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Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

ABSTRACT: Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

PROVIDER: PRJEB8718 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR776679.fastq.gz	Fastqsanger.gz
	ERR776680.fastq.gz	Fastqsanger.gz
	ERR776681.fastq.gz	Fastqsanger.gz
	ERR776682.fastq.gz	Fastqsanger.gz

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Similar Datasets

Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315

Project description:Burkholderia cenocepacia is an opportunistic pathogenic bacterium intrinsically resistant to most antibiotics and biocides. The aim of this study is to map transcription start sites and 5'UTRs, and to discover novel non-coding small RNAs expressed in biofilms. The experimental approach used for this study is differential sequencing, where RNA samples are split into two aliquots, one of which is then treated with a 5' monophosphate-dependent exonuclease. Two separate libraries are created from exonuclease-treated and -untreated sub-samples, using illumina sequencing from the 5'end, without fractionation step and without depletion of abundant rRNAs. Transcription start sites can then be identified by comparing exonuclease-treated with untreated RNA-seq libraries.

2015-09-03 | E-MTAB-3381 | biostudies-arrayexpress

Expression data from Burkholderia cenocepacia J2315 hfq and hfq2 mutants

2014-01-01 | GSE47344 | GEO

Genome-wide transcription start site profiling in biofilm-grown Burkholderia cenocepacia J2315.

Project description:Burkholderia cenocepacia is a soil-dwelling Gram-negative Betaproteobacterium with an important role as opportunistic pathogen in humans. Infections with B. cenocepacia are very difficult to treat due to their high intrinsic resistance to most antibiotics. Biofilm formation further adds to their antibiotic resistance. B. cenocepacia harbours a large, multi-replicon genome with a high GC-content, the reference genome of strain J2315 includes 7374 annotated genes. This study aims to annotate transcription start sites and identify novel transcripts on a whole genome scale.RNA extracted from B. cenocepacia J2315 biofilms was analysed by differential RNA-sequencing and the resulting dataset compared to data derived from conventional, global RNA-sequencing. Transcription start sites were annotated and further analysed according to their position relative to annotated genes.Four thousand ten transcription start sites were mapped over the whole B. cenocepacia genome and the primary transcription start site of 2089 genes expressed in B. cenocepacia biofilms were defined. For 64 genes a start codon alternative to the annotated one was proposed. Substantial antisense transcription for 105 genes and two novel protein coding sequences were identified. The distribution of internal transcription start sites can be used to identify genomic islands in B. cenocepacia. A potassium pump strongly induced only under biofilm conditions was found and 15 non-coding small RNAs highly expressed in biofilms were discovered.Mapping transcription start sites across the B. cenocepacia genome added relevant information to the J2315 annotation. Genes and novel regulatory RNAs putatively involved in B. cenocepacia biofilm formation were identified. These findings will help in understanding regulation of B. cenocepacia biofilm formation.

| S-EPMC4603805 | biostudies-literature

Burkholderia cenocepacia J2315

Project description:Burkholderia cenocepacia J2315 Genome sequencing

| PRJNA326479 | ENA

Transcription profiling by array of Burkholderia cenocepacia J2315 grown at 20C or 37C

Project description:B. cenocepacia J2315 was grown on LB medium to mid-stationary phase at O.D. 0.5 at 150 rpm in a shaking incubator at two different temperatures: 37 degrees and 20 degrees centigrade.

2012-01-01 | E-MEXP-2789 | biostudies-arrayexpress

Expression data from Burkholderia cenocepacia J2315 hfq and hfq2 mutants

Project description:Hfq proteins are RNA chaperones that play a critical role in post-transcription regulation of gene expression. Bacteria of the Burkholderia cepacia complex harbor two distinct and functional Hfq proteins, the Hfq and Hfq2. We have previously performed the functional analysis of Hfq and Hfq2 in the pathogen Burkholderia cenocepacia J2315. In order to examine the impacts of each RNA chaperone on the global transcriptome of B. cenocepacia J2315, we performed comparative transcriptome profile of mutants on the hfq and hfq2 genes, using as reference the wild-type strain. For expression profiling, over-night cultures of the Burkholderia cenocepacia J2315 wild-type strain and the isogenic mutants hfq::Tp and M-NM-^Thfq2 grown in LB medium were diluted to an initial OD640 nm of 0.25 into LB medium. Triplicate samples were cultured at 37M-BM-:C with 250 r.p.m. agitation for 16 h and RNA extracted from the three bacterial isolates.

2014-01-01 | E-GEOD-47344 | biostudies-arrayexpress

Transcription profiling by array of Burkholderia cenocepacia J2315 grown to mid-log phase in different media

Project description:B. cenocepacia J2315 was grown to mid-log phase in different media: LB broth, iso-sensitest broth, basal salt medium with glucose<br>at pH 7 and pH 6, basal salt medium at pH 7 with a reduced iron content, and basal salt medium with glycerol

2012-01-01 | E-MEXP-2762 | biostudies-arrayexpress

Identification of potential therapeutic targets for Burkholderia cenocepacia by comparative transcriptomics

Project description:[1] Transcription profiling of one Burkholderia cenocepacia clinical isolate, J2315, versus a soil isolate, HI2424, in conditions mimicking CF sputum [2] Transcription profiling of Burkholderia cenocepacia isolates J2315 and HI2424 in media mimicking CF sputum or the soil environment

2009-12-01 | GSE15817 | GEO

Response of Burkholderia cenocepacia J2315 to subinhibitory concentration of chlorhexidine

Project description:Burkholderia cenocepacia J2315 was grown in LB broth with and without the presence of the desinfectant chlorhexidine in the subinhibitory concentration of 5mg/L. Four biological replicates for each control and test conditions were performed. The experiment was designed as a direct comparison with dye swap of two replicates.

2012-05-10 | E-MEXP-3207 | biostudies-arrayexpress

Transcription profiling by array of Burkholderia cenocepacia J2315 grown to mid-stationary phase in basal salt medium with glucose or glycerol substrates

Project description:B. cenocepacia J2315 was grown to mid-stationary phase in basal salt medium with two different substrates: 20 mM glucose or 40 mM glycerol. Cells were harvested after 30 hours incubation at 37 degrees centigrade. <br>The expression profile was compared to cells grown on the same medium and harvested in mid-log phase.

2012-01-01 | E-MEXP-2772 | biostudies-arrayexpress

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