Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNAseq analysis of the serotype M1 group A Streptococcus strain MGAS2221

ABSTRACT: We recovered RNA from exponential and stationary phase cell cultures of MGAS2221 and utilized two distinct methods to remove rRNA from our samples, the RiboZero kit from Epicenter, and the terminator- 5--Phosphate-Dependent Exonuclease (TEX). This gave us 4 distinct RNAs with which we performed RNAseq analysis. Both rRNA removal methods worked well, with only a small percentage of the final total read counts being derived from rRNA sequences. A single group A Streptococcus strain was investigated.

ORGANISM(S): Streptococcus pyogenes

SUBMITTER: Paul Sumby

PROVIDER: E-GEOD-45325 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

RNA-seq analysis of Xenorhabdus nematophila

Project description:Analysis of size selected RNA samples to identify sRNAs using wild-type and rpoS mutant strains. Four experiments, two from each of two strains using two protocols.

2013-03-26 | E-GEOD-45298 | biostudies-arrayexpress

RNA-seq analysis of Escherichia coli str. K-12 substr. MG1655

Project description:Expression profiles of wild-type and SgrR mutant E. coli strains under aMG and 2-DG-induced stress. Expression profiles of E. coli overexpressing SgrS sRNA. Illumina RNA-Seq of total RNA extracted from wild-type, SgrR/SgrS mutant and SgrS overexpressing E. coli strains grown in different conditions.

2013-03-26 | E-GEOD-45443 | biostudies-arrayexpress

Computational Analysis of Bacterial RNA-Seq Data

Project description:RNA-seq analysis was carried out on N. gonorrhoeae grown in vitro to verify accuracy of a novel RNA-seq analysis program, Rockhopper Three replicates of N. gonorrhoeae grown in vitro

2013-03-26 | E-GEOD-45444 | biostudies-arrayexpress

RNA-seq analysis of Salmonella enterica Typhimurium LT2

Project description:We performed whole-genome transcriptomic analyses of the Salmonella Typhimimurium genome during glucose-phosphate stress. In particular, we wanted to elucidate the role of the the small RNA SgrS and protein regulator SgrT in the stress response. Wild-type Salmonella cells, mutants of Salmonella either lacking sgrS or lacking SgrS RNA/ SgrT peptide function were subject to glucose-phoshate stress

2013-03-26 | E-GEOD-45445 | biostudies-arrayexpress

Transcriptional control in Candidatus Pelagibacter ubique and other marine bacterial taxa

Project description:Bacteria respond to stimuli in the environment using transcriptional control, but this may not be the case for most marine bacteria having small, streamlined genomes. Candidatus Pelagibacter ubique, a cultivated representative of the SAR11 clade, which is the most abundant clade in the oceans 4, has a small, streamlined genome and possesses an unusually small number of transcriptional regulators. This observation leads to the hypothesis that transcriptional control is low in Pelagibacter and limits its response to environmental conditions. However, the extent of transcriptional control in Pelagibacter is unknown. Here we show that transcriptional control is extremely low in Pelagibacter and another oligotroph (SAR92) compared to two marine copiotrophic bacterial taxa, Polaribacter MED152 and Ruegeria pomeroyi. We found that ~0.1% of protein-encoding genes in Pelagibacter are under transcriptional control compared to >10% of genes in other marine bacteria. Regardless of the growth condition, the same genes were highly expressed while most genes were always expressed at very low levels. Quantitative RNA sequencing revealed that abundances of most Pelagibacter transcripts were <0.01 copies per cell whereas transcript abundances were 1 to 10 copies per cell in some other bacteria. Our results demonstrate that Pelagibacter can change growth without shifts in transcript levels, suggesting that transcriptional control plays a minimal role in the adaptive strategy for one of the most successful organisms in the biosphere. Bacteria were grown in batch culture and sampled twice during the initial, rapid phase of exponential growth and twice during the phase of slower growth that followed.

