Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Homo sapiens

ABSTRACT: Elucidating the genetic mechanisms governing cytosine base editing outcomes through CRISPRi screens

PROVIDER: PRJNA1081436 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR28574700.fastq.gz	Fastqsanger.gz
	SRR28579600_1.fastq.gz	Fastqsanger.gz
	SRR28579600_2.fastq.gz	Fastqsanger.gz
	SRR28580300_1.fastq.gz	Fastqsanger.gz
	SRR28580300_2.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 692

Similar Datasets

Enhanced genome-wide knockout screens in bacteria with CRISPR base editors

Project description:Genome-wide knockout or knockdown screens have become powerful tools for the investigation of genotype-to-phenotype relationships. In bacteria, these screens commonly rely on transcriptional repression by dCas9, gene knockouts through Cas9 editing or random transposon mutagenesis, but depending on the technique, suffer from incomplete gene silencing, low editing efficiencies or they require massive library sizes. Here, we take a distinct approach with base editing to introduce premature stop codons or mutate start codons in Escherichia coli using a ScCas9 nickase derived base editor (ScBE3) that exhibits flexible PAM recognition. We then derive guide design rules by applying machine learning to a gene essentiality screen conducted in E. coli. For further improvement, we combined base-editing with Cas9-induced cleavage of the unedited cell fraction. The efficiency of this dual system was validated through a screen of conditionally essential E. coli genes. This improved setup that decouples the gene editing from the screening leads to more efficient guide depletion and confirmed previously published conditionally essential genes. Overall, base editing represents a useful tool for genome-wide knockout screens in bacteria and will eventually enable genome-wide knockout screens in a broader range of bacterial species to study their diverse genetics.

2024-02-05 | GSE225335 | GEO

Massively parallel base editing to map variant effects in human hematopoiesis

Project description:Systematic evaluation of the impact of genetic variants is critical for the study and treatment of human physiology and disease. While specific mutations can be introduced by genome engineering, we still lack scalable approaches that are applicable to the important setting of primary cells, such as blood and immune cells. Here, we describe the development of massively parallel base-editing screens in human hematopoietic stem and progenitor cells. Such approaches enable functional screens for variant effects across any hematopoietic differentiation state. Moreover, they allow rich phenotyping through single-cell RNA sequencing readouts, and separately, characterization of editing outcomes through pooled single-cell genotyping. We efficiently design improved leukemia immunotherapy approaches, comprehensively identify non-coding variants modulating fetal hemoglobin expression, define mechanisms regulating hematopoietic differentiation, and probe the pathogenicity of uncharacterized disease-associated variants. These strategies will advance effective and high-throughput variant-to-function mapping in human hematopoiesis to identify the causes of diverse diseases.

2023-05-02 | GSE215253 | GEO

Project description:Comprehensive evaluation and prediction of base editing outcomes for near-PAMless adenine and cytosine base editors

| PRJNA1046210 | ENA

Bimodal Adenine and Cytosine CRISPR Base Editing on DNA

Project description:Adenine and cytosine base editors (ABEs and CBEs) represent a new genome editing technology that allows the programmable installation of A-to-G or C-to-T alterations on DNA. We engineered Streptococcus pyogenes Cas9-based adenine and cytosine base editor (SpACE) that enables efficient simultaneous introduction of A-to-G and C-to-T substitutions in the same base editing window on DNA.

2020-07-02 | GSE137411 | GEO

Project description:Base editing sensor screens and validation

| PRJNA746395 | ENA

Streptomyces coelicolor strain:M145

Project description:Cytosine base editing data for Streptomyces coelicolor M145

| PRJNA1064385 | ENA

Project description:Engineered APOBEC3A deaminase for highly accurate cytosine base editing.

| PRJNA1042830 | ENA

Project description:Engineered APOBEC3A deaminase for highly accurate cytosine base editing.

| PRJNA938572 | ENA

Project description:Engineered APOBEC3A deaminase for highly accurate cytosine base editing.

| PRJNA938284 | ENA

Project description:Engineered APOBEC3A deaminase for highly accurate cytosine base editing.

| PRJNA938523 | ENA

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