Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity II

ABSTRACT: 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.

ORGANISM(S): Homo sapiens

PROVIDER: GSE298534 | 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

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity IV

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 | GSE307892 | GEO

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity V

2025-11-05 | GSE308237 | GEO

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity III

Project description: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.

2025-11-05 | GSE307740 | GEO

CHANGE-seq-BE enables simultaneously sensitive and unbiased in vitro profiling of Cas-dependent base editor genome-wide off-target activity I

Project description:By CHANGE-seq-BE, we identified a total of 81 potential off-targets and confirmed 95.4% frequencies of on-target editing with no evident off-targets above the detection threshold compared to controls (rhAmp-seq, IDT).

2025-11-05 | GSE298465 | GEO

Project description:Multiplex Digenome-seq

| PRJNA900689 | ENA

Gene expression profile at the single cell level of wild type and Cbl and Cblb knock-out organoids isolated from mouse intestional crypts.

Project description:Organoid grown from intestinal crypts of Cbl flox/flox; Cbl-bflox/flox; R26Cre ERT2 mice were in presence or absence of 4-hydroxy-tamoxifen to delete Cbl and Cblb. Single cell RNA sequencing were performed in these two conditions to undestand the change in cell populations due to Cbl and Cblb depeletion.

2023-07-01 | GSE236186 | GEO

Gene expression profiling of Hodgkin lymphoma cell line KMH2: Comparison of CIITA-BX648577 knockdown cultures with non-silencing controls

Project description:Description of differentially expressed genes between KMH2 CIITA-BX648577 knockdown cultures and non-silencing controls To determine the change in gene expression after siRNA interference with the fusion transcript CIITA-BX 648577 identified in KMH2 cells.

2010-12-11 | E-GEOD-25987 | biostudies-arrayexpress

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

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 | GSE129893 | GEO

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

2019-07-11 | GSE129889 | GEO

CIITA regulated genes in human B cells

Project description:The MHC class II transactivator (CIITA) is essential for the expression of MHC-II genes. CIITA functions as a transcriptional activator when bound to genes although repressive roles have been reported at some loci in other cell types. To define the role of CIITA in gene regulation in human B cells, we performed ChIP-seq for CIITA using three independent antibodies, the histone marks H3K4me3 and H3K27ac, and ATAC-seq in the Raji human B cell line. Additionally, we profiled H3K27ac and ATAC-seq in the CIITA-null RJ2.2.5 cell line. A core set of CIITA peaks were identified that overlapped in all antibodies. Using the H3K27ac, H3K4me3, and ATAC-seq profiles generated in CIITA+ Raji and CIITA-null RJ2.2.5 cells CIITA dependent chromatin modifications were identified. These data define the CIITA regulated genes in human B cells.

2015-03-06 | GSE52941 | 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