2015-03-03 | E-GEOD-66443 | biostudies-arrayexpress

Expression comparison between MGAS2221 and isogenic spyCEP mutant

Project description:Expression analysis was performed to confirm that spyCEP is the only gene differentially regulated between parental strain MGAS2221 and isogenic spyCEP mutant 2221DELTACEP. Keywords: expression comparison 4 cultures of each strain were analyzed.

2010-05-26 | E-GEOD-9793 | biostudies-arrayexpress

Co-cultivation and transcriptome sequencing of two co-existing fish pathogens Moritella viscosa and Aliivibrio wodanis.

Project description:Aliivibrio wodanis and Moritella viscosa have often been isolated together from fish with winter ulcer. Little is known about the interaction between the two bacterial species and how the presence of one bacterial species affects the behaviour of the other. The impact on bacterial growth in co-culture was investigated in vitro, and the presence of A. wodanis has a strong inhibitorial effect on M. viscosa. Further, we have sequenced the complete genomes of these two marine Gram-negative species, and have performed transcriptome analysis of the bacterial gene expression levels from in vivo samples. Using bacterial implants in the fish abdomen, we demonstrate that the presence of A. wodanis is altering the gene expression levels of M. viscosa compared to when the bacteria are implanted separately. The impeding effect on growth and the change in the global gene expression pattern of M. viscosa when the two pathogens co-exists is discussed in this paper.

2014-11-30 | E-MTAB-2851 | biostudies-arrayexpress

Transcriptome comparison of Streptococcus pyogenes strain MGAS2221 with that of an isogenic PEL mutant

Project description:PEL is a small regulatory RNA that is present within the S. pyogenes genome. In some strains of S. pyogenes, the PEL sRNA regulates many of the known virulence factors produced by this pathogen. A genome-wide analysis of PEL-regulated genes had not been performed previously so we analyzed this by comparing the parental M1T1 isolate MGAS2221 with an isogenic PEL mutant. Comparing gene transcript levels between these two strains at the exponential and stationary phases of growth, we identified that PEL has no regulatory function in MGAS2221. Three cultures of each GAS strain were grown in THY broth to exponential (O.D. 0.5) and stationary (O.D. 1.7) phases of growth. Two volumes of RNA protect were added to samples recovered at these O.D.'s, the samples incubated at room temperature for 5 minutes, and the bacteria collected through centrifugation. Total RNA was isolated via a mechanical disruption method, converted to cDNA, fragmented, labeled, and hybridized to our Affymetrix microarray. Estimates of gene expression were calculated using GCOS software v1.4.

2009-08-25 | E-GEOD-17767 | biostudies-arrayexpress

RNAseq analysis of the serotype M1 group A Streptococcus strain MGAS2221

Project description:We recovered RNA from exponential and stationary phase cell cultures of MGAS2221 and utilized two distinct methods to remove rRNA from our samples, the RiboZero kit from Epicenter, and the terminator- 5--Phosphate-Dependent Exonuclease (TEX). This gave us 4 distinct RNAs with which we performed RNAseq analysis. Both rRNA removal methods worked well, with only a small percentage of the final total read counts being derived from rRNA sequences.

2013-03-20 | GSE45325 | GEO

Mating response of three yeast species (S. cerevisiae, S. paradoxus and S. mikatae)

Project description:We examined the mating response of three yeast species, by subjecting a-type cells from each of them to alpha-factor (6uM). The expression of cells before and after (60min) addition of alpha-factor were compared using S. cerevisiae cDNA microarrays. In addition, we verified our results with a true mating experiment: the expression of a-type and alpha-type cells from S. cerevisiae were compared before and after mixing them for 90 minutes (i.e. allowing them to mate). Keywords: yeast mating response, comparison among species Three (or four) samples were processed in parallel for each species (biological replicates). All samples were measured by hybridization to S. cerevisiae cDNA microarray

2010-06-11 | E-GEOD-7525 | 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