Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sox32 Alleles Generated from Four-guide Cas9 RNP Targeting in G0 Zebrafish Embryos

ABSTRACT: We report long-read sequencing results from the sox32 allele targeted with a multi-guide Cas9 RNP strategy. Embryos were cell-injected with Cas9 RNP programmed with 4 guides simultaneously targeting different portions of the sox32 gene. Genomic DNA was extracted from each embryo and the sox32 coding sequence and intron were amplified and sequenced. Six individual embryos were evaluated. We found that the majority of sequences were unique and most involved mutations confined to the target sites rather than larger lesions spanning two or more target sites. We also found that alleles accumulated mutations over several DNA replication cycles, which may in part explain the diversity of alleles that were generated. This study is the first to use high-throughput sequencing to evaluate of an allele of this size mutated by a multi-guide Cas9 RNP strategy and provides insights into the dynamics of CRISPR-Cas9 RNP gene editing in vivo.

ORGANISM(S): Danio rerio

PROVIDER: GSE115233 | GEO | 2018/07/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

sox32 Alleles Generated from Four-guide Cas9 RNP Targeting in G0 Zebrafish Embryos

Project description:sox32 Alleles Generated from Four-guide Cas9 RNP Targeting in G0 Zebrafish Embryos

| PRJNA474217 | ENA

Dynamics and Competition of CRISPR-Cas9 RNP and AAV donors Mediated Genome Editings

Project description:The CRISPR system identified in Streptococcus pyogenes (Sp) has been widely applied in genome editing. In this system, under the direction of gRNA, endonuclease SpCas9 cut both strands of the cognate DNA. These processes may disrupt the open reading frame of the gene and generate a knockout (KO) allele or achieve precise gene knockin (KI). Here we report the dynamics and DNA repair profiles after the delivery of Cas9-guide RNA ribonucleoprotein (RNP) with or without the adeno-associated virus serum type 6 (AAV6) template in four cell types. We show that editing profiles have distinct differences between cell lines. We reveal AAV6-mediated HDR effectively outcompetes MMEJ-mediated longer deletions but not NHEJ-mediated indels. However, a combination of the small molecule compounds M3814 and Trichostatin A (TSA), which potently inhibits predominant NHEJ repairs, leads to an up to a 3-fold increase in HDR efficiency.

2020-12-14 | GSE155891 | GEO

RNP-MaP: In-cell analysis of protein interaction networks defines functional hubs in RNA

Project description:RNAs interact with networks of proteins to form complexes (RNPs) that govern many biological processes, but inter-protein networks on RNA are currently impossible to examine in a comprehensive way. We developed a live-cell RNP-MaP (RNP network analysis by mutational profiling) chemical probing strategy for mapping simultaneous binding by and cooperative interactions among multiple proteins with single RNA molecules at nucleotide resolution. RNP-MaP revealed that two structurally related, but sequence-divergent noncoding RNAs, RNase P and RMRP, share nearly identical RNP networks and, further, that protein-mediated structural communication identifies function-critical network hubs in these RNAs. RNP-MaP identified previously unknown protein interaction networks within the XIST long noncoding RNA that are conserved between mouse and human RNAs and defined silencing, compartmentalization and splicing communities of proteins whose binding sites are networked together on XIST. The XIST E region contains a dense network of protein interactions, and including PTBP1, MATR3, and TIA1 proteins , which RNP-MaP revealed to each bind the XIST E region via two distinct interaction modes.; Depletion of PTBP1 and MATR3 caused native XIST particles to disperse and disappear in a human cell line. the The highly networked XIST E region was sufficient to mediate XIST RNA-like foci formation in cells. RNP-MaP enables discovery and prioritization of in-cell protein interaction networks critical for function in long RNAs, in the absence of pre-existing knowledge about protein binding sites.

2020-07-05 | GSE152483 | GEO

RIP-seq of polyribosomal SLBP RNP

Project description:UV cross-linking and immunoprecipiatation with high throughput sequencing of cytoplasmic SLBP RNP Polyclonal Î±-SLBP antibody was used to immunoprecipitate SLBP RNP from polyribosomal fractions of HeLa S3 lysates. Mock immunoprecipitation were also performed and serve as a negative control.

2015-12-16 | E-GEOD-62076 | biostudies-arrayexpress

HITS-CLIP of cytoplasmic SLBP RNP

Project description:UV cross-linking and immunoprecipiatation with high throughput sequencing of cytoplasmic SLBP RNP Polyclonal Î±-SLBP antibody was used to immunoprecipitate UV-crosslinked SLBP RNP from cytoplasmic HeLa lysates. Mock immunoprecipitation were also performed and serve as a negative control.

2015-12-16 | E-GEOD-61958 | biostudies-arrayexpress

RIP-seq of polyribosomal SLBP RNP

Project description:UV cross-linking and immunoprecipiatation with high throughput sequencing of cytoplasmic SLBP RNP

2015-12-16 | GSE62076 | GEO

HITS-CLIP of cytoplasmic SLBP RNP

Project description:UV cross-linking and immunoprecipiatation with high throughput sequencing of cytoplasmic SLBP RNP

2015-12-16 | GSE61958 | GEO

SNP array for Cas9 treated human oocytes and embryos

Project description:Human eggs were fertilized with sperm carrying a homozygous mutation in the EYS gene at rs758109813 and treated with a Cas9 RNP targeting this mutation at either fertilization or at the 2-cell stage. The purpose of this analysis was to determine loss of heterozygosity due to CRISPR-induced chromosomal changes. We find that However, in half of the embryos, the break remains unrepaired throughout the first cell cycle, resulting in both segmental, as well as whole chromosome loss. These embryos appear as corrected non-mosaic wild type embryos in an on-target sequence analysis, but are not viable. These results show a surprising tolerance of the human embryo for mitotic entry with unrepaired DNA double strand breaks, and suggest that pericentromeric cleavage by Cas9 may enable the allele-specific removal of chromosomes in trisomic embryos.

2020-10-29 | GSE148488 | GEO

RIP-chip analysis of the C. elegans GLD-2 and RNP-8 protein

Project description:C. elegans GLD-2 forms an active PAP with multiple RNA-binding partners to regulate diverse aspects of germline and early embryonic development. One GLD-2 partner, RNP-8, was previously shown to influence oocyte fate specification. To identify transcripts selectively associated with both GLD-2 and RNP-8, we employ a genomic approach using the method of RNA immunoprecipitation followed by microarray analysis (RIP-chip). We used microarrays to identify mRNAs selectively associated with either GLD-2 or RNP-8. Worm extracts were prepared from synchronized adult C. elegans (15 h after L4 stage). For GLD-2 IP, an immoblized anti-GLD-2 antibody was then used to purify the GLD-2 complexes from either wild-type (N2) or gld-2(RNAi) worm extracts. RNA was then extracted from the pellets and analyzed on C.elegans Affymetrix genechip. Four biological replicates were performed, each sample processed in parallel. For RNP-8 IP, an immoblized anti-RNP-8 antibody was then used to purify the RNP-8 complexes from either wild-type (N2) or rnp-8(q784) worm extracts and three biological replicates were performed. For wt or gld-2(RNAi) samples, total RNA was extracted from worm extracts and hybridized on C.elegans Affymetrix genechip.

2010-09-21 | E-GEOD-23843 | biostudies-arrayexpress

Detection of RNAs binding to Vg1 RNP

Project description:We report the application of NGS for high-throughput profiling of transcripts assoicated with the ribonuleoprotein (RNP) formed on Vg1 mRNA in oocytes of Xenopus Laevis.

2020-07-21 | GSE154766 | GEO

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