Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Combinatorial single-cell profiling of major chromatin types with MAbID

ABSTRACT: Gene expression programs result from the collective activity of numerous regulatory factors. Studying their cooperative mode of action is imperative to understand gene regulation, but simultaneously measuring these factors within one sample has been challenging. Here, we introduce MAbID, a method for combinatorial genomic profiling of histone modifications and chromatin-binding proteins. MAbID employs antibody-DNA conjugates to insert genomic barcodes at sites of epitope occupancy, enabling combined incubation of multiple antibodies to reveal the genomic distributions of many epigenetic markers simultaneously. We used MAbID to profile all major chromatin types and multiplexed measurements without loss of individual data quality. Moreover, we obtained joint measurements of six epitopes in single cells of mouse bone marrow and during mouse in vitro differentiation, capturing associated changes in multifactorial chromatin states. Thus, MAbID holds the potential to gain unique insights into the interplay between gene regulatory mechanisms, especially for low-input samples and in single cells.

ORGANISM(S): Mus musculus Homo sapiens

PROVIDER: GSE218476 | GEO | 2023/09/20

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Comparative genomic hybridization of plasmids containing genomic library clones grown in E. coli to monitor copy number changes over time

Project description:We report a genome-wide, multi-scale approach to simultaneously measure the effect that the increased copy of each gene and/or operon has on a desired trait or phenotype. The method involves i) growth selections on a mixture of several different plasmid based genomic libraries of defined insert sizes or SCALEs, ii) micro-array studies of enriched plasmid DNA, and a ii) mathematical multi-scale analysis (MSA) that precisely identifies the relevant genetic elements. This approach allows for identification of all single open reading frames and larger multi-gene fragments within a genomic library that alter the expression of a given phenotype. We have demonstrated this method in E. coli by monitoring, in parallel, a population of >106 genomic library clones of different insert sizes, throughout continuous selections over a period of 100 generations.

2006-10-26 | E-TABM-143 | biostudies-arrayexpress

High throughput joint profiling of chromatin accessibility and protein levels in single cells [marrow]

Project description:Recent technological advances have enabled massively parallel single-cell Assay for Transposase Accessible Chromatin by sequencing (scATAC-seq) to simultaneously profile the epigenomic landscape in thousands of individual cells. scATAC-seq methods sample genomic DNA accessible to transposases, but have not previously been combined with measurement of protein levels. Here, we present ATAC with Select Antigen Profiling by sequencing, ASAP-seq, a tool to simultaneously profile accessible chromatin and protein levels in thousands of single cells, pairing sparse scATAC data with robust detection of hundreds of cell surface and intracellular protein markers, and optionally, enriched mtDNA coverage for lineage tracing (mtscATAC-seq) with minimal impact on ATAC-seq data quality. ASAP-seq makes use of a novel bridging approach to utilize existing commercially available antibody:oligo conjugates developed for CITE-seq and related technologies. We demonstrate the utility of ASAP-seq in the context of hematopoietic differentiation, cell surface marker dynamics following peripheral blood mononuclear cell stimulation, and as a combinatorial decoder of multiplexed perturbations in primary T cells.

2020-09-08 | GSE156477 | GEO

High throughput joint profiling of chromatin accessibility and protein levels in single cells [Tcell KO]

2020-09-08 | GSE156476 | GEO

High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMCs]

2020-09-08 | GSE156474 | GEO

High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMC_Stim_Multiome]

2021-05-14 | GSE166188 | GEO

High throughput joint profiling of chromatin accessibility and protein levels in single cells [PBMC stimulation]

2020-09-08 | GSE156473 | GEO

High throughput joint profiling of chromatin accessibility and protein levels in single cells [Species mix]

2020-09-08 | GSE156475 | GEO

High throughput joint profiling of chromatin accessibility and protein levels in single cells [Tcell_Intra]

2021-05-14 | GSE166191 | GEO

Simultaneous profiling of multiple chromatin proteins in the same cells

Project description:Methods derived from CUT&RUN and CUT&Tag enable genome-wide mapping of the localization of proteins on chromatin from as few as one cell. These and other mapping approaches focus on one protein at a time, preventing direct measurements of co-localization of different chromatin proteins in the same cells and requiring prioritization of targets where samples are limiting. Here we describe multi-CUT&Tag, an adaptation of CUT&Tag that overcomes these hurdles by using antibody-specific barcodes to simultaneously map multiple proteins in the same cells. Highly specific multi-CUT&Tag maps of histone marks and RNA Polymerase II uncovered sites of co-localization in the same cells, active and repressed genes, and candidate cis-regulatory elements. Single-cell multi-CUT&Tag profiling facilitated identification of distinct cell types from a mixed population and inference of cell type-specific gene expression. In sum, multi-CUT&Tag increases the “per cell” information content of epigenomic maps, facilitating direct analysis of the interplay of different proteins on chromatin.

2021-09-06 | GSE171554 | GEO

NOMe-HiC: joint profiling of genetic variants, DNA methylation, chromatin accessibility, and 3D genome in the same DNA molecule

Project description:Cis-regulatory elements coordinate the regulation of their targeted genes’ expression. However, the joint measurement of cis-regulatory elements’ activities and their interactions in spatial proximity is limited by the current sequencing approaches. We describe a method, NOMe-HiC, which simultaneously captures single nucleotide polymorphisms, DNA methylation, chromatin accessibility (GpC methyltransferase footprints), and chromosome conformation changes from the same DNA molecule, together with the transcriptome, in a single assay. NOMe-HiC shows high concordance with state-of-the-art mono-omic assays across different molecular measurements and reveals coordinated chromatin accessibility at distal genomic segments in spatial proximity and novel types of long-range allele-specific chromatin accessibility.

2023-02-28 | GSE189158 | 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