Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Joint single-cell profiling of Cas9 edits and transcriptomes reveals on- and off-target effects on gene expression (RNA-seq)

ABSTRACT: A longstanding barrier in genome engineering with CRISPR-Cas9 has been the inability to characterize editing outcomes at single-cell resolution. We present "Superb-seq", a new scRNA-seq method that measures on-target and off-target genome edits and associated transcriptomes. In contrast to Perturb-seq that captures single-cell guide information, Superb-seq directly captures single-cell edit profiles by T7 in situ transcription. We demonstrate and validate this method through two Superb-seq experiments in 30,000 cells of three cell types, amplicon sequencing (rhAmpSeq), and bulk RNA-seq. Superb-seq uses off-the-shelf kits, standard laboratory equipment, and requires no virus, which will improve CRISPR screens in diverse tissues and functional characterization of CRISPR therapeutics.

ORGANISM(S): Homo sapiens

PROVIDER: GSE313958 | GEO | 2025/12/17

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Joint single-cell profiling of Cas9 edits and transcriptomes reveals on- and off-target effects on gene expression (rhAmpSeq)

Project description:A longstanding barrier in genome engineering with CRISPR-Cas9 has been the inability to characterize editing outcomes at single-cell resolution. We present "Superb-seq", a new scRNA-seq method that measures on-target and off-target genome edits and associated transcriptomes. In contrast to Perturb-seq that captures single-cell guide information, Superb-seq directly captures single-cell edit profiles by T7 in situ transcription. We demonstrate and validate this method through two Superb-seq experiments in 30,000 cells of three cell types, amplicon sequencing (rhAmpSeq), and bulk RNA-seq. Superb-seq uses off-the-shelf kits, standard laboratory equipment, and requires no virus, which will improve CRISPR screens in diverse tissues and functional characterization of CRISPR therapeutics.

2025-12-17 | GSE313955 | GEO

Joint single-cell profiling of Cas9 edits and transcriptomes reveals on- and off-target effects on gene expression (Superb-seq)

Project description:A longstanding barrier in genome engineering with CRISPR-Cas9 has been the inability to measure Cas9 edit outcomes at single-cell resolution. Here we present Superb-seq, a new technology for joint measurement of on-target and off-target Cas9 edits and transcriptomes by single-cell RNA sequencing. In contrast to Perturb-seq methods that read each cell’s guide RNA, Superb-seq directly reads Cas9 edits by leveraging T7 in situ transcription. We performed Superb-seq on 9,500 K562 cells, targeting four chromatin remodeler genes with seven guide RNAs. Superb-seq identified 11,891 edit events in 6,230 edited cells at all seven on-target sites and at 36 off-target sites. One notable off-target edit fell within the first intron of the deubiquitinase gene USP9X, which decreased its expression and perturbed the expression of downstream genes. Superb-seq uses off-the-shelf kits, standard equipment, and requires no virus, which will enable CRISPR screens in virus-intolerant cell types and functional characterization of off-target events.

2025-02-25 | GSE284207 | GEO

Joint single-cell profiling of Cas9 edits and transcriptomes reveals on- and off-target effects on gene expression (Superb-seq)

Project description:Joint single-cell profiling of Cas9 edits and transcriptomes reveals on- and off-target effects on gene expression (Superb-seq)

| PRJNA1197977 | ENA

Transcriptome wide edits after split-engineered base editor treatment

Project description:We report transcriptome wide edits comparison between split-engineered base editors and intact base editors. Our results show that, split-engineered base editors show backgound levels of unique C>U edits when compared to intact base editors.

2021-10-18 | GSE181109 | GEO

Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase [Nanopore]

Project description:Genome editing enables sequence-function profiling of endogenous cis-regulatory elements, driving understanding of their mechanisms. However, these approaches lack direct, scalable readouts of chromatin accessibility across long single-molecule chromatin fibers. Here we leverage double-stranded DNA cytidine deaminases to profile chromatin accessibility at endogenous loci of interest through targeted PCR and long-read sequencing, a method we term targeted deaminase-accessible chromatin sequencing (TDAC-seq). With high sequence coverage at targeted loci, TDAC-seq can be integrated with CRISPR perturbations to link genetic edits and their effects on chromatin accessibility on the same single chromatin fiber at single-nucleotide resolution. We employed TDAC-seq to parse CRISPR edits that activate fetal hemoglobin in human CD34+ hematopoietic stem and progenitor cells (HSPCs) during erythroid differentiation as well as in pooled CRISPR and base-editing screens tiling an enhancer controlling the globin locus. We further scaled the method to interrogate 947 variants in a GFI1B-linked enhancer associated with myeloproliferative neoplasm risk in a single pooled CRISPR experiment in CD34+ HSPCs. Together, TDAC-seq enables high-resolution sequence-function mapping of single-molecule chromatin fibers by genome editing.

2025-07-04 | GSE284033 | GEO

Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase [ATAC-seq]

2025-07-04 | GSE284031 | GEO

Selict-seq profiles genome-wide off-target effects in adenosine base editing

Project description:Adenosine base editors (ABEs) facilitate the conversion of A•T base pairs to G•C base pairs, demonstrating significant potential for correcting pathogenic point mutations in humans. However, the off-target editing effects of ABEs remain inadequately characterized. In this study, we present a biochemical method, Selict-seq, designed to evaluate genome-wide off-target editing by ABEs. Selict-seq specifically captures dI-containing single-stranded DNA (ssDNA) and precisely identifies dA-to-dI mutation sites, thereby elucidating the off-target effects induced by ABEs. Through investigations involving three single-guide RNAs (sgRNAs), we identified numerous unexpected off-target edits both within and outside the protospacer regions. Analysis of these off-target sites revealed distinct characteristics of the ABE8e(V106W). These findings significantly advance our understanding of the off-target landscape associated with ABE8e. In summary, our approach enables an unbiased analysis of the ABE editome and provides a widely applicable tool for specificity evaluation of various emerging genome editing technologies.

2025-03-25 | GSE278492 | GEO

Project description:Deep Sequencing CRISPR edits

| PRJNA757741 | ENA

Project description:Deep Sequencing CRISPR edits

| PRJNA758082 | ENA

Project description:Deep Sequencing CRISPR edits

| PRJNA758048 | ENA