Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Cloning vector pUC19

ABSTRACT: Protospacer integration into plasmid DNA by Cas1–Cas2

PROVIDER: PRJNA317579 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR3341836.fastq.gz	Fastqsanger.gz
	SRR3341837.fastq.gz	Fastqsanger.gz
	SRR3341838.fastq.gz	Fastqsanger.gz

Items per page:

1 - 3 of 3

Similar Datasets

Sequencing of reaction products from protospacer integration by Cas1-Cas2

Project description:We report the sites of protospacer integration into plasmids by Cas1-Cas2. The goal of this study is to determine the role of sequence elements on protospacer integration. Methods: Cas1-Cas2 integration products were fragmented, end-repaired, adapter ligated, PCR amplified, and analyzed by Illumina sequencing. Protospacer-containing reads were selected by Cutadapt and mapped to the plasmid with Bowtie.

2015-01-30 | E-GEOD-64552 | biostudies-arrayexpress

Cloning vector pUC19

Project description:Sequencing of reaction products from protospacer integration by Cas1-Cas2

| PRJNA271290 | ENA

Sequencing of reaction products from protospacer integration by Cas1-Cas2

Project description:We report the sites of protospacer integration into plasmids by Cas1-Cas2. The goal of this study is to determine the role of sequence elements on protospacer integration.

2015-01-30 | GSE64552 | GEO

Protospacer integration into plasmid DNA by Cas1–Cas2

Project description:We report the integration site specificity of Cas1–Cas2 into target plasmid DNA encoding a CRISPR locus. The goal of this study is to determine the effect of IHF on target site selection of Cas1–Cas2.

2016-05-27 | GSE79992 | GEO

Cas1-Cas2 and DnaK physically and functionally interact to modulate CRISPR Adaptation

Project description:Prokaryotic Cas1-Cas2 protein complexes generate adaptive immunity to mobile genetic elements (MGEs), by capture and integration of MGE DNA in to CRISPR sites. De novo immunity relies on Cas1-Cas2 targeting MGE DNA, without the aid of pre-existing immunity complexes, through mechanisms of ‘naive adaptation’ that are not clear. Using E. coli we show that the chaperone DnaK inhibits Cas1-Cas2 from DNA binding and integration, and that DnaK expression prevents naïve adaptation from chromosomal self-targeting. We show that that inhibition of naïve adaptation is reversible by eliminating DnaK from cells, by mutation of the DnaK substrate binding domain, and by expression of an MGE (phage )protein. We show that a fluorescently labelled Cas1 fusion can be visualised in living cells. Formation of foci depends on active DNA replication, and that the number of foci per cell is much increased in cells lacking DnaK. We discuss a model in which DnaK provides a mechanism for restraining naïve adaptation from self-targeting. This restraint is released once MGE DNA is present in the cell.

2023-05-18 | PXD042090 | Pride

Casposase structure and the mechanistic link between DNA transposition and spacer acquisition by CRISPR-Cas

Project description:Key to CRISPR-Cas adaptive immunity is maintaining an ongoing record of invading nucleic acids that are encountered, a process carried out by the Cas1-Cas2 complex that integrates short segments of foreign genetic material (spacers) into the CRISPR locus. It is hypothesized that Cas1 evolved from casposases, a novel class of transposases. We show here that casposase integration in vitro recapitulates several properties of CRISPR-Cas integrases. The X-ray structure of Methanosarcina mazei casposase bound to DNA representing the product of integration reveals a tetramer with target DNA bound snugly between two dimers in which single-stranded casposon end binding resembles that of spacer 3'-overhangs. The differences between transposase and CRISPR-Cas integrase are largely architectural, and it appears that evolutionary change involved changes in protein-protein interactions to favor Cas2 binding over tetramerization and the separation of Cas1 dimers. This, in turn, led to preferred integration of single spacers over two transposon ends.

2020-02-03 | GSE139037 | GEO

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

Escherichia coli BL21(DE3)

Project description:Record-seq: Recording transcriptional histories using FsRT-Cas1–Cas2

| PRJNA510019 | ENA

Cloning vector pVK100

Project description:Sequence of the cos-npt region of pVK100

| PRJEB36156 | ENA

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