Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency and patterns

ABSTRACT: Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency and patterns

PROVIDER: PRJNA525279 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Similar Datasets

Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency and patterns

Project description:Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR/Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. We leverage our TRIP technology to integrate ~1k barcoded reporter genes in the genomes of mouse embryonic stem cells. We target the integrated reporters (IRs) using RNA-guided Cas9 and characterize induced mutations by sequencing. We report that gRNA-sequence and IR locus explain most variation in mutation efficiency. Predominant insertions of a gRNA-specific nucleotide are consistent with template-dependent repair of staggered DNA ends with 1-bp 5′ overhangs. We confirm that such staggered ends are induced by Cas9 in mouse pre-B cells. To explain observed insertions, we propose a model generating primarily blunt and occasionally staggered DNA ends. Mutation patterns indicate that gRNA-sequence controls the fraction of staggered ends, which could be used to optimize Cas9-based insertion efficiency.

2019-03-08 | GSE127752 | GEO

Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency.

Project description: Not available

| S-EPMC6453899 | biostudies-literature

RNASeq of Arg2 gRNA or scrambled gRNA CRISPR'd Tregs

Project description:RNASeq of Arg2 gRNA or scrambled gRNA CRISPR'd Tregs

| PRJNA588065 | ENA

Cas9 gRNA engineering for selectable genome editing, activation and repression

Project description:RNA-Seq after Cas9-gRNA transfection with different length gRNAs we performed PolyA Selection and RNA-Seq on cells transfected with dCas9-VPR and a gRNA of each length (20nt, 16nt, or 14nt) targeting ACTC1, MIAT, or HBG1/2

2015-07-15 | E-GEOD-70694 | biostudies-arrayexpress

Zebrafish 22 hpf embryos: WT vs. MO-grnA injected

Project description:Transcriptional profiling of zebrafish embryos comparing wild type untreated embryos with embryos injected with morpholino of zf-grna. This assay is used for the determination of expression profiling at 22 hpf under GRN-A deficiency. Two-condition experiment: wild type vs. MO-grnA treated cells. 3 biological replicates: each group contains 200 embryos.

2013-03-28 | E-GEOD-28318 | biostudies-arrayexpress

WT vs MO-grnA injected: 16, 24, 48, 72 hpf trunk region of zebrafish embryos

Project description:Transcriptional profiling of zebrafish embryo comparing wild type untreated embryos with embryos injected with morpholino of zf-grna. This assay is used for determination of expression profiling of trunk muscle at 16, 24, 48, 72 hpf under GRN-A deficiency. Two-condition experiment, wild type vs. MO-grnA treated cells. Biological replicates: each group contains 200 embryos.

2013-06-01 | E-GEOD-38441 | biostudies-arrayexpress

Highly multiplexed genome engineering using CRISPR/Cas9 gRNA arrays.

Project description: Not available

| S-EPMC6141065 | biostudies-literature

IDLV capture for gRNA off-target analysis

Project description:IDLV capture for gRNA off-target analysis

| PRJNA552824 | ENA

IDLV capture for gRNA off-target analysis

Project description:Vector capturing was used for experimental identification of potential off-target sites of 2 gRNA targeting alpha globin genes

2020-05-26 | GSE133861 | GEO

Genome Editing with Tyrosinase gRNA

Project description:We confirmed Tyrosinase genome insertions or deletions of the three Tg mice by deep sequencing using MiSeq. These mice generated gene editing mice by using Tol2 transposon to introduce tyrosinase guide RNA (gRNA) into fertilized eggs obtained by crossing LSL (loxP-stop-loxP)-Cas9 mice with CAG-CreER mice.

2023-02-27 | GSE225711 | 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