Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

7 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Illumina Genome Analyzer

ORGANISM(S): Burkholderia cenocepacia

SUBMITTER: Andrea Sass

PROVIDER: E-MTAB-3381 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

dRNA-seq of Shewanella oneidensis MR-1

Project description:We combined high-resolution tiling microarrays and 5'-end RNA sequencing to obtain a genome-wide map of transcription start sites (TSSs) for Shewanella oneidensis MR-1. To test the reliability of these TSSs, we compared our result to those from differential RNA sequencing (dRNA-seq), which discriminates primary and processed ends of transcripts. We found that our identified TSSs tend to have significantly more mapped reads in the TEX(+) sample than the TEX(-) sample. Overall, the dRNA-seq results support the validity of our predictions for TSS. S. oneidensis MR-1 was grown to mid-log phase in Luria-Bertani broth (LB) or defined lactate minimal medium, and total RNA was isolated and used for differential RNA-sequencing (dRNA-seq) by next-generation sequencing, which is used to verify genome-wide transcription start sites. For dRNA-seq, total RNA was partially treated with Terminator Exonuclease (TEX) to digest processed RNA and thereby enrich for primary transcript ends.

2014-06-12 | E-GEOD-58292 | biostudies-arrayexpress

Differential RNA-seq (dRNA-seq) for annotation of transcriptional start sites and small RNAs in Helicobacter pylori

Project description:In this study transcriptional start sites (TSS) for H. pylori 26695 were determined To detect the complement of transcripts expressed from H. pylori, we collected three independent biological replicates (B1 – B3) from 26695 wild type strain grown to mid-exponential (OD 600 ~0.6) phase under microaerophilic conditions at 37°C in BHI medium. For all three samples, total RNA was extracted and subjected to differential RNA-seq (dRNA-seq) library preparation for primary transcriptome analysis as described previously (Sharma et al., 2010). Specifically, prior to cDNA library construction half of each RNA sample was treated with 5’ terminator exonuclease (+TEX samples), which degrades RNAs containing a 5’-monophosphate (5’-P) and, thus, enriches for primary transcripts containing 5’-triphosphates (5’-PPP). The other half of each sample was left untreated (-TEX samples) and thus contains both primary transcripts (5’-PPP) and processed RNAs (5’-P).

2015-07-01 | E-GEOD-67564 | biostudies-arrayexpress

Genome-wide identification of transcriptional start sites in the haloarchaeon Haloferax volcanii based on differential RNA-Seq (dRNA-Seq)

Project description:Three biological replicates of H. volcanii grown under optimal conditions to mid-exponential growth phase were used to determine the primary transcriptome and map 5â-ends of transcripts. In total, 4,749 potential transcriptional start sites (TSS) were detected. A position weight matrix was derived for promoter prediction, showing that 64% of the TSS were preceded by stringent or relaxed basal promoters. 1,851 TSS belonged to protein-coding genes, showing that less than half (46%) of the 4040 protein-coding genes are expressed under optimal growth conditions. 72% of all protein-coding transcripts were leaderless, underscoring that this is the default pathway for translation initiation in haloarchaea. The 5â-UTRs of transcripts with leaders had a widely varying length distribution without any optimum. 2,898 of the TSS belong to potential non-coding RNAs, representing an unexpectedly high fraction (61%) among all transcripts. 2792 of the non-coding TSS had not been described before and were thus novel (59% of all TSS). A large fraction of the potential novel non-coding transcripts are cis-antisense RNAs (1,244 aTSS). There was a strong negative correlation between the levels of antisense transcripts and cognate sense mRNAs, suggesting that negative regulation of gene expression via antisense RNAs may play an important role in haloarchaea. The other types of novel non-coding transcripts correspond to internal transcripts overlapping with mRNAs (1,153 iTSS) and intergenic small RNA (sRNA) candidates (395 TSS). Three biological replicates were performed with slight differences in library preparation. In each case, part of the sample was treated with terminator 5'-phosphate-dependent exonuclease (+TEX), while part of the sample remained untreated (-TEX). Therefore, in total, six samples were analysed by high-throughput sequencing.

