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| Status |
Public on Mar 01, 2018 |
| Title |
CRISPR RNA-dependent binding and cleavage of endogenous RNAs by the Campylobacter jejuni Cas9 |
| Organisms |
Campylobacter jejuni; Escherichia coli K-12 |
| Experiment type |
Expression profiling by high throughput sequencing
Other
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| Summary |
This study investigates the RNA targets and cleavage sites of endogenous Cas9 in the food-borne pathogen Campylobacter jejuni. Direct RNA binding targets of Cas9 in C. jejuni strain NCTC11168 were determined using RIP-seq. The Cleavage sites were then predicted in the RNA targets by comparing total transcriptome data from WT and deletion (cas9, crRNA3, tracrRNA, CRISPR-tracrRNA) strains. PAMs for the CjeCas9 were enriched using the PAM-SCANR platform, which operates through a GFP reporter gene. Upon GFP (and thus functional PAM) enrichment, fluorescing cells were isolated using FACS and prepared plasmid DNA was amplified and prepared for sequencing.
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| Overall design |
Identification of Cas9 binding and cleavage sites in C. jejuni strain NCTC11168. Four total files are included for the PAM-SCANR dataset. Raw reads are available for both biological replicates, both pre- and post-FACS. After extracting the variable PAM region from the reads, enrichment was calculated by comparing the pre-FACS PAM counts to the post-FACS counts. These calculations are presented in the included processed data file.
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| Contributor(s) |
Dugar G, Leenay RT, Eisenbart SK, Bischler T, Aul BU, Beisel CL, Sharma CM |
| Citation(s) |
29499139 |
| |
| Submission date |
Nov 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Thorsten Bischler |
| E-mail(s) |
thorsten.bischler@uni-wuerzburg.de
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| Organization name |
University of Wuerzburg
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| Department |
Core Unit SysMed
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| Street address |
Josef-Schneider-Straße 2 / D15
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| City |
Würzburg |
| ZIP/Postal code |
97080 |
| Country |
Germany |
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| Platforms (2) |
| GPL19168 |
Illumina MiSeq (Escherichia coli K-12) |
| GPL19974 |
Illumina HiSeq 2500 (Campylobacter jejuni) |
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| Samples (13)
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| Relations |
| BioProject |
PRJNA418174 |
| SRA |
SRP124876 |
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