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 resolves 5mC and 5hmC and reveals their distinct gene regulatory effects

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Mus musculus

PROVIDER: GSE236798 | GEO | 2023/07/13

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 resolves 5mC and 5hmC and reveals their distinct gene regulatory effects.

Project description:Oxidative modification of 5-methylcytosine (5mC) by ten-eleven translocation (TET) DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here, we present joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A toward 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multimodal single-cell data integration, enable accurate identification of neuronal subtypes and uncover context-specific regulatory effects on cell-type-specific genes by TET enzymes.

| S-EPMC11525041 | biostudies-literature

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [snhmCseq]

Project description:Oxidative modification of 5-methylcytosine (5mC) by TET DNA dioxygenases generates 5-hydroxymethylcytosine (5hmC), the most abundant form of oxidized 5mC. Existing single-cell bisulfite sequencing methods cannot resolve 5mC and 5hmC, leaving the cell-type-specific regulatory mechanisms of TET and 5hmC largely unknown. Here we present Joint single-nucleus (hydroxy)methylcytosine sequencing (Joint-snhmC-seq), a scalable and quantitative approach that simultaneously profiles 5hmC and true 5mC in single cells by harnessing differential deaminase activity of APOBEC3A towards 5mC and chemically protected 5hmC. Joint-snhmC-seq profiling of single nuclei from the mouse brains reveals an unprecedented level of epigenetic heterogeneity of both 5hmC and true 5mC at single-cell resolution. We show that cell-type-specific profiles of 5hmC or true 5mC improve multi-modal single-cell data integration, enable accurate identification of neuronal subtypes, and uncover context-specific regulatory effects of cell-type-specific genes by TET enzymes.

2023-07-14 | GSE236776 | GEO

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [snRNAseq]

2023-07-14 | GSE236769 | GEO

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [Joint-snhmC-seq: snhmCseq2.split]

2023-07-14 | GSE236784 | GEO

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [Joint-snhmC-seq: snmCseq2.split]

2023-07-14 | GSE236789 | GEO

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects

Project description:Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects

| PRJNA992435 | ENA

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [snhmCseq]

Project description:Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [snhmCseq]

| PRJNA992415 | ENA

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [snRNAseq]

Project description:Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [snRNAseq]

| PRJNA992409 | ENA

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [Joint-snhmC-seq: snhmCseq2.split]

Project description:Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [Joint-snhmC-seq: snhmCseq2.split]

| PRJNA992426 | ENA

Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [Joint-snhmC-seq: snmCseq2.split]

Project description:Joint single-cell profiling resolves 5mC and 5hmC and reveals their distinct gene regulatory effects [Joint-snhmC-seq: snmCseq2.split]

| PRJNA992433 | 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