Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of non-coding RNAs expressed by Burkholderia cenocepacia during Caenorhabditis elegans infection

ABSTRACT: We investigated the transcriptome of B. cenocepacia under infection of the nematode Caenorhabditis elegans. RNAs fractions extracted from C. elegans infected with B. cenocepacia were used for Illumina high throughput sequencing using the CappableSeq method. The main objective of this work was to identify small non-coding RNAs (sRNAs) expressed by B. cenocepacia under infection conditions.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Burkholderia cenocepacia

SUBMITTER: Tiago Pita

PROVIDER: E-MTAB-12592 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Shared Molecules

Only show the datasets with similarity scores above: 0.5

Threshold

0.5

Similar Datasets

Cappable-seq of Sinorhizobium meliloti ECF/anti-σ-free free strains overexpressing heterologous ecf genes compared to an empty vector control strain

Project description:Bacterial σ factors are dissociable subunits of the core RNA polymerase and important for promoter recognition and transcription initiation. Extracytoplasmic function (ECF) σ factors (σs) represent the most minimalistic and diverse group of alternative σs within the σ70 protein family. It has been shown that heterologous ECF σs hold great potential as context independent regulators in a variety of bacterial species and we implemented a core set of 12 heterologous ECF σs and their cognate promoters in Sinorhizobium meliloti. To analyze if heterologous ECF σs affect transcription from the host genome, we overexpressed the ecf02_2817 gene encoding σE from E. coli and the ecf11_0987 gene from Vibrio parahaemolyticus from ~20 copy number plasmid in RFF625c, a S. meliloti Rm1021 strain deleted for all native ECF/anti-σ genes (Lang et al. 2018, DOI: 10.1128/mSphereDirect.00454-18) . We employed Cappable-Seq to globally determine transcription start sites (TSS) in theses strains and compared it to the TSS profile of an empty vector control strain.

2023-01-26 | E-MTAB-12127 | biostudies-arrayexpress

Cappable RNA Sequencing of Streptomyces formicae to annotate transcription start sites under formicamycin producing conditions

Project description:Total RNA was extracted from Streptomyces formicae grown on SFM (soy flour, mannitol agar) on day 2, 3 and 4 and subjected to cappable RNA sequencing by Vertis Biotechnologie for annotation of TSSs across the genome.

2019-05-18 | E-MTAB-7975 | biostudies-arrayexpress

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

Cappable-seq analysis of Myxococcus xanthus at various developmental time points

Project description:Myxococcus xanthus is a model organism for studying social behaviors and cell differentiation in bacteria. Upon nutrient depletion, M. xanthus cells initiate a developmental program that culminates in formation of spore-filled fruiting bodies and peripheral rods outside of fruiting bodies. Completion of this developmental program depends on fine-tuned spatial and temporal regulation of gene expression, intercellular communication, signaling by nucleotide-based second messengers, and motility. In order to understand regulation of gene expression during growth and development, transcription start sites were identified using Cappable-seq. To this end, we extracted total RNA from vegetative cells (referred as 0 h of development) and from cells developed for 6, 12, 18 and 24 h under submerged conditions in two replicates.

2021-10-20 | E-MTAB-11042 | biostudies-arrayexpress

Response of Burkholderia cenocepacia H111 to micro-oxia

Project description:B. cenocepacia is an opportunistic human pathogen that is particularly problematic for patients suffering from cystic fibrosis (CF). In the CF lung, bacteria grow to high densities within the viscous mucus that is limited in oxygen. Pseudomonas aeruginosa, the dominant pathogen in CF patients, is known to grow and survive under oxygen-limited to anaerobic conditions by using micro-oxic respiration, denitrification and fermentative pathways. In contrast, inspection of the genome sequences of available B. cenocepacia strains suggested that B. cenocepacia is an obligate aerobic and non-fermenting bacterium. In accordance with the bioinformatics analysis, we observed that B. cenocepacia H111 is able to grow with as little as 0.1% O2 but not under strictly anoxic conditions. Phenotypic analyses revealed that H111 produced larger amounts of biofilm, pellicle and proteases under micro-oxic conditions (0.5% - 5% O2, i.e. conditions that mimic those encountered in CF lung infection), and was more resistant to several antibiotics. RNA-Seq and shotgun proteomics analyses of cultures of B. cenocepacia H111 grown under micro-oxic and aerobic conditions showed up-regulation of genes involved in the synthesis of the exopolysaccharide (EPS) cepacian as well as several proteases, two isocitrate lyases and other genes potentially important for life in micro-oxia. Oxygen regulation in Burkholderia cenocepacia was investigated using RNA-Seq of cells grown under aerobic or micro-oxic conditions.

2013-07-15 | E-GEOD-48585 | biostudies-arrayexpress

Determination of Transcription Start Sites (TSS) in Azotobacter vinelandii grown with iron, vanadium or molybdenum for 6 hours after nitrogen step-down

Project description:This experiment was to determine genome wide qualitative and quantitative differences in transcription starts under conditions of availability of iron or vanadium or molybdenum which act as co-factors for different nitrogenase isoenzymes. In response to availability of the co-factors transcription initiation is mediated by three paralogs of vanadium nitrogenase activator VnfA1, VnfA2 and, VnfA3. ChIP-Seq data for VnfA1 and VnfA3 will be submitted separately.

2022-06-23 | E-MTAB-11706 | biostudies-arrayexpress

B. cenocepacia transcriptome in vivo

Project description:The adaptation of B. cenocepacia to the host environment was assessed in a rat chronic respiratory infection model and compared to that of high cell-density in vitro-grown cultures using transcriptomics

2011-12-12 | E-MEXP-3367 | biostudies-arrayexpress

Mapping the quorum sensing regulon of Burkholderia cenocepacia H111

Project description:Comparative transcriptional profiling of the Burkholderia cenocepacia H111 wild type, the cepR mutant H111-R and the complemented cepR mutant H111-R (pBAH27).

2011-05-01 | E-MTAB-509 | biostudies-arrayexpress

Transciption profiling of Burkholderia cenocepacia K56-2 and shvR mutant

Project description:Transcriptome comparison of Burkholderia cenocepacia K56-2 and shvR (BCAS0225) mutant

2010-11-08 | E-MEXP-2939 | biostudies-arrayexpress

Transcription profiling of Burkholderia cenocepacia K56-2 wild type and quorum sensing mutants

Project description:Comparative transcriptional profiling of Burkholderia cenocepacia K56-2 (wildtype) and cepR, cciR and cepRcciIR mutants.

2009-09-18 | E-MEXP-2303 | biostudies-arrayexpress