Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatial epigenome-transcriptome co-profiling of mammalian tissues [RNA-Seq]

ABSTRACT: We present spatially resolved high-spatial-resolution genome-wide co-mapping of epigenome and transcriptome by simultaneously profiling of chromatin accessibility and gene expression (spatial-ATAC-RNA-seq), as well as histone modification and gene expression (spatial-CUT&Tag-RNA-seq) on the same tissue section at cellular level by combining the microfluidic deterministic barcoding strategy in DBiT-seq and the chemistry used in ATAC-seq/CUT&Tag.

ORGANISM(S): Mus musculus

PROVIDER: GSE205054 | GEO | 2023/01/29

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Spatial epigenome-transcriptome co-profiling of mammalian tissues [spatial CUT&Tag]

Project description:We present spatially resolved high-spatial-resolution genome-wide co-mapping of epigenome and transcriptome by simultaneously profiling of chromatin accessibility and gene expression (spatial-ATAC-RNA-seq), as well as histone modification and gene expression (spatial-CUT&Tag-RNA-seq) on the same tissue section at cellular level by combining the microfluidic deterministic barcoding strategy in DBiT-seq and the chemistry used in ATAC-seq/CUT&Tag.

2023-01-29 | GSE217091 | GEO

Spatial epigenome-transcriptome co-profiling of mammalian tissues

2023-01-29 | GSE218593 | GEO

Spatial epigenome-transcriptome co-profiling of mammalian tissues [Human RNA-Seq]

2023-01-29 | GSE205181 | GEO

Spatial epigenome-transcriptome co-profiling of mammalian tissues [Human ATAC-Seq]

2023-01-29 | GSE205180 | GEO

Spatial epigenome-transcriptome co-profiling of mammalian tissues [ATAC-Seq]

2023-01-29 | GSE205052 | GEO

Spatial epigenome-transcriptome co-profiling of mammalian tissues [CUT&TAG]

2023-01-29 | GSE205051 | GEO

Spatial profiling of chromatin accessibility in mouse and human tissues

Project description:We present spatially resolved chromatin accessibility profiling of tissue sections via next-generation sequencing by combining in situ ATAC-seq chemistry and microfluidic deterministic barcoding. Mouse and human tissues were profiled by spatial-ATAC-seq.

2022-05-20 | GSE171943 | GEO

Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level

Project description:Spatial omics emerged as a new frontier of biological and biomedical research. Here, we present spatial-CUT&Tag for spatially resolved genome-wide profiling of histone modifications by combining in situ CUT&Tag chemistry, microfluidic deterministic barcoding, and next-generation sequencing. Spatially resolved chromatin states in mouse embryos revealed tissue-type-specific epigenetic regulations in concordance with ENCODE references and provide spatial information at tissue scale. Spatial-CUT&Tag revealed epigenetic control of the cortical layer development and spatial patterning of cell types determined by histone modification in mouse brain. Single-cell epigenomes can be derived in situ by identifying 20-micrometer pixels containing only one nucleus using immunofluorescence imaging. Spatial chromatin modification profiling in tissue may offer new opportunities to study epigenetic regulation, cell function, and fate decision in normal physiology and pathogenesis.

2022-02-10 | GSE165217 | GEO

Spatially exploring RNA biology in archival formalin-fixed paraffin-embedded tissues

Project description:The capability to spatially explore RNA biology in formalin-fixed paraffin-embedded (FFPE) tissues holds transformative potential for histopathology research. Here, we present pathology-compatible deterministic barcoding in tissue (Patho-DBiT) by combining in situ polyadenylation and computational innovation for spatial whole transcriptome sequencing, tailored to probe the diverse RNA species in clinically archived FFPE samples. It permits spatial co-profiling of gene expression and RNA processing, unveiling region-specific splicing isoforms, and high-sensitivity transcriptomic mapping of clinical tumor FFPE tissues stored for five years. Furthermore, genome-wide single nucleotide RNA variants can be captured to distinguish malignant subclones from non-malignant cells in human lymphomas. Patho-DBiT also maps microRNA regulatory networks and RNA splicing dynamics, decoding their roles in spatial tumorigenesis. Cellular-level Patho-DBiT dissects the spatiotemporal cellular dynamics driving tumor clonal architecture and progression. Patho-DBiT stands poised as a valuable platform to unravel rich RNA biology in FFPE tissues to aid in clinical pathology evaluation.

2024-08-12 | GSE274641 | GEO

High spatial resolution multi-omics atlas sequencing of mouse embryos

Project description:Microfluidic deterministic barcoding of mRNAs and proteins in tissue slides followed by high throughput sequencing enables the construction of high-spatial-resolution multi-omics atlas at the genome scale. Applying it to mouse embryo tissues revealed major tissue (sub)types in early-stage organogenesis, brain micro-vasculatures, and the fine structure of an optical vesicle at the single-cell-layer resolution.

2020-09-16 | GSE137986 | 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