Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Dissecting cellular crosstalk by sequencing physically interacting cells

ABSTRACT: Dissecting cellular crosstalk by sequencing physically interacting cells

PROVIDER: PRJNA558696 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9906150_1.fastq.gz	Fastqsanger.gz
	SRR9906150_2.fastq.gz	Fastqsanger.gz
	SRR9906160_1.fastq.gz	Fastqsanger.gz
	SRR9906160_2.fastq.gz	Fastqsanger.gz
	SRR9906170_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 218

Similar Datasets

Dissecting cellular crosstalk by sequencing physically interacting cells

Project description:Crosstalk between neighboring cells underlines many biological processes, such as cell activation, differentiation and signaling. Current single-cell genomic technologies lack information of cell-cell interactions, as each cell is profiled separately following tissue dissociation. Here we present Physically Interacting Cells sequencing (PIC-seq), which combines fluorescently activated cell sorting of physically interacting cells along with massively parallel single-cell RNA-sequencing and computational modeling to systematically map in situ cellular interactions and characterize their molecular crosstalk. Focusing on interactions between T cells and dendritic cells (DC) in vitro and in vivo, we map T-DC interaction preferences, and discover regulatory T cells as the major T cell subtype interacting with DC. Analysis of T-DC pairs characterized interaction-specific transcription, including upregulation of a costimulatory program in rare interactions between pathogen-presenting DC and T cells. In summary, PIC-seq provides a new technology to profile cell-cell interactions and characterize interaction-specific pathways and target genes at high resolution.

2020-03-12 | GSE135382 | GEO

Physically interacting cell sequencing of mouse embryonic endoderm at E7.5, E8.5, and E9.5

Project description:Physically interacting cell sequencing of mouse embryonic endoderm at E7.5, E8.5, and E9.5

| PRJNA756041 | ENA

Physically interacting cell sequencing of mouse embryonic endoderm at E7.5, E8.5, and E9.5

Project description:Cells continuously communicate with the neighboring cells during development. Direct interaction of different cell types can induce molecular signals dictating lineage specification and cell fate decisions. The current single-cell RNAseq (scRNAseq) technology cannot study cell contact dependent (or niche specific) gene expression due to the loss of spatial information. To overcome this issue and determine cell contact specific gene expression during embryogenesis, we performed RNA sequencing of physically interacting cells (PICseq) and assessed alongside our single cell transcriptomes (scRNAseq) derived from developing mouse embryos between embryonic day (E) 7.5 and E9.5. Analysis of PICseq data identifies an interesting suite of gene expression signatures depending on neighboring cell types. For instance, neural progenitor (NP) cells expressed Nkx2-1 when interacting with definitive endoderm (DE) and DE cells expressed Gsc when interacting with NP. Based on the identified cell contact specific genes, we devised a means to predict the neighboring cell types from individual cell transcriptome. We further developed spatial-tSNE to show the pseudo-spatial distribution of cells in a 2-dimensional space. In sum, we suggest an approach to study niche specific gene regulation during embryogenesis.

2022-08-03 | GSE182393 | GEO

Physically interacting beta-delta pairs in the regenerating pancreas revealed by single-cell sequencing

Project description:Physically interacting beta-delta pairs in the regenerating pancreas revealed by single-cell sequencing

| PRJNA762008 | ENA

Dissecting autoimmune cellular and molecular networks in vitiligo

Project description:Dissecting autoimmune cellular and molecular networks in vitiligo

| PRJNA735301 | ENA

Dissecting autoimmune cellular and molecular networks in vitiligo

Project description:Dissecting autoimmune cellular and molecular networks in vitiligo

| PRJNA735302 | ENA

Sequencing of Physically Interacting Cells in Human Kidney Allograft Rejection Reveals Insights into Immune Cell Interactions

Project description:Sequencing of Physically Interacting Cells in Human Kidney Allograft Rejection Reveals Insights into Immune Cell Interactions

| PRJNA783343 | ENA

Dissecting crosstalk between embryonic and extra-embryonic tissues with stem cell co-culture

Project description:Dissecting crosstalk between embryonic and extra-embryonic tissues with stem cell co-culture

| PRJNA1008219 | ENA

Dissecting crosstalk between embryonic and extra-embryonic tissues with stem cell co-culture [II]

Project description:Dissecting crosstalk between embryonic and extra-embryonic tissues with stem cell co-culture [II]

| PRJNA976913 | ENA

Dissecting crosstalk between embryonic and extra-embryonic tissues with stem cell co-culture [I]

Project description:Dissecting crosstalk between embryonic and extra-embryonic tissues with stem cell co-culture [I]

| PRJNA739152 | 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