Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Small RNA sequencing of Pyrobaculum species in exponential and stationary phases

ABSTRACT: Small RNA sequencing of Pyrobaculum species in exponential and stationary phases

PROVIDER: PRJNA415954 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR6223660.fastq.gz	Fastqsanger.gz
	SRR6223661.fastq.gz	Fastqsanger.gz
	SRR6223662.fastq.gz	Fastqsanger.gz
	SRR6223663.fastq.gz	Fastqsanger.gz
	SRR6223664.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 12

Similar Datasets

Small RNA sequencing of Pyrobaculum species in exponential and stationary phases

Project description:A great diversity of small, non-coding RNA (ncRNA) molecules with roles in gene regulation and RNA processing have been intensely studied in eukaryotic and bacterial model organisms, yet our knowledge of possible parallel roles for small RNAs (sRNA) in archaea is limited. We employed RNA-seq to identify novel sRNA across multiple species of the hyperthermophilic genus Pyrobaculum, known for unusual RNA gene characteristics. By comparing transcriptional data collected in parallel among five species, we were able to identify conserved RNA genes fitting into known and novel families and found a large increase in the number of conserved C/D box sRNA genes over what had been previously recognized; many of these genes are encoded antisense to protein coding genes. We also used the genome of Pyrobaculum neutrophilum for comparative genomics. The conserved opposition to orthologous genes across the Pyrobaculum genus suggests similarities to other cis-antisense regulatory systems. We used the improved C/D box sRNA annotations to conduct a deep study of the evolution of archaeal C/D box sRNAs by organizing them into 110 families within the Pyrobaculum based on synteny and conservation of guide sequences. We examined gene duplications and rearrangements, including one family that has expanded in a pattern similar to retrotransposed repetitive elements in eukaryotes. New training data provided by this set of C/D box sRNAs enabled creation of an improved search model. Our analyses provide the most comprehensive, dynamic view of C/D box sRNA evolutionary history within a genus, in terms of modification function, feature plasticity, and gene mobility.

2017-10-27 | GSE106228 | GEO

Defining the impact of exoribonucleases in the shift between exponential and stationary phases

Project description:The transition between exponential and stationary phase is a natural phenomenon for all bacteria and requires a massive readjustment of the bacterial transcriptome. Exoribonucleases are key enzymes in the transition between the two growth phases. PNPase, RNase R and RNase II are the major degradative exoribonucleases in Escherichia coli. We analysed the whole transcriptome of exponential and stationary phases from the WT and mutants lacking these exoribonucleases (Δpnp, Δrnr, Δrnb, and ΔrnbΔrnr). When comparing the cells from exponential phase with the cells from stationary phase more than 1000 transcripts were differentially expressed, but only 491 core transcripts were common to all strains. There were some differences in the number and transcripts affected depending on the strain, suggesting that exoribonucleases influence the transition between these two growth phases differently. Interestingly, we found that the double mutant RNase II/RNase R is similar to the RNase R single mutant in exponential phase while in stationary phase it seems to be closer to the RNase II single mutant. This is the first global transcriptomic work comparing the roles of exoribonucleases in the transition between exponential and stationary phase.

2019-11-13 | GSE117635 | GEO

Transcriptomic profiling of Salmonella during lag, exponential and stationary phases of growth

Project description:Transcriptional profiles during all phases of growth of Salmonella Typhimurium SL1344 were obtained and used to investigate growth phase-dependent alterations in gene expression. Viable count growth curve analysis of the growth system showed a culture lag time of 2.09 hours, and profiles at 4, 20, 40, 60, 90 and 120 minutes were measured accordingly. For comparison, profiles of the inoculum (0 min), mid-exponential (380 min), late-exponential (630 min), early-stationary (900 min) and late-stationary phase (2880 min) were also obtained. Large-scale gene-expression changes were seen, with substantial changes within 4 minutes of inoculation, indicating the speed and sophistication at which Salmonella senses its new environment during lag phase.

