Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Construction of Reusable Plasmid Libraries for Strain Construction

ABSTRACT: Construction of Reusable Plasmid Libraries for Strain Construction

PROVIDER: PRJNA189258 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Construction of Reusable Plasmid Libraries for Strain Construction

Project description:Test whether it is possible to conjugate a whole plasmid library into a recipient strain without loss of fidelity (as judged by aCGH analysis)

2013-12-31 | GSE44258 | GEO

Construction of Reusable Plasmid Libraries for Strain Construction

Project description:Test whether it is possible to conjugate a whole plasmid library into a recipient strain without loss of fidelity (as judged by aCGH analysis) Donor and Recipient Libraries are compared with array CGH to detect copy number differences, a simple selection experiment is also performed

2013-12-31 | E-GEOD-44258 | biostudies-arrayexpress

RNAseq of ∆yacP (∆rae1) mutant and plasmid complemented strain

Project description:To identify the substrates of YacP (Rae1) by determine which RNAs are affected in a ∆yacP mutant and plasmid complemented strain

2017-03-28 | GSE93894 | GEO

The expression profiles analysis of a virulence plasmid-cured strain of shigella flexneri

Project description:In this study, we analyzed the expression profiles of a virulence plasmid-cured strain and wild-type strain of shigella flexneri. The results showed that the genes of glp regulon were upregulated in mutant bacteria in stationary phase cultures.

2008-12-22 | GSE12535 | GEO

Enhanced plasmid mediated bioaugmentation of RDX contaminated matrices in column studies using donor strain Gordonia sp. KTR9 [exp 2]

Project description:To further explore potential molecular mechanisms and pathways by which the presence or absence of the pGKT2 plasmid may be affecting the overall fitness cost in the native Gordonia sp KTR9 strain, transcriptome studies were performed. Transcriptome experiments comparing KTR9 wild-type and mutant strains grown in rich media confirmed the loss of the pGKT2 plasmid and also indicated the loss of the 90 kb pGKT1 plasmid.

2019-07-31 | GSE125550 | GEO

Enhanced plasmid mediated bioaugmentation of RDX contaminated matrices in column studies using donor strain Gordonia sp. KTR9 [exp1]

Project description:To further explore potential molecular mechanisms and pathways by which the presence or absence of the pGKT2 plasmid may be affecting the overall fitness cost in a transconjugant Rhodococcus jostii RHA1 strain, transcriptome studies were performed. Transcriptome experiments comparing RHA1 wild-type and RHA1 transconjugant strains grown in rich media confirmed the presence of the pGKT2 plasmid.

2019-07-31 | GSE125548 | GEO

Transposon-based construction of strand-specific RNA-seq libraries

Project description:We have developed two methods for efficiently consructing RNA-seq libraries using transposition. Each method constructs high quality RNA-seq libraries when compared to standard approaches. One of the methods (Directional Tn-RNA-seq) maintains strand-of-origin information and exhibits strand specificity comparable to current approaches. RNA-seq libraries were constructed from ECC-1, a human cell line, and Universal Human Reference RNA using transposon-based and standard RNA-seq library construciton methods.

2011-10-10 | E-GEOD-32307 | biostudies-arrayexpress

Transposon-based construction of strand-specific RNA-seq libraries

2011-10-10 | GSE32307 | GEO

TELP, a sensitive and versatile library construction method for next-generation sequencing

Project description:Next-generation sequencing has been widely used for the genome-wide profiling of histone modifications, transcription factor binding and gene expression through chromatin immunoprecipitated DNA sequencing (ChIP-seq) and cDNA sequencing (RNA-seq). Here, we describe a versatile library construction method that can be applied to both ChIP-seq and RNA-seq on the widely used Illumina platforms. Standard methods for ChIP-seq library construction require nanograms of starting DNA, substantially limiting its application to rare cell types or limited clinical samples. By minimizing the DNA purification steps that cause major sample loss, our method achieved a high sensitivity in ChIP-seq library preparation. Using this method, we achieved the following: (1) generated high-quality epigenomic and transcription factor-binding maps using ChIP-seq for murine adipocytes; (2) successfully prepared a ChIP-seq library from as little as 25 pg of starting DNA; (3) achieved paired-end sequencing of the ChIP-seq libraries; (4) systematically profiled gene expression dynamics during murine adipogenesis using RNA-seq; and (5) preserved the strand specificity of the transcripts in RNA-seq. Given its sensitivity and versatility in both double-stranded and single-stranded DNA library construction, this method has wide applications in genomic, epigenomic, transcriptomic and interactomic studies. Pre-adipocytes and mature adipocytes were collected. Their chromatin and RNA were subjected to ChIP and mRNA extraction. Sequencing libraries from ChIP DNA or mRNA were generated following either standard protocols or TELP method. The quality and features of TELP libraries were proved and demonstrated in comparison with standard libraries or other published data.

2015-12-15 | E-GEOD-75966 | biostudies-arrayexpress

Inducible meiotic cDNA libraries for genome-wide studies of gene isoforms

Project description:We report the construction of 5 yeast meiotic cDNA libraries and perform proof-of-principle screens to show that these yeast cDNA libraries can be used to identify genes and gene isoforms that are important for competitive fitness. Samples 1-25 are from different stages of cDNA library construction and deep sequencing was used to characterize gene representation in each yeast cDNA library. Samples 26-175 are from proof-of-principle competitive fitness screens.

2021-05-12 | GSE174268 | GEO

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