimurium strain Keller, Staphloccocus epidermidis and Yersinia pseudotuberculosis) Study of miRNA expression dynamics of monocyte-derived dendritic cells upon bacterial infection using RNA sequencing

2015-02-18 | E-GEOD-64142 | biostudies-arrayexpress

Transcriptome-wide effects of NusA on RNA polymerase pausing in Bacillus subtilis

Project description:In this work we conducted RNET-seq on Wild Type, NusA depletion, nusG deletion, and NusA depletion nusG deletion strains of B. subtilis. Using this data we analysed the transcriptome-wide effects of NusA on RNA polymerase pausing and found that NusA has modest pause stimulating as well as suppressing effects throughout the genome.

2021-10-22 | GSE186285 | GEO

Genome-wide profiling of miRNA expression dynamics in monocyte-derived dendritic cells following infection with a panel of intra-cellular bacteria

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Proteogenomic analysis of Mycobacterium smegmatis using high resolution mass spectrometry

Project description:Biochemical evidence is vital for accurate genome annotation. The integration of experimental data collected at the proteome level using high resolution mass spectrometry allows for improvements in genome annotation by providing evidence for novel gene models, while validating or modifying others. Here we report the results of a proteogenomic analysis of a reference strain of Mycobacterium smegmatis (mc2155), a fast growing model organism for the pathogenic Mycobacterium tuberculosis, the causative agent for Tuberculosis. By integrating high throughput LC/MS/MS proteomic data with genomic six frame translation and ab initio gene prediction databases, a total of 2887 ORFs were identified, including 2810 ORFs annotated to a Reference protein, and 63 ORFs not previously annotated to a Reference protein. Further, the translational start site (TSS) was validated for 558 Reference proteome gene models, while upstream translational evidence was identified for 81. In addition, N-terminus derived peptide identifications allowed for downstream TSS modification of a further 24 gene models. We validated the existence of 6 previously described interrupted coding sequences at the peptide level, and provide evidence for 4 novel frameshift positions. Analysis of peptide posterior error probability (PEP) scores indicate high-confidence novel peptide identifications and indicate that the genome of M. smegmatis is not yet fully annotated.

2016-03-31 | PXD003500 | Pride

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