Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [CHANGE-seq-BE for ABE targets]

ABSTRACT: To assess CHANGE-seq-BE performance, we used it to characterize ABE8e-NRCH base editor activity targeting sickle mutation (HBBS) in the HBB gene and identified additional 29 (53% more) bona fide off-targets than CIRCLE-seq. Furthermore, CHANGE-seq-BE applied for ABE8e targeting five therapeutically relevant loci (B2M, CBLB, CD7, CIITA, and PDCD1) in human primary T-cells and compared with Digenome-seq. CHANGE-seq-BE is highly sensitive and capable of detecting bona fide off-targets while requiring approximately 20-fold less sequencing reads.

ORGANISM(S): Homo sapiens

PROVIDER: GSE307740 | GEO | 2025/11/05

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [Hybrid Capture Sequencing for CBE and ABE]

Project description:To assess genome-wide off-target activity of base editors and Cas9 nucleases identified by CHANGE-seq-BE, Digenome-seq, and CHANGE-seq, we performed hybrid capture sequencing for five therupatic loci (B2M, CBLB, CD7, CIITA, PDCD1) in human primary T-cells and PCSK9 in human hepatocytes. We observed high on-target editing for ABE, CBE, Cas9 mRNA edited cells and potential off-targets confirmed by hybrid capture sequencing. Our results demonstrate that CHANGE-seq-BE is highly sensitive than Digenome-seq to detect more bona fide off-targets with cellular activity ranging from 0.5% to 92.2%. Moreover, ABE exhibit more off-targets than Cas9 under same delivery conditions.

2025-11-05 | GSE308237 | GEO

Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [Hybrid Capture Sequencing for Cas9]

2025-11-05 | GSE307892 | GEO

Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [CHANGE-seq-BE for CBE targets]

Project description:To adapt and apply for cytosone base editors (CBEs), we perfomed CHANGE-seq-BE using eA3A-BE3 to target B2M, CBLB, CD7, CIITA and PDCD1 regions at different loci. CHANGE-seq-BE identified low frequency off-target editing rates ranging from 1.7% to 7.5% that are not identified by Digenome-seq further implies CHANGE-seq-BE is highly sensitive and can identify true off-targets while requiring 20-fold fewer sequencing reads.

2025-11-05 | GSE298534 | GEO

Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [Digenome-seq]

Project description:To compare the sensitivity of CHANGE-seq-BE to another leading off-target discovery method, we performed Digenome-seq on the same ABE and CBE targets and evaluated them with matching analysis parameters. Many low-frequency off-target sites with editing rates were not identified by Digenome-seq and were only discovered by CHANGE-seq-BE.

2025-12-03 | GSE312238 | GEO

CHANGE-seq reveals the genome-wide activity of CRISPR-Cas9 [RNA-seq]

Project description:We recently developed CHANGE-seq (Circularization for High-throughput Analysis of Nuclease Genome-wide Effects by Sequencing), a fast, streamlined, Tn5 tagmentation-based assay for measuring the genome-wide activity of Cas9 in vitro that is easily scalable to many targets and samples. In this study, we directly compare CIRCLE-seq to CHANGE-seq and systematically evaluate Cas9 genome-wide activity on 110 targets across 13 therapeutically-relevant loci leveraging CHANGE-seq. We validate the sensitivity of CHANGE-seq for identifying sites of bona fide cellular off-target mutations using GUIDE-seq and sensitive targeted tag sequencing. Additionally, we sought to evaluate the impact of chromatin accessibility on cellular off-target activity by comparing CHANGE-seq with matched GUIDE-seq cellular off-target, chromatin, and transcriptional profiles generated from the same human primary T-cells.

2020-09-22 | GSE149362 | GEO

CHANGE-seq reveals the genome-wide activity of CRISPR-Cas9 [ATAC-seq]

2020-09-22 | GSE149361 | GEO

CHANGE-seq reveals the genome-wide activity of CRISPR-Cas9 [ChIP-seq]

2020-06-15 | GSE149295 | GEO

Sensitive and unbiased genome-wide profiling of base-editor-induced off-target activity with CHANGE-seq-BE [gRNA sequencing for ABE targets]

Project description:To identify potential contaminating gRNAs, we adapted a gRNA sequencing assay based on an established SMARTer smRNA sequencing technology. We evaluated five research-grade gRNAs from three synthetic gRNA manufacturer suppliers (A, B and C). We detected the presence of contaminating gRNAs in CBLB and CIITA gRNAs from supplier A (batch 1), with frequency ranging from 0.09% to 2.71%.

2025-11-27 | GSE311547 | GEO

CD74-NRG1 fusion as an bona fide oncogene

Project description:CD74-NRG1 fusion as an bona fide oncogene

| PRJNA762691 | ENA

The role of DOT1L in Th cells

Project description:ChIP sequencing of naïve Th, bona fide Th1 and bona fide Th2 cells

2020-12-15 | GSE138821 | GEO