Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Illumina sequencing analysis of mutagenicity of eMutaT7[transition]

ABSTRACT: We created a mutator protein, eMutaT7[transition] with targeted in vivo hypermutation in E. coli. To investigate the gene-specific mutagenesis, we sequenced ~3.3 kb DNA around the target gene from cells taken at cycle 0 (n = 1) and cycle 20 (n = 3) by Illumina sequencing.

INSTRUMENT(S): TruSeq Nano DNA Kit, Illumina NovaSeq 6000, Cosmogenetech

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Seokhee Kim

PROVIDER: E-MTAB-12258 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Illumina sequencing analysis of mutagenicity of EvoluGene

Project description:We created a mutator protein, Evolugene with very fast in vivo mutation rate and gene specificity in E. coli. To comprehensively analyze the specificity and mutagenicity, we sequenced ~3.3 kb DNA around the target gene from cells taken at cycle 27 by Illumina sequencing.

2020-10-24 | E-MTAB-9677 | biostudies-arrayexpress

Parallel monitoring of the integration efficiency and stability of mini-TLCΦ plasmids with different attachment sites

Project description:Define the sequence requirement for FtsK-driven and XafT-driven Xer recombination reactions

2022-03-09 | E-MTAB-10951 | biostudies-arrayexpress

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: Plasmid Loss

Project description:We generated a collection of 13 plasmids, with each plasmid containing a variant of a CRISPR protospacer targeted by spacer 8 of the E. coli CRISPR-I array. We transformed the plasmids as a pool into delta cas3 E. coli cells expressing all other cas genes constitutively. We then transformed these cells with either an empty vector or a plasmid expressing the Cas3 nuclease. DNA surrounding the protospacers was PCR-amplified and sequenced.

2017-08-24 | E-MTAB-5969 | biostudies-arrayexpress

Whole genome sequencing analysis of evolved E.coli

Project description:We created a mutator protein. The mutator, was prepared by fusing a PmCDA1 (Petromyzon marinus Cytidine DeAminase) and E.coli RNA polymerase alpha subunit(EcoRNAP alpha). After 120 cycles, whole genome sequencing was performed on the wild type and evolved sample. After characterization of the mutation capacity of our mutator, we evolved a sucrose utilization strain and we sequenced Suc strain.

2021-05-03 | E-MTAB-10368 | biostudies-arrayexpress

Transcription Termination and Antitermination of Bacterial CRISPR Arrays

Project description:V. cholerae A50 has a functional CRISPR-cas system with a conserved boxA sequence. Plasmids harboring protospacers that are perfect targets for each spacer of the array are introduced into wt and boxA mutant V. cholerae. After a period of growth without selection, cells are collected and the protospacer plasmids are sequenced in a high throughput manner.

2020-10-08 | E-MTAB-9631 | biostudies-arrayexpress

Threonine dehydratase couples L-cysteine metabolism to cadmium resistance in Pseudomonas stutzeri 273 through cadmium sulfide nanoparticle biomineralization

Project description:Cysteine is an amino acid containing sulfhydryl (-SH) group which is the basis of cysteine involved in sulfur metabolism and heavy metal detoxification in microorganisms. Here, we demonstrate that adding L-cysteine significantly improves the cadmium resistance and removal ability of Pseudomonas stutzeri 273. Threonine dehydratase (TSD) connects L-cysteine metabolism and cadmium resistance through CdS nanoparticle biomineralization with the ability of catalyzing L-cysteine desulfuration and H2S generation in P. stutzeri 273. Gene knockout of TSD in P. stutzeri 273 results in the decrease of L-cysteine and cadmium resistance, decline of H2S generation, and reduction of CdS biosynthesis ability.

2022-03-01 | PXD011469 | Pride

RNA-seq for identifying toxin MazF and MqsR cleavage sites in toxin expression and subsequent recovery cultures of Escherichia coli (mRNA and ncRNA excluding rRNA)

Project description:Bacterial toxin-antitoxin systems are thought to help bacteria to reduce their metabolism in various stressful conditions. Many toxins of the bacterial toxin-antitoxin systems are ribonucleases. Such toxins have been mostly viewed as degraders of mRNA, however recently it was demonstrated that they are also capable of cleaving non-coding RNA. MazF toxin is also hypothesized to reprogram E. colis translational machinery. Current cDNA libraries are part of a project which aims to identify the major RNA cleavage sites (in mRNA, rRNA and regulatory non-coding RNA) of MazF and MqsR toxins in E. coli. We wanted to elaborate on the roles of MazF and MqsR in E. coli: is MazF really involved in reprogramming the translational machinery or is MazF, along with MqsR, just a robust cleaver of RNA? We extracted total RNA from cultures where the expression of MazF or MqsR was induced for 2h and from cultures that had been recovering from toxin production for 30 minutes; RNA from log phase culture was used as the control. We used strand specific random primed paired end RNA sequencing data to locate the major cleavage sites. To map the cleavage sites, we counted 5’ end stacks of forward reads in each genomic position and compared them with total coverage. MazF and MqsR cleave at specific recognition sequences, ˇACA and GˇC respectively, which allowed us to eliminate the false positives. One of our initial aims was also to look for irregular RNA ligation events following toxin expression, thus we used long, 300 base reads in sequencing.

2018-10-11 | E-MTAB-6993 | biostudies-arrayexpress

The identification of bacterial protein interaction partners pointed out to new intracellular functions of Francisella tularensis glyceraldehyde-3-phosphate dehydrogenase

Project description:Glyceraldehyde-3-phopshate dehydrogenase (GAPDH) is well-known for its involvement in numerous non-metabolic processes inside the mammalian cells. Alternative functions of prokaryotic GAPDH are mainly deduced from its extracellular localization and the ability to bind to selected host proteins. Data on its participation in intracellular bacterial processes are scarce as there is so far only one study dealing with this issue. We previously reported several evidence that the GAPDH homologue of Francisella tularensis, GapA, might also exert additional non-enzymatic functions. To follow up our former observation, here we decided to find out GapA’s interacting partners within the bacterial proteome to explore its new roles at the intracellular level. The quantitative proteomics approach based on stable isotope labelling of amino acids in cell culture (SILAC) in combination with affinity purification and mass spectrometry enabled us to identify 18 proteins potentially interacting with GapA, six of those interactions were further confirmed by alternative methods. Half of the identified proteins were involved in non-metabolic processes. Further analysis together with the quantitative label-free comparative analysis of proteomes isolated from the wild-type strain and strain with deleted gapA gene suggests that the GapA is implicated in DNA repair processes. The absence of GapA promotes secretion of its most potent interaction partner, the hypothetical protein with peptidase propeptide domain (PepSY) indicating its impact on subcellular distribution of some proteins.

2020-08-31 | PXD019739 | Pride

Comparative proteomics for the secretome of Vibrio proteolyticus T6SS3

Project description:Identifying the secreted effector proteins of type VI secretion system 3 (T6SS3) in the bacterium Vibrio proteolyticus.

2023-04-13 | PXD040610 | Pride

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: ChIP Library-seq

Project description:We generated a collection of 13 plasmids, with each plasmid containing a variant of a CRISPR protospacer targeted by spacer 8 of the E. coli CRISPR-I array. We transformed the plasmids as a pool into delta cas3 E. coli cells expressing all other cas genes constitutively, with FLAG-tagged casA. We then used ChIP to enrich for CasA-bound protospacers. DNA surrounding the protospacers was PCR-amplified from input (pre-immunocrecipitation) and ChIP (post-immunoprecipitation) samples and sequenced.

2017-08-24 | E-MTAB-5972 | biostudies-arrayexpress

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