Marker Frequency data of genomic loci extracted from N16961 V. cholerae strain grown fro 10h in M9-fructose + 0.2% L-Arabinose, in M9-fructose to exp phase and to stationary phase
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Illumina MiSeq
ORGANISM(S): Vibrio cholerae
SUBMITTER: Elisa Galli
PROVIDER: E-MTAB-13450 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Marker Frequency data of genomic loci extracted from N16961 V. cholerae strain grown fro 10h in M9-fructose + 0.2% L-Arabinose, in M9-fructose to exp phase and to stationary phase
| PRJEB67525 | ENA
Project description:Study of the possible existence of a replication fork trap in Vibrio cholerae. 1- FX85: EPV50(WT) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 2- FX86: EPV50(WT) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 3- FX288: EGV140 (oriL3) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 4- FX289:EGV140 (oriL3) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 5- FX290: EGV111 (oriR4) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 6- FX291:EGV111 (oriR4) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 7- FX355:EPV50 (WT) grown in LB medium to exponential phase (0.2 OD 650nm) 8- FX356:EPV50 (WT) grown in LB medium to stationary phase (overnight) 9- FX286:EGV140 (oriL3) grown in LB medium to exponential phase (0.2 OD 650nm) 10- FX287:EGV140 (oriL3) grown in LB medium to stationary phase (overnight) 11- FX292:EGV111 (oriR4) grown in LB medium to exponential phase (0.2 OD 650nm) 12- FX49: MCH1 (WT monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 13- FX48: MCH1 (WT monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to stationary phase (long overnight). 14- FX11: EGV369 (oriL3 monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 15- FX12: EGV366 (oriR4 monochromosome) grown in M9 minimal medium supplemented with 0.4 % fructose to exponential phase (0.2 OD 650 nm). 16- FX296 EPV50 M9 Exp 17- FX294 EPV50 M9 Stat 18-FX316 EGV140 M9 Exp 19- FX315 EGV111 M9 Exp 20-FX318 MCH1 M9 Exp 21- FX317 MCH1 M9 Stat 22- FX320 EGV369 M9 Exp 23- FX319 EGV366 M9 Exp Chromosomal DNA was extracted using the Sigma GenElute bacterial genomic DNA kit. 5 μg of DNA were used to generate a genomic library according to Illumina's protocol. The libraries and the sequencing were performed by the High-throughput Sequencing facility of the I2BC (http://www.i2bc.paris-saclay.fr/spip.php?article399〈=en,CNRS, Gif-sur-Yvette, France). Genomic DNA libraries were made with the ‘Nextera DNA library preparation kit’ (Illumina) following the manufacturer’s recommendations. Library quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit (Agilent technologies). Libraries were pooled in equimolar proportions. 75 bp single reads were generated on an Illumina MiSeq instrument, using a MiSeq Reagent kit V2 (500 cycles) (Illumina), with an expected depth of 217X. Reads were aligned on the in silico reconstituted genome of the cognate strain using BWA software. An in-lab written MATLAB-based script was used to perform marker frequency analysis. Data were normalized by dividing uniquely mapping sequence reads by the total number of reads. Enrichment of uniquely mapping sequence reads in 1 kb non-overlapping windows were calculated and plotted against the chromosomal coordinates.
2021-05-07 | E-MTAB-7193 | biostudies-arrayexpress
Project description:The evolutional trajectory of gut microbial colonization from birth has been shown to prime for health later in life. Here, we combined cultivation-independent 16S rRNA gene sequencing and metaproteomics to investigate the functional maturation of gut microbiota in faecal samples from full-term healthy infants collected at 6 and 18 months of age. Phylogenetic analysis of the metaproteomes showed that Bifidobacterium provided the highest number of distinct protein groups. Considerable divergences between taxa abundance and protein phylogeny were observed at all taxonomic ranks. Age had a profound effect on early microbiota where compositional and functional complexity of less dissimilar communities increased with time. Comparisons of the relative abundances of proteins revealed the transition of taxon-associated saccharolytic and carbon metabolism strategies from catabolic pathways of milk and mucin-derived monosaccharides feeding acetate/propanoate synthesis to complex food sugars fuelling butyrate production. Furthermore, co-occurrence network analysis uncovered two anti-correlated modules of functional taxa. A low-connected Bifidobacteriaceae-centred guild of facultative anaerobes was succeeded by a rich club of obligate anaerobes densely interconnected around Lachnospiraceae, underpinning their pivotal roles in microbial ecosystem assemblies. Our findings establish a framework to visualize whole microbial community metabolism and ecosystem succession dynamics, proposing opportunities for microbiota-targeted health-promoting strategies early in life.
2018-07-16 | PXD009056 | Pride
Project description:Salmonella typhimurium 14028s Transposon library recovered after three consecutive rounds of growth to late log phase in M9 minimal medium (arabinose 0.4%) at 37°C with aeration, compared to an expansion of the initial library selected on Luria agar plates + kanamycin (50ug/ml), O/N at 37°C Keywords: Transposon tag analysis
2008-09-01 | GSE7058 | GEO
Project description:The aim of this study is to investigate whether there is selection for myeloid cells in our mouse models based on X chromosome choice. The mice are heterozygous at each allele for 129 & Bl6 mouse strains. We are investigating whether granulocyte RNA of female aged mice show a skewing towards one strain or the other at polymorphic loci of the X chromosome. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/
2014-05-06 | E-ERAD-245 | biostudies-arrayexpress
Project description:Investigation of whole genome gene expression level in E. coli rpoS knock-out strain grown up to stationary phase in M9 minimal media supplemented with 0.2% glucose E. coli rpoS deletion mutant grown up to OD600nm 1.5 (stationary phase) in M9 minimal media supplemented with 0.2% glucose. The high-density oligonucleotide tiling arrays used were consisted of 371,034 oligonucleotide. Data for wild type controls are GSM389302, GSM389303, and GSM389304.
2014-02-05 | E-GEOD-46543 | biostudies-arrayexpress
Project description:Transcriptional profiling comparing a V. cholerae cpxA* mutant relative to WT at an OD600 of 1.
2014-05-03 | GSE55037 | GEO
Project description:In the title compound, C(12)H(9)NOS, the sulfoxide O atom is disordered over two sites with occupancies of 0.907?(4) and 0.093?(4). The dihedral angle betweeen the two aromatic rings is 18.40?(14)°. Different types of supramolecular interactions including inter-molecular N-H?O hydrogen bonds and ?-? contacts [centroid-centroid distances = 3.9096?(16) and 4.1423?(16)?Å] between the aromatic rings of symmetry-related mol-ecules are observed in the crystal structure.
| S-EPMC3011726 | biostudies-literature
Project description:Nucleic Acid Sequencing for the study of division induced double strand breaks in the terminus region of Escherichia coli cells lacking RecBCD DNA repair enzymes.
2017-09-18 | E-MTAB-6030 | biostudies-arrayexpress
Project description:Pseudoxanthomonas sp. 10H Genome sequencing
| PRJNA1147402 | ENA