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

Transcription Start Site (TSS) mapping and total RNAseq of Streptomyces scabies wild-type (WT) versus Streptomyces scabies ΔbtmL

ABSTRACT: The aim of this experiment was to map the transcription start sites (TSSs) in the bottromycin biosynthetic gene cluster from Streptomyces scabies, qualitatively assess the expression levels of this cluster within the bacterium's transcriptome and evaluate whether deletion of a potential regulatory gene in the cluster, btmL affects gene cluster expression.

INSTRUMENT(S): NextSeq 500

ORGANISM(S): Streptomyces scabiei

SUBMITTER: Natalia Miguel-Vior

PROVIDER: E-MTAB-8236 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

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

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

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

Identification of transcript starts in Desulfovibrio alaskensis G20

Project description:5' RNASeq of mRNA from G20 in defined lactate/sulfate media (LS4D) 5' RNASeq of a single sample

2013-08-03 | E-GEOD-49484 | biostudies-arrayexpress

Role assessment of the type VI secretion systems during disease interactions of Erwinia amylovora with its plant host by comparing the in planta and in vitro RNA-seq transcriptomes of wildtype CFBP 1430 and its T6SS double mutant (T6-d1d3)

Project description:To assess the contribution of type VI secretion systems to virulence and potential transcriptomic changes of E. amylovora CFBP 1430, a double mutant in two structural genes was generated (T6-d1d3). An in vitro RNA-seq transcriptome comparison of the wildtype to the T6-d1d3 mutant was made by growing the bacteria to the mid-log phase in minimal M9 medium supplemented with sucrose. An in planta RNA-seq transcriptome comparison was performed by inoculating a bacterial suspension on the hypanthium of apple flowers and collecting at two days post inoculation.

2017-08-07 | E-MTAB-5444 | biostudies-arrayexpress

RNA-Seq of roseoflavin producer Streptomyces davaonensis reveals transcription of unusual high number of riboflavin biosynthetic genes (rib genes) in exponential and stationary growth phase

Project description:RNA-Seq of roseoflavin producer Streptomyces davaonensis reveals transcription of unusual high number of riboflavin biosynthetic genes (rib genes) in exponential and stationary growth phase. In this study mRNA from three biological replicates of Streptomyces davaonensis harvested in exp. (after 18 h of growth) and stationary growth phase (after 48 h of growth) were sequenced after Illumina Ribozero treatment via Illumina TruSeq stranded mRNA libs on Illumina HiSeq1500. Moreover primary 5′-end-enriched cDNA libraries were prepared according to Peifer-Sancar et al. (2013) and sequenced on Illumina MiSeq system.

2020-01-31 | E-MTAB-8679 | 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

Strand-specific RNA-seq analysis of three streptomycetes

Project description:We report the mRNA and small RNA transcriptomes of Streptomyces coelicolor, Streptomyces avermitilis, and Streptomyces venezuelae. We identified dozens of new conserved sRNAs and antisense RNAs, including a prominent group of antisense RNAs termed ‘cutoRNAs’ that result from overlap of the 3′ ends of convergently transcribed mRNAs. In addition, we observed abundant unique ncRNAs, including many within secondary metabolic gene clusters. For each of the three species (S. coelicolor, S. avermitilis, S. venezuelae) two libraries were created. The first was a long-read library, where total RNA was depleted of rRNA. The second was a short read library, where total RNA was size selected (40-300 nucleotides) prior to library creation. The long-read library allowed the profiling of mRNAs and asRNAs, while the short-read library was enriched for small RNAs (sRNAs).

2013-08-01 | E-GEOD-46008 | biostudies-arrayexpress

Transcription start site analysis for Thermotoga maritima [RNA-seq]

Project description:Investigation of 5' transcripts using strand specific sequencing for T. maritima under logphase, maltose minimal media growth conditions Two replicate samples were sequenced after isolating total RNA of cultures grown in maltose minimal media. Cells were harvested in logphase growth.

2013-08-02 | E-GEOD-37461 | biostudies-arrayexpress

Genome sequencing coupled with iPSC technology identifies GTDC1 as a novel candidate gene involved in Neurodevelopmental Disorders

Project description:We identified genomic structural alterations of six patients with signs of neurodevelopmental disorder (NDDs) that harbour chromosomal rearrangements using large-insert paired-end tag sequencing (DNA-PET). This technique allowed the refinement of chromosomal breakpoints and lead to the identification of seven disrupted genes (GNAQ, RBFOX3, UNC5D, TMEM47, NCAPG2, GTDC1 and XIAP). For one patient we filtered the entire panel of structural variations (SVs) with his parents and identified a unique SV that disrupted a single gene: GTDC1. We then validated the functional consequences of the chromosomal breakpoint disruption of GTDC1 by using patient-derived iPSCs. By differentiating these cells into neural progenitor cells (NPCs) and neurons, we interrogated the disease process at the cellular level and observed defects in the proliferation and glycosylation status of NPCs and also defects in neuronal maturation and function. We compared these results with GTDC1-deficient wild-type human NPCs and neurons, and observed similar phenotypic features as in the patient-derived cells which confirm that GTDC1 is involved in the patient’s phenotype. We show here that the combination of genomic screening with iPSCs technology provides a mechanistic insight into possible contributory effects of candidate genes implicated in NDDs and for personalized medicine. Structural variations were identified by long insert DNA paired-end tag (DNA-PET) sequencing, a mate-pair sequencing approach.

2014-09-03 | E-GEOD-51430 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

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