Browse
Submit Data
Databases
API
Help

Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Illumina MiSeq

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

SUBMITTER: Anne Stringer

PROVIDER: E-MTAB-5969 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

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

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

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

Vibrio Cholerae CRISPR-cas PAM requirements

Project description:Plasmids were constructed harboring protospacers that are perfect targets for spacers #4 and #21 of the array, but contain NNN (all possible PAM combinations) immediately upstream of the protospacer. The plasmids were introduced into V. cholerae with or without a functional CRISPR-cas system and cells were plated on selective media. Cells were collected and the protospacer plasmids were sequenced in a high throughput manner. PAMs were counted using a custom python script

2024-05-06 | E-MTAB-14044 | biostudies-arrayexpress

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: RNA-Seq

Project description:We measured global RNA levels using RNA-seq in cas3+ E. coli cells with intact CRISPR arrays or cells with the CRISPR-I array deleted to determine if off-target events driven by endogenous spacers affect RNA levels.

2018-02-10 | E-MTAB-6446 | biostudies-arrayexpress

Sequence Requirements for Cascade Function in a Type I-E CRISPR System: RNA-Seq

Project description:We measured global RNA levels using RNA-seq in cas3 E. coli cells with intact CRISPR arrays or cells with the CRISPR-I array deleted to determine if off-target events driven by endogenous spacers affect local gene expression.

2017-08-24 | E-MTAB-5971 | biostudies-arrayexpress

CRISPR Cas3 Plasmid degradation assays

Project description:CRISPR Cas3 Plasmid degradation assays

| PRJEB13999 | ENA

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

Project description:We used ChIP-seq to map binding of the CRISPR surveillance complex, Cascade, in an E. coli strain lacking the endonuclease Cas3. These data enabled us to determine the precise sequence requirements for Cascade binding.

2017-08-24 | E-MTAB-5970 | biostudies-arrayexpress

Characterization of primed adaptation in the Escherichia coli type I-E CRISPR-Cas system

Project description:We determined the set of newly acquired CRISPR spacers during naive and primed adaptation in E. coli. We compared primed adaptation when targeting different plasmid and chromosomal sites. These data provide insight into the sequence features that impact the efficiency of primed adaptation in E. coli.

2020-02-06 | E-MTAB-8700 | biostudies-arrayexpress

Total proteome of AB1157 with RA-inducing plasmid pTn5053

Project description:Bacterial defence systems are tightly regulated to avoid autoimmunity. In Type I restriction-modification (R-M) systems, a specific mechanism called restriction alleviation (RA) controls the activity of the restriction module. In the case of the Escherichia coli Type I R-M system EcoKI, RA proceeds through ClpXP-mediated proteolysis of restriction complexes bound to non-methylated sites that appear after replication or reparation of host DNA. Here, we show that RA is also induced in the presence of plasmids carrying EcoKI recognition sites, a phenomenon we refer to as plasmid-induced RA. Further, we show that the anti-restriction behavior of plasmid-borne non-conjugative transposons such as Tn5053, previously attributed to their ardD loci, is due to plasmid-induced RA. Plasmids carrying both EcoKI and Chi sites induce RA in RecA- and RecBCD-dependent manner. However, inactivation of both RecA and RecBCD restores RA, indicating that there exists an alternative, RecA-independent, homologous recombination pathway that is blocked in the presence of RecBCD. Indeed, plasmid-induced RA in a RecBCD-deficient background does not depend on the presence of Chi sites. We propose that processing of random dsDNA breaks in plasmid DNA via homologous recombination generates non-methylated EcoKI sites, which attract EcoKI restriction complexes channeling them for ClpXP-mediated proteolysis.

2024-06-23 | PXD050621 | Pride

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