Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identifying gene combinations for targeting innate immune cells to enhance T cells activation [CITE-seq]

ABSTRACT: Identifying gene combinations for targeting innate immune cells to enhance T cells activation [CITE-seq]

PROVIDER: PRJNA1017473 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR26061300_1.fastq.gz	Fastqsanger.gz
	SRR26061300_2.fastq.gz	Fastqsanger.gz
	SRR26061301_1.fastq.gz	Fastqsanger.gz
	SRR26061301_2.fastq.gz	Fastqsanger.gz
	SRR26061302_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 162

Similar Datasets

Identifying gene combinations for targeting innate immune cells to enhance T cells activation [CITE-seq]

Project description:Genetic engineering of hematopoietic cells ex-vivo opens new opportunities for programming immune cells and improving their functionality in response to illness and infections. Molecular methods for genetic manipulation are constantly improving, but it is challenging to reveal which genes are the most beneficial to target and whether multiple genes tackling can further improve the desired outcome. Current screening methods are limited by scale, the number of perturbations, and low content readouts. We developed a hybrid platform called “high multiplicity of perturbations and cellular indexing of transcriptomes and epitopes by sequencing (HMPCITE-seq)” that allows for finding combinations of genes to target and improves desired cellular functions. We used antigen-presenting cells and performed two genome-wide CRISPR screens to enhance the activation and co-stimulation programs and restrict the suppressive programs. Five genes were found in both screens including Cebpb gene. We showed that targeting Cebpb in antigen-presenting cells enhances the expression of costimulatory molecules, prevents attenuate cell migration and phagocytosis, improves T cell proliferation, and restricts tumor growth. To find the genetic interactions between validated targeted genes, and identify gene combinations for targeting, we performed high-order perturbations of validated genes from the screens with single-cell RNA-seq readouts. We found that targeting both Cebpb and Med12 genes shows a better phenotype compared to the single KOs. Thus, the HMPCITE-seq platform, starting from a genome-wide screen, allows the finding of gene combinations to target as demonstrated by functional experiments in-vitro and in-vivo.

2023-09-17 | GSE243244 | GEO

Identifying gene combinations for targeting innate immune cells to enhance T cells activation

Project description:Identifying gene combinations for targeting innate immune cells to enhance T cells activation

| PRJNA869561 | ENA

Identifying gene combinations for targeting innate immune cells to enhance T cells activation [DNA]

Project description:Identifying gene combinations for targeting innate immune cells to enhance T cells activation [DNA]

| PRJNA852272 | ENA

Identifying gene combinations for targeting innate immune cells to enhance T cells activation [RNA-Seq]

Project description:Identifying gene combinations for targeting innate immune cells to enhance T cells activation [RNA-Seq]

| PRJNA869564 | ENA

Identifying gene combinations for targeting innate immune cells to enhance T cells activation [Med12 and Cebpb KO]

Project description:Identifying gene combinations for targeting innate immune cells to enhance T cells activation [Med12 and Cebpb KO]

| PRJNA978003 | ENA

Identifying gene combinations for targeting innate immune cells to enhance T cells activation [Cebpb-KO CRISPR screen]

Project description:Identifying gene combinations for targeting innate immune cells to enhance T cells activation [Cebpb-KO CRISPR screen]

| PRJNA972701 | ENA

Identifying gene combinations for targeting innate immune cells to enhance T cells activation [DNA]

Project description:Genetic engineering of hematopoietic cells ex-vivo opens new opportunities for programming immune cells and improving their functionality in response to illness and infections. Molecular methods for genetic manipulation are constantly improving, but it is challenging to reveal which genes are the most beneficial to target and whether multiple genes tackling can further improve the desired outcome. Current screening methods are limited by scale, the number of perturbations, and low content readouts. We developed a hybrid platform called “high multiplicity of perturbations and cellular indexing of transcriptomes and epitopes by sequencing (HMPCITE-seq)” that allows for finding combinations of genes to target and improves desired cellular functions. We used antigen-presenting cells and performed two genome-wide CRISPR screens to enhance the activation and co-stimulation programs and restrict the suppressive programs. Five genes were found in both screens including Cebpb gene. We showed that targeting Cebpb in antigen-presenting cells enhances the expression of costimulatory molecules, does not attenuate cell migration and phagocytosis, improves T cell proliferation, and restricts tumor growth. To find the genetic interactions between validated targeted genes, and identify gene combinations for targeting, we performed high-order perturbations of validated genes from the screens with single-cell RNA-seq readouts. We found that targeting both Cebpb and Med12 genes shows a better phenotype compared to the single KOs. Thus, the HMPCITE-seq platform, starting from a genome-wide screen, allows the finding of gene combinations to target as demonstrated by functional experiments in-vitro and in-vivo.

2023-09-13 | GSE206832 | GEO

Identifying gene combinations for targeting innate immune cells to enhance T cells activation [RNA-Seq]

2023-09-13 | GSE211213 | GEO

Identifying gene combinations for targeting innate immune cells to enhance T cells activation [Med12 and Cebpb KO]

2023-09-13 | GSE233796 | GEO

Identifying gene combinations for targeting innate immune cells to enhance T cells activation [Cebpb-KO CRISPR screen]

Project description:Genetic engineering of hematopoietic cells ex-vivo opens new opportunities for programming immune cells and improving their functionality in response to illness and infections. Molecular methods for genetic manipulation are constantly improving, but it is challenging to reveal which genes are the most beneficial to target and whether multiple genes tackling can further improve the desired outcome. Current screening methods are limited by scale, the number of perturbations, and low content readouts. We developed a hybrid platform called “high multiplicity of perturbations and cellular indexing of transcriptomes and epitopes by sequencing (HMPCITE-seq)” that allows for finding combinations of genes to target and improves desired cellular functions. We used antigen-presenting cells and performed two genome-wide CRISPR screens to enhance the activation and co-stimulation programs and restrict the suppressive programs. Five genes were found in both screens including Cebpb gene. We showed that targeting Cebpb in antigen-presenting cells enhances the expression of costimulatory molecules, does not attenuate cell migration and phagocytosis, improves T cell proliferation, and restricts tumor growth. To find the genetic interactions between validated targeted genes, and identify gene combinations for targeting, we performed high-order perturbations of validated genes from the screens with single-cell RNA-seq readouts. We found that targeting both Cebpb and Med12 genes shows a better phenotype compared to the single KOs. Thus, the HMPCITE-seq platform, starting from a genome-wide screen, allows the finding of gene combinations to target as demonstrated by functional experiments in-vitro and in-vivo.

2023-09-13 | GSE232543 | 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