Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling

ABSTRACT: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling

PROVIDER: PRJNA785812 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR16575500_1.fastq.gz	Fastqsanger.gz
	SRR16575500_2.fastq.gz	Fastqsanger.gz
	SRR16575600_1.fastq.gz	Fastqsanger.gz
	SRR16575600_2.fastq.gz	Fastqsanger.gz
	SRR16575700_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8380

Similar Datasets

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human tonsil]

Project description:Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human tonsil]

| PRJNA778815 | ENA

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human kidney]

Project description:Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human kidney]

| PRJNA785816 | ENA

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 resolved epigenomic profiling of single cells in complex tissues

Project description:The recent development of spatial omics enables single-cell profiling of the transcriptome and the 3D organization of the genome in a spatially resolved manner. A spatial epigenomics method would expand the repertoire of spatial omics tools and accelerate our understanding of the spatial regulation of cellular processes and tissue functions. Here, we developed an imaging approach for spatially resolved profiling of epigenetic modifications in single cells

2022-12-16 | GSE191069 | GEO

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [E13.5 mouse embryo]

Project description:Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [E13.5 mouse embryo]

| PRJNA774737 | ENA

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [mouse organ array]

Project description:Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [mouse organ array]

| PRJNA777262 | ENA

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human tonsil]

Project description:Emerging spatial profiling technology has enabled high-plex molecular profiling in biological tissues, preserving the spatial and morphological context of gene or protein expression. Here we describe expanded chemistry for the Digital Spatial Profiling platform to quantify whole transcriptomes in human and mouse tissues using a wide range of spatial profiling strategies and sample types. We designed multiplexed in situ hybridization probe pools targeting the protein-coding genes in the human and mouse transcriptomes, hereafter referred to as the human or mouse Whole Transcriptome Atlas (WTA). We validated the human and mouse WTA assays using cell lines to demonstrate concordance with orthogonal gene expression profiling methods in profiled region sizes ranging from ∼10-500 cells. By benchmarking against bulk RNAseq and single-molecule fluorescence in situ hybridization, we demonstrate robust transcript detection possible down to ∼100 transcripts per region. To assess the performance of WTA across tissue and sample types, we applied WTA to biological questions in cancer, molecular pathology, and developmental biology. We show that spatial profiling with WTA can detect expected spatial gene expression differences between tumor and tumor microenvironment, identify spatial disease-specific heterogeneity in gene expression in histological structures of the human kidney, and comprehensively map transcriptional programs in anatomical substructures of nine organs in the developing mouse embryo. Digital Spatial Profiling technology with the WTA assays provides a flexible method for spatial whole transcriptome profiling applicable to diverse tissue types and biological contexts.

2022-03-01 | GSE188451 | GEO

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human kidney]

2022-03-01 | GSE190088 | GEO

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human cell pellet array]

Project description:Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [human cell pellet array]

| PRJNA775634 | ENA

Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [mouse cell pellet array]

Project description:Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling [mouse cell pellet array]

| PRJNA777246 | 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