2016-08-10 | E-GEOD-82206 | biostudies-arrayexpress

The social and structural architecture of the yeast protein interactome

Project description:Nearly all cellular functions are mediated by protein-protein interactions and mapping the interactome provides fundamental insights into the regulation and structure of biological systems. In principle, affinity purification coupled to mass spectrometry (APMS) is an ideal and scalable tool, however, it has been difficult to identify low copy number complexes, membrane complexes and those disturbed by protein-tagging. As a result, our current knowledge of the interactome is far from complete, and assessing the reliability of reported interactions is challenging. Here we develop a sensitive, high-throughput, and highly reproducible AP-MS technology combined with a quantitative two-dimensional analysis strategy for comprehensive interactome mapping of Saccharomyces cerevisiae. We reduced required cell culture volumes thousand-fold and employed 96-well formats throughout, allowing replicate analysis of the endogenous green fluorescent protein (GFP) tagged library covering the entire expressed yeast proteome. The 4159 pull-downs generated a highly structured network of 3,909 proteins connected by 29,710 interactions. Compared to previous large-scale studies, we double the number of proteins (nodes in the network) and triple the number of reliable interactions (edges), including very low abundant epigenetic complexes, organellar membrane complexes and non-taggable complexes interfered by abundance correlation. This nearly saturated interactome reveals that the vast majority of yeast proteins are highly connected, with an average of 15 interactors, the majority of them unreported so far. Similar to social networks between humans, the average shortest distance is 4.2 interactions. A web portal (www.yeastinteractome.org) enables exploration of our dataset by the network and biological communities and variations of our AP-MS technology can be employed in any organism or dynamic conditions.

2023-09-11 | PXD031940 | Pride

RAMPAGE dataset for the human K562 cell line

Project description:5'-complete cDNA sequencing on ribosome-depleted total RNA from the human K562 cell line. Provides high-quality, genome-wide single-base resolution profiling of transcription start sites and their expression levels. This dataset represents a whole-genome, single-base resolution profiling of transcription start site (TSS) expression in the human K562 cell line. These profiles were established using RAMPAGE, a high-throughput, high-accuracy 5'-complete cDNA sequencing method implemented on the Illumina platform. The data was analyzed using custom scripts and algorithms that are all available upon request.

2012-08-30 | E-GEOD-36200 | biostudies-arrayexpress

Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis

Project description:In this study we have combined RNA-seq analysis of genome-wide transcriptional start sites with regular RNA-seq to study the transcriptional landscape of Mycobacterium tuberculosis during exponential culture and growth arrest using a starvation model where exponentially growing cells are incubated in PBS for 24 hours. Three independent biological replicates were used in this experiment.

2013-11-22 | E-MTAB-1616 | biostudies-arrayexpress

Identification of transcription start sites in Streptomyces venezuelae at 10, 14, 18 and, 24 hours of culture by 5' tag RACE.

Project description:Identification of transcription start sites in Streptomyces venezuelae genome after 10, 14, 18 and, 24 hours of culture 5' tag RACE. The 4 time points correspond to late vegetative growth, initiation of sporulation, maturation of spores and, completion of sporulation.

2021-07-09 | E-MTAB-10690 | biostudies-arrayexpress

Expression Analysis of Bisphenol A and 17Î²-estradiol Exposure in Embryonic Zebrafish

Project description:Investigation of whole genome expression pattern of 24 hours post fertilization Danio rerio embryos exposed to bisphenol A, 17Î²-estradiol, or 0.1% DMSO vehicle control This data represents 2 experiments using 2 separate microarrays. Microarray 1 [Low]: Embryos were exposed to 0.1 ÂµM BPA, 0.1 ÂµM E2, or control from 8 hpf to 24 hpf. Three biological replicates were collected for each treatment. 40 embryos were pooled to comprise a replicate. Microarray 2 [High]: Embryos were exposed to 80 ÂµM BPA, 15 ÂµM E2, or control from 8 hpf to 24 hpf. Two biological replicates were collected for each treatment. 40 embryos were pooled to comprise a replicate. These 2 microarray experiments are cross-comparable, as described in the associated publication.

2013-03-25 | E-GEOD-38960 | biostudies-arrayexpress

Sessile burkholderia cepacia complex cells survive antibiotic treatment by avoiding production of reactive oxygen species

Project description:In the present study we wanted to investigate the molecular mechanisms responsible for the tobramycin tolerance in Burkholderia cenocepacia J2315 biofilms.

2012-02-01 | E-MEXP-3532 | biostudies-arrayexpress

Transcription start site identification in Bacillus subtilis

Project description:Cappable-seq was used to map transcription start sites globally in wild type Bacillus subtilis. Total RNA was isolated from cells grown in LB media until exponential phase. RNA corresponding to transcription start sites was capped with a 5' biotin tag, which was used for enrichment via a pull down with streptavidin beads. Enriched RNA was converted to cDNA and then subjected to illumina sequencing.

2021-04-16 | E-MTAB-8582 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data