Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Studying the phosphosugar stress in Bacillus subtilis using differential gene expression analysis of wildtype and manA deletion mutant grown on LB mannose medium

ABSTRACT: Studying the phosphosugar stress in Bacillus subtilis using differential gene expression analysis of wildtype and manA deletion mutant grown on LB mannose medium

PROVIDER: PRJEB28870 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR2818361_1.fastq.gz	Fastqsanger.gz
	ERR2818361_2.fastq.gz	Fastqsanger.gz
	ERR2818362_1.fastq.gz	Fastqsanger.gz
	ERR2818362_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 4 of 4

Similar Datasets

Studying the phosphosugar stress in Bacillus subtilis using differential gene expression analysis of wildtype and manA deletion mutant grown on LB mannose medium

Project description:Bacillus subtilis has different response systems to cope with external and internal stressors. In this study, we investigated the effect of phosphosugar stress caused by accumulation of phosphosugars in B. subtilis. To do so, manA, the encoding gene of mannose-6-phosphate isomerase, was deleted in B. subtilis KM0 to construct strain KM642. Next, strains KM0 and KM642 were cultured in LB with 1% mannose and the cell pellets were isolated after 3.5 h of incubation at 37 °C for transcriptome analysis by RNA-Seq. Differential gene expression analysis was performed based on the RNA-Seq data generated by paired end sequencing (2 x 75nt read length) of Illumina TruSeq stranded mRNA-cDNA libraries on Illumina MiSeq system from control strain and manA deletion mutant.

2019-06-06 | E-MTAB-7262 | biostudies-arrayexpress

Gene Expression profiles of E.coli grown in LB and Minimal medium

Project description:Gene Expression profiles of E.coli grown in LB and Minimal medium (DM) at OD 600 =1 Keywords: ordered

2005-02-28 | GSE1981 | GEO

Gene Expression profiles of E.coli grown in LB and Minimal medium

Project description:Gene Expression profiles of E.coli grown in LB and Minimal medium (DM) at OD 600 =1

2010-06-10 | E-GEOD-1981 | biostudies-arrayexpress

P. aeruginosa PA14 WT in LB medium vs in LB with 10 mM adenosine medium

Project description:To investigate the impact of adenosine on gene expression of wild-type PA14. To investigate the impact of adenosine on gene expression of wild-type PA14, cells were harvested after incubating for 7 h in LB medium and LB with 10 mM adenosine medium, and RNA was extracted with the RNeasy Mini Kit (Qiagen, Valencia, CA) using a bead beater (Biospec, Bartlesville, OK ) with RNAlater buffer (Applied Biosystems, Foster City, CA) to stabilize the RNA.

2012-05-22 | E-GEOD-29665 | biostudies-arrayexpress

A mannose-sensing AraC-type transcriptional activator regulates intestinal colonization of Vibrio cholerae

Project description:In this study, we show that ManR (VC1825) activates the transcription of the mannose operon in M9 medium supplemented with fructose or mannose, and when manR is impaired Vibrio cholerae cells fail to colonize the intestine and host survival is significantly prolonged in a fruit fly Drosophila melanogaster infection model. To identify other target genes of ManR, transcriptome analysis was performed in wild-type V. cholerae and manR mutant strains, , grown on M9 medium supplemented with glucose, fructose, or mannose.

2022-01-05 | GSE192900 | GEO

RNA-seq of Klebsiella pneumoniae SGH10 grown in LB or DMEM medium

Project description:SGH10 bacteria were grown under DMEM (Dulbecco's Modified Eagle Medium) and LB(Lysogeny broth). Bacteria were harvested by centrifugation, the pellet was resuspended in TE buffer, mixed with lysosyme (SigmaAldrich) in a final concentration of 0.9 mg/ml, and immediately frozen in liquid nitrogen. The frozen pellet was subjected to two cycles of thaw and freeze at 37°C and in liquid nitrogen, respectively, and RNA was extracted using Tri-Reagent (Sigma-Aldrich). RNA-seq libraries were constructed by the RNAtag-seq method. RNA-seq libraries were sequenced by single end sequencing using Nextseq 500 Sequencer (Illumina). sequence fragments were mapped to SGH10 which contains a chromosome NZ_CP025080.1 and a plasmid NZ_CP025081.1. For each growth condition, three biological repeats were done.

2023-12-01 | E-MTAB-13341 | biostudies-arrayexpress

RIL-seq of Klebsiella pneumoniae SGH10 grown in LB or DMEM medium

Project description:RIL-seq experiment allows identification of pairs of interacting RNA molecules while bound to the Hfq protein. SGH10 bacteria were grown under DMEM (Dulbecco's Modified Eagle Medium) and LB (Lysogeny broth) conditions. RIL-seq was performed as previously described in Melamed et al. 2018 with adaptation of the computational analysis to the SGH10. It was applied to three biological replicates, for each growth condition. Libraries were sequenced by paired-end sequencing using Nextseq 500 Sequencer (Illumina). sequence fragments were mapped to SGH10 which contains a chromosome NZ_CP025080.1 and a plasmid NZ_CP025081.1. RIL-seq derived sequence fragments that mapped to the same locus or to two different loci were defined as single and chimeric fragments respectively. Chimeric fragments that appeared statistically significantly more than expected at random (S-chimeras) were considered as representing putative interacting RNAs.

2023-12-01 | E-MTAB-13342 | biostudies-arrayexpress

Transcription profiling of wild type and crc mutant Pseudomonas putida growing exponentially in LB medium

Project description:Effect of inactivating the crc gene (PP_5292) on the transcriptome of cells growing exponentially in LB medium

2009-11-03 | E-MEXP-1886 | biostudies-arrayexpress

SigX ECF sigma factor deletion mutant expression profile in Pseudomonas aeruginosa H103 in LB medium

Project description:Analysis of a SigX knockout mutant of Pseudomonas aeruginosa H103 strain in LB.

2018-12-01 | GSE117438 | GEO

Listeria monocytogenes EGD after growth BHI vs. LB vs. MM

Project description:Transcriptional profile of prfA, the dependent genes and the PTS genes after growth in BHI (brain-heart-infusion), LB (Luria Bertani broth) and MM (minimal medium (Premaratne et al. 2001) (each supplemented with 50 mM Glucose). Keywords: media comparison

2008-12-01 | GSE12143 | 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