2011-12-13 | GSE22294 | GEO

Transcription profiling by array of E. coli MG1655 strains with deletions of fis and hns in early-exponential, mid-exponential, transition-to-stationary and stationary phases

Project description:Differential expression of genes in E. coli MG1655 strains with deletions of fis and hns was assessed under early-exponential, mid-exponential, transition-to-stationary and stationary phases of growth in LB medium.

2010-09-01 | E-MEXP-2838 | biostudies-arrayexpress

Defining the impact of exoribonucleases in the shift between exponential and stationary phases

Project description:Defining the impact of exoribonucleases in the shift between exponential and stationary phases

| PRJNA482775 | ENA

Transcriptome analysis of S. maltophilia in the exponential and stationary phases and after a treatment with quorum sensing autoinducers.

Project description:Stenotrophomonas maltophilia is an emerging opportunistic multidrug-resistant pathogen frequently co-isolated with other relevant nosocomial pathogens in respiratory tract infections. S. maltophilia uses the endogenous DSF quorum sensing (QS) system to regulate virulence processes but can also respond to exogenous AHL signals produced by neighboring bacteria. A whole-transcriptome sequencing analysis was performed for S. maltophilia strain K279a in the exponential and stationary phases and in exponential cultures after a treatment with exogenous DSF or AHLs. Our first analysis reveals that during the beginning of the stationary phase 1673 genes are differentially expressed representing 37% of total genomic content. COG analysis showed that most of these genes were enriched for energetic metabolism processes and regulation of gene expression. In a second analysis, and after adding DSF or AHLs to cultures in exponential phase, 82 and 28 were found deregulated respectively, 22 of which were commonly upregulated by both autoinducers. Interestingly, among these genes affected by both DSFs and AHLs, 14 functional genes were also upregulated in the stationary phase. Gene functions regulated by all tested conditions include lipid and amino acid metabolism, stress response and signal transduction mechanisms, nitrogen and iron metabolism, and adaptation to microoxic conditions. Overall, our findings provide clues on the role that the QS could have in the transition from the exponential to the stationary phase in S. maltophilia and for the bacterial fitness for high-density growth.

2023-05-16 | GSE206442 | GEO

RNA-seq of Chlorella sp. HS2: Comparison between freshwater and marine conditions at exponential and stationary growth phases

Project description:Chlorella sp. HS2 is a halotolerant microalga exhibiting relatively high biomass productivity and substantially high lipid accumulation in marine growth media, which suggests this alga as an important crop for industrial algal cultivation systems. To determine pathways leading to HS2's acclimation responses to salt stress, we performed RNA-seq analysis with triplicated cultures grown in freshwater and marine media at both exponential and stationary growth phases. We then run de novo assembly to obtain HS2 transcriptome, which in turn was annotated and processed to extract dysregulated pathways. Results showed a large proportion of down-regulated genes, for instance photosynthesis and TCA pathways. Photosynthesis appeared, however, to recover at the stationary phase, while the general down-regulation pattern was maintained.

2020-03-12 | GSE146789 | GEO

Transcriptomic profiling of Salmonella during lag, exponential and stationary phases of growth

2011-12-13 | E-GEOD-22294 | biostudies-arrayexpress

Proteomic profiling of the exponential and stationary of phases of CHO cell culture.

Project description:A non-mAb producing CHO-K1GS cell line was cultured for 7 days, samples were acquired for proteomics at 96 h post-seeding when the cells were in exponential growth (n = 4) and at 168 h when the cells had entered stationary phase (n = 4).

2024-08-10 | PXD053511 | Pride

GAS M3 serotype, exponential versus stationary phase

Project description:MGAS315 is a wild type strain. RNA isolated in exponential phase and stationary phase were compared Keywords: Growth phase comparison

2007-06-28 | GSE5179 | GEO

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