Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Saturation Mutagenesis-Reinforced Functional Assays (SMuRF) Data

PROVIDER: PRJNA993285 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other
	SRR25223776_1.fastq.gz	Fastqsanger.gz
	SRR25223776_2.fastq.gz	Fastqsanger.gz
	SRR25223777_1.fastq.gz	Fastqsanger.gz
	SRR25223777_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 11

Similar Datasets

Saturating mutagenesis with assembled CRISPR-Cas9 ribonucleoprotein complexes.

Project description:The CRISPR-Cas9 system enables efficient sequence-specific mutagenesis for creating germline mutants of model organisms. Key constraints in vivo remain the expression and delivery of active Cas9-guideRNA ribonucleoprotein complexes (RNPs) with minimal toxicity, variable mutagenesis efficiencies depending on targeting sequence, and high mutation mosaicism. Here, we established in vitro-assembled, fluorescent Cas9-sgRNA RNPs in stabilizing salt solution to achieve maximal mutagenesis efficiency in zebrafish embryos. Sequence analysis of targeted loci in individual embryos reveals highly efficient bi-allelic mutagenesis that reaches saturation at several tested gene loci. Such virtually complete mutagenesis reveals preliminary loss-of-function phenotypes for candidate genes in somatic mutant embryos for subsequent generation of stable germline mutants. We further show efficient targeting of functional non-coding elements in gene-regulatory regions using saturating mutagenesis towards uncovering functional control elements in transgenic reporters and endogenous genes. Our results suggest that in vitro assembled, fluorescent Cas9-sgRNA RNPs provide a rapid reverse-genetics tool for direct and scalable loss-of-function studies beyond zebrafish applications.

2016-05-01 | E-MTAB-4143 | biostudies-arrayexpress

Project description:Saturation Mutagenesis of MlaC

| PRJNA849600 | ENA

Project description:DNCR1 single-site saturation mutagenesis

| PRJNA421812 | ENA

Mycobacterium tuberculosis H37Rv

Project description:Mycobacterium tuberculosis PncA saturation mutagenesis

| PRJNA352866 | ENA

Project description:Stabilizing proteins through saturation suppressor mutagenesis

| PRJNA766786 | ENA

Saturation mutagenesis of disease-associated regulatory elements

Project description:The majority of common variants associated with common diseases, as well as an unknown proportion of causal mutations for rare diseases, fall in noncoding regions of the genome. Although catalogs of noncoding regulatory elements are steadily improving, we have a limited understanding of the functional effects of mutations within them. Here, we performed saturation mutagenesis in conjunction with massively parallel reporter assays on 20 disease-associated gene promoters and enhancers, generating functional measurements for over 30,000 single nucleotide substitution and deletion mutations. We find that the density of putative transcription factor binding sites varies widely between regulatory elements, as does the extent to which evolutionary conservation or various integrative scores predict functional effects. These data provide a powerful resource for interpreting the pathogenicity of clinically observed mutations in these disease-associated regulatory elements, and also comprise a gold-standard dataset for the further development of algorithms that aim to predict the regulatory effects of noncoding mutations.

2019-02-15 | GSE126550 | GEO

Saturation mutagenesis of disease-associated regulatory elements

Project description:Saturation mutagenesis of disease-associated regulatory elements

| PRJNA522353 | ENA

Site saturation mutagenesis of 500 human protein domains

Project description:Site saturation mutagenesis of 500 human protein domains

| PRJNA1105013 | ENA

Saturation mutagenesis reveals manifold determinants of exon definition

Project description:Saturation mutagenesis reveals manifold determinants of exon definition

| PRJNA415408 | ENA

Transcriptional Characterization of Streptococcus pneumoniae Interacting with Human Pharyngeal Cells

Project description:We used a combination of adherence assays, mutagenesis and functional genomics to identify novel factors involved in adherence. This work identifies a list of novel potential pneumococcal adherence determinants.

2013-09-30 | GSE44947 | 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