Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

ABSTRACT: Haploid Genetic Screen for functional cell-surface levels of CD47

PROVIDER: PRJNA459485 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7119494.fastq.gz	Fastqsanger.gz
	SRR7119495.fastq.gz	Fastqsanger.gz

Items per page:

1 - 2 of 2

Similar Datasets

Project description:Haploid genetic screen

| PRJNA485887 | ENA

Project description:Haploid screen beta1 Integrin surface level

| PRJNA952841 | ENA

Genome-wide CRISPR screen for comprehensive identification of human factors involved in alternative polyadenylation based on differential localization of CD47 protein

Project description:At least 70% of the human protein-coding genes possess more than one poly(A) site (PAS) and undergo a phenomenon known as alternative polyadenylation (APA), leading to distinct transcripts from a single gene. Previously, it has been demonstrated that shortening or lengthening of mRNA, resulting from the APA, could be observed in physiological and pathological conditions. Nevertheless, factors and cellular mechanisms responsible for the APA are largely unknown. CD47 protein localization was previously demonstrated to be regulated by APA. Here, we showed that core 3′ end processing factors regulate the different CD47 mRNA transcripts. This finding led us to develop an immunofluorescence staining method that simultaneously detects cell surface and intracellular CD47 protein and visualizes altered APA. Using this method, we detected the alterations of CD47 protein localization upon the depletion of the long 3′ untranslated region (UTR) mRNA isoform of CD47 or CFIm25. To systematically elucidate potential novel regulators of APA, we integrated an approach using immunofluorescence staining of cell surface and intracellular CD47 with genome-wide CRISPR screen coupled with pooled single guide RNA (sgRNA) libraries targeting human protein-coding genes. The functional genetic screens and systematic analysis of RNA-seq data revealed POLDIP2 as the potential novel regulator of APA that has global impact on APA regulation. These findings suggest that the study of novel identified APA regulators could lead to a deeper understanding of detailed molecular mechanisms governing APA under physiological and pathological conditions.

2025-08-11 | GSE288919 | GEO

Homo sapiens strain:HAP1

Project description:HAP1 haploid genetic screen for LUJV

| PRJNA395972 | ENA

Haploid genetic screen for components of MLKL-mediated cell death

Project description:Haploid genetic screen for components of MLKL-mediated cell death

| PRJEB26694 | ENA

CD47 expression in natural killer cell regulates homeostasis and modulates immune response to lymphocytic choriomeningitis virus

Project description:CD47 is a ubiquitous cell surface receptor that limits cell clearance by phagocytes that express its counter-receptor signal-regulatory protein-α and directly regulates T cell immunity by interacting with its inhibitory ligand thrombospondin-1. Murine natural killer (NK) cells express higher levels of CD47 than other lymphocytes, but the role of CD47 in regulating NK cell homeostasis and immune function remains unclear. Cd47-/- mice exhibited depletion of NK precursors in bone marrow, but antisense Cd47 knockdown or gene disruption resulted in a dose dependent accumulation of immature and mature NK cells in spleen. Cd47-/- mice were impaired in controlling chronic Clone-13 lymphocytic choriomeningitis virus (LCMV) infection, which was associated with depletion of splenic NK cells and loss of effector cytokine and interferon response gene expression in Cd47-/- NK cells. These data identify CD47 as a cell-intrinsic and systemic regulator of NK cell homeostasis and NK cell responses to viral infection.

2019-03-11 | GSE113980 | GEO

Expression data from mouse optic nerve and optic tract

Project description:A membrane protein SIRPα (CD172a) interacts with another membrane protein CD47 and thereby constitutes a cell–cell contact signal. To investigate the functional role of CD47-SIRPα signal in the brain, we analyzed the effect of genetic ablation of CD47-SIRPα signal on the gene expression profile in specific brain regions by the use of microarrays.

2019-03-22 | GSE118804 | GEO

Expression data from mouse brain mononuclear cells

2019-03-22 | GSE118805 | GEO

CD47 Inhibits Self-renewal and Reprogramming by Regulating c-Myc and Other Stem Cell Transcription Factors

Project description:Signaling through the thrombospondin-1 receptor CD47 broadly limits cell and tissue survival of stress, but the molecular mechanisms are incompletely understood. We now show that loss of CD47 permits sustained proliferation of primary murine endothelial cells and enables these cells to spontaneously reprogram to form multipotent embryoid bodies. c-Myc, Klf4, Oct4, and Sox2 expression is elevated in CD47-null endothelial cells, in several tissues of CD47- or thrombospondin-1-null mice, and in a human T cell line lacking CD47. CD47 knockdown acutely increases mRNA levels of c-Myc and other stem cell transcription factors in cells and in vivo, whereas CD47 ligation by thrombospondin-1 suppresses c-Myc expression. The inhibitory effects of increasing CD47 levels can be overcome by maintaining c-Myc expression and are absent in cells with dysregulated c-Myc. Thus, CD47 antagonists enable cell self-renewal and reprogramming by overcoming negative regulation of c-Myc and other stem cell transcription factors. To identify gene expression changes associated with CD47 null cells, we compared the gene expression profile of these cells with WT endothelial cell, CD47 null Embryoid bodies cells and an established Embryonic Stem cell line.

2013-07-10 | E-GEOD-43133 | biostudies-arrayexpress

Haploid genome-wide screens for essential components and negative regulators of interferon lambda signaling in human cells

Project description:We undertook a unbiased genome-wide haploid genetic screen to identify new components in interferon lambda signaling. In addition, we performed a genome-wide screen to identify genes that repress spontaneous activation of interferon stimulated genes in the absence of interferon. Both of these screens were performed using a HAP1 cell line containing GFP reporter under the transcriptional regulation of the Interferon-Stimulated Response Element from IFIT2. We also overexpressed IL28RA (IFNLR1) in this cell line, in order to sensitize the cells to type III interferon

2017-07-25 | E-MTAB-5866 | biostudies-arrayexpress

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