Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

PROVIDER: PRJNA1046210 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR26974430_1.fastq.gz	Fastqsanger.gz
	SRR26974430_2.fastq.gz	Fastqsanger.gz
	SRR26974431_1.fastq.gz	Fastqsanger.gz
	SRR26974431_2.fastq.gz	Fastqsanger.gz
	SRR26974432_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 52

Similar Datasets

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

Transcriptome-wide effects of cytosine and adenine deaminases on gene expression induced by base editors

Project description:We used RNA-sequencing data to explore the transcriptome-wide effects of cytosine and adenine deaminases on gene expression induced by base editors.

2021-06-01 | GSE158693 | GEO

Project description:Cas12a based cytosine base editors (CBEs) and adenine base editors (ABEs) in rice

| PRJNA910189 | ENA

Precise adenine base editors that exhibit minimized cytosine catalysis

Project description:Precise adenine base editors that exhibit minimized cytosine catalysis

| PRJNA693459 | ENA

Comprehensive evaluation of adenine base editors induced mutations at genomic and transcriptional level

Project description:Comprehensive evaluation of adenine base editors induced mutations at genomic and transcriptional level

| PRJNA769274 | ENA

One-step generation of tumor models by base editor multiplexing in adult stem cell-derived organoids

Project description:Optimization of CRISPR/Cas9-mediated genome engineering has resulted in base editors that hold promise for mutation repair and disease modeling. Here, we demonstrate the application of base editors for the generation of complex tumor models in human ASC-derived organoids. First we show Efficacy of cytosine and adenine base editors in modelingCTNNB1hot-spot mutations in hepatocyte organoids. Next, we use C>T base editors to insert nonsense mutations inPTENin endometrial organoids and demonstrate tumorigenicity even in the heterozygous state. Moreover, drug screening assays on organoids harboring eitherPTENorPTENandPIK3CAmutations reveal the mechanism underlying the initial stages of endometrial tumorigenesis. To further increase the scope of base editing we combine SpCas9 and SaCas9 for simultaneous C>T and A>G editing at individual target sites. Finally, we show that base editor multiplexing allow modeling of colorectal tumorigenesis in a single step by simultaneously transfecting sgRNAs targeting five cancer genes.

2023-07-30 | GSE236490 | GEO

Comprehensive evaluation of adenine base editors induced mutations at genomic and transcriptional level [transcriptome]

Project description:Comprehensive evaluation of adenine base editors induced mutations at genomic and transcriptional level [transcriptome]

| PRJNA769277 | ENA

Comprehensive evaluation of adenine base editors induced mutations at genomic and transcriptional level [WGS]

Project description:Comprehensive evaluation of adenine base editors induced mutations at genomic and transcriptional level [WGS]

| PRJNA769278 | ENA

CRISPR adenine and cytosine base editors with reduced RNA off-target activities [ABE]

Project description:CRISPR-guided DNA base editors enable the efficient installation of targeted single-nucleotide changes. Cytosine or adenine base editors (CBEs or ABEs), which are fusions of cytidine or adenosine deaminases to CRISPR-Cas nickases, can efficiently induce DNA C-to-T or A-to-G alterations in DNA, respectively. We recently demonstrated that both the widely used CBE BE3 (harboring a rat APOBEC1 cytidine deaminase) and the optimized ABEmax editor can induce tens of thousands of guide RNA-independent, transcriptome-wide RNA base edits in human cells with high efficiencies. In addition, we showed the feasibility of creating SElective Curbing of Unwanted RNA Editing (SECURE)-BE3 variants that exhibit substantially reduced unwanted RNA editing activities while retaining robust and more precise on-target DNA editing. Here we describe structure-guided engineering of SECURE-ABE variants that not only possess reduced off-target RNA editing with comparable on-target DNA activities but are also the smallest Streptococcus pyogenes Cas9 (SpCas9) base editors described to date. In addition, we tested CBEs composed of cytidine deaminases other than APOBEC1 and found that human APOBEC3A (hA3A) cytidine deaminase CBE induces substantial transcriptome-wide RNA base edits with high efficiencies. By contrast, a previously described “enhanced” A3A (eA3A) cytidine deaminase CBE or a human activation-induced cytidine deaminase (hAID) CBE induce substantially reduced or near background levels of RNA edits. In sum, our work describes broadly useful SECURE-ABE and -CBE base editors and reinforces the importance of minimizing RNA editing activities of DNA base editors for research and therapeutic applications.

2019-07-11 | GSE129889 | GEO

CRISPR adenine and cytosine base editors with reduced RNA off-target activities [CBE]

2019-07-11 | GSE129893 | GEO