Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nanobody-tethered transposition for dual profiling of chromatin accessibility and DNA methylation

ABSTRACT: DNA methylation and histone modifications are critical epigenetic regulators that orchestrate gene expression and modulate various physiological and pathological processes. However, existing methodologies for simultaneous profiling of these epigenetic marks often require high cell input and suffer from data loss due to bisulfite conversion. In this study, we present advanced multimodal chromatin profiling methods, MethylTag and Multi-MethylTag, that address these challenges by integrating Tn5 transposase with methylated adaptors and optimizing post-bisulfite library preparation. These methods enable high-resolution, multi-dimensional chromatin profiling with reduced cell input and improved data integrity. We validated these techniques in various human and mouse cell lines, revealing complex interactions between DNA methylation and histone modifications. Our findings highlight the utility of these approaches in enhancing epigenetic research and deepening our understanding of the regulatory mechanisms underlying gene expression.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE278068 | GEO | 2026/01/10

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution

Project description:Chromatin states are functionally defined by a complex combination of histone modifications, transcription factor binding, DNA accessibility, and other factors. However, most current single-cell-resolution methods are unable to measure more than one aspect of chromatin state in a single experiment, limiting our ability to accurately measure chromatin states. Here, we introduce nanobody-tethered transposition followed by sequencing (NTT-seq), a new assay capable of measuring the genome-wide presence of multiple histone modifications and protein-DNA binding sites at single-cell resolution. NTT-seq utilizes recombinant Tn5 transposase fused to a set of secondary nanobodies (nb). Each nb-Tn5 fusion protein specifically binds to different immunoglobulin-G antibodies, enabling a mixture of primary antibodies binding different epitopes to be used in a single experiment. We apply bulk- and single-cell NTT-seq to generate high-resolution multimodal maps of chromatin states in cell culture and cells of the human immune system, demonstrating the high accuracy and sensitivity of the method. We further extend NTT-seq to enable simultaneous profiling of cell-surface protein expression alongside multimodal chromatin states to study cells of the immune system.

2022-09-21 | GSE212588 | GEO

Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution

Project description:Nanobody-tethered transposition enables multifactorial chromatin profiling at single-cell resolution

| PRJNA876138 | ENA

Nanobody-tethered Transposition Allows for Multifactorial Chromatin Profiling at Single-cell Resolution

Project description:Nanobody-tethered Transposition Allows for Multifactorial Chromatin Profiling at Single-cell Resolution

| PRJNA884477 | ENA

Nanobody-tethered Transposition Allows for Multifactorial Chromatin Profiling at Single-cell Resolution

Project description:Nanobody-tethered Transposition Allows for Multifactorial Chromatin Profiling at Single-cell Resolution

| PRJNA884478 | ENA

Direct transposition of native DNA for sensitive multimodal single-molecule sequencing IV

Project description:Concurrent readout of sequence and base modifications from long unamplified DNA templates by PacBio single-molecule sequencing requires large amounts of input material. Here we adapt Tn5 transposition to introduce hairpin oligonucleotides and fragment (tagment) limiting quantities of DNA for generating PacBio-compatible circular molecules. We developed two methods that implement tagmentation and use 90–99% less input than current protocols: (1) single-molecule real-time sequencing by tagmentation (SMRT-Tag), which allows detection of genetic variation and CpG methylation; and (2) single-molecule adenine-methylated oligonucleosome sequencing assay by tagmentation (SAMOSA-Tag), which uses exogenous adenine methylation to add a third channel for probing chromatin accessibility. SMRT-Tag of 40 ng or more human DNA (approximately 7,000 cell equivalents) yielded data comparable to gold standard whole-genome and bisulfite sequencing. SAMOSA-Tag of 30,000–50,000 nuclei resolved single-fiber chromatin structure, CTCF binding and DNA methylation in patient-derived prostate cancer xenografts and uncovered metastasis-associated global epigenome disorganization. Tagmentation thus promises to enable sensitive, scalable and multimodal single-molecule genomics for diverse basic and clinical applications.

2024-05-01 | GSE245946 | GEO

Direct transposition of native DNA for sensitive multimodal single-molecule sequencing I

2022-08-08 | GSE210136 | GEO

Direct transposition of native DNA for sensitive multimodal single-molecule sequencing III

2024-05-01 | GSE225311 | GEO

Direct transposition of native DNA for sensitive multimodal single-molecule sequencing II

2024-05-01 | GSE225310 | GEO

Neurulation of the cynomolgus monkey embryo achieved from 3D blastocyst culture [Bisulfite-Seq]

Project description:To further reveal the major cell types of developing pIVC embryos and underlying epigenetic dynamics, the optimized single-cell based multi-omics sequencing method scChaRM-seq was performed (Yan et al., 2021b). 1,862 single cells Bisulfite-seq datasets were further analyzed. We then performed multi-omics profiling analysis using data obtained from9 pIVC embryos at 8 sequential developmental stages.

2023-03-24 | GSE218524 | GEO

Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase

Project description:Here we present APOBEC-coupled epigenetic sequencing (ACE-seq), a bisulfite-free method for localizing 5-hydroxymethylcytosine (5hmC) at single-base resolution with low DNA input. The method builds on the observation that AID/APOBEC family DNA deaminase enzymes can potently discriminate between cytosine modification states and exploits the non-destructive nature of enzymatic, rather than chemical, deamination. ACE-seq yielded high-confidence 5hmC profiles with at least 1,000-fold less DNA input than conventional methods. Applying ACE-seq to generate a base-resolution map of 5hmC in tissue-derived cortical excitatory neurons, we found that 5hmC was almost entirely confined to CG dinucleotides. The whole-genome map permitted cytosine, 5-methylcytosine (5mC) and 5hmC to be parsed and revealed genomic features that diverged from global patterns, including enhancers and imprinting control regions with high and low 5hmC/5mC ratios, respectively. Enzymatic deamination overcomes many challenges posed by bisulfite-based methods, thus expanding the scope of epigenome profiling to include scarce samples and opening new lines of inquiry regarding the role of cytosine modifications in genome biology.

2018-10-08 | GSE116016 | 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