Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Nuclear GFP ChIP-seq from bone marrow-derived dendritic cells of GFP-cGAS knock-In mice

ABSTRACT: Nuclear GFP ChIP-seq from bone marrow-derived dendritic cells of GFP-cGAS knock-In mice

PROVIDER: PRJNA516356 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR8470235_1.fastq.gz	Fastqsanger.gz
	SRR8470235_2.fastq.gz	Fastqsanger.gz
	SRR8470236_1.fastq.gz	Fastqsanger.gz
	SRR8470236_2.fastq.gz	Fastqsanger.gz
	SRR8470237_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 8

Similar Datasets

Nuclear GFP ChIP-seq from bone marrow-derived dendritic cells of GFP-cGAS knock-In mice

Project description:Cytosolic DNA activates cyclic GMP-AMP (cGAMP) synthase (cGAS), an innate immune sensor pivotal in anti-microbial defense, senescence, auto-immunity and cancer. cGAS is considered a sequence-independent DNA sensor with limited access to nuclear DNA because of compartmentalization. However, the nuclear envelope is a dynamic barrier and cGAS is present in the nucleus. Here, we identify determinants of nuclear cGAS localization and activation. We show that nuclear-localized cGAS synthesizes cGAMP and induces innate immune activation of dendritic cells, but cGAMP levels are 200-fold lower than following transfection with exogenous DNA. Using cGAS ChIP-seq and a GFP-cGAS knock-in mouse, we find nuclear cGAS enrichment on centromeric satellite DNA, confirmed by imaging, and to a lesser extent with LINE elements. The non-enzymatic N-terminal domain of cGAS determines nucleo-cytoplasmic localization, enrichment on centromeres and activation of nuclear-localized cGAS. These results reveal a preferential functional association of nuclear cGAS with centromeres.

2019-02-27 | GSE125432 | GEO

Nuclear GFP ChIP-seq from human Monocyte Derived Dendritic Cells transduced with GFP-NLS-cGAS or GFP-NLS

2019-02-27 | GSE125431 | GEO

Nuclear GFP ChIP-seq from human Monocyte Derived Dendritic Cells transduced with GFP-NLS-cGAS or GFP-NLS

Project description:Nuclear GFP ChIP-seq from human Monocyte Derived Dendritic Cells transduced with GFP-NLS-cGAS or GFP-NLS

| PRJNA516357 | ENA

NONO detects the nuclear HIV capsid to promote cGAS-mediated innate immune activation

Project description:Detection of viruses by innate immune sensors induces protective antiviral immunity. The viral DNA sensor cGAS is necessary for detection of HIV by human dendritic cells and macrophages. However, synthesis of HIV DNA during infection is not sufficient for immune activation. The capsid protein, which associates with viral DNA, has a pivotal role in enabling cGAS-mediated immune activation. We now find that NONO is an essential sensor of the HIV capsid in the nucleus. NONO protein directly binds capsid with higher affinity for weakly pathogenic HIV-2 than highly pathogenic HIV-1. Upon infection, NONO is essential for cGAS activation by HIV and cGAS association with HIV DNA in the nucleus. NONO recognizes a conserved region in HIV capsid with limited tolerance for escape mutations. Detection of nuclear viral capsid by NONO to promote DNA sensing by cGAS reveals an innate strategy to achieve distinction of viruses from self in the nucleus.

2018-09-28 | GSE109554 | GEO

Gene induction in STAT1-/- fibroblasts transduced with lentiviruses expressing human cGAS

Project description:The hypothesis tested was that lentiviral driven cGAS expression activates antiviral gene expression. Cells were transduced with lentiviruses expressing cGAS or a control (firefly luciferase). Total RNA was harvested 48 h post-transduction and processed for Illumina BeadArray.

2013-12-01 | E-GEOD-52241 | biostudies-arrayexpress

Expression data of GFP-high or low cells of LGR5-GFP or KRT20-GFP knock-in human colorectal tumor organoids.

Project description:We analyzed gene expression of 3 lines LGR5-GFP, 2 lines KRT20-GFP knock-in colorectal tumor organdies. The cancer stem cell (CSC) theory highlights a self-renewing subpopulation of cancer cells that fuels tumour growth. The existence of human CSCs is mainly supported by xenotransplantation of prospectively isolated cells, but their clonal dynamics and plasticity remain unclear. Here, we show that human LGR5+ colorectal cancer cells serve as CSCs in growing cancer tissues. Lineage-tracing experiments with a tamoxifen inducible Cre knock-in allele of LGR5 reveal the self-renewal and differentiation capacity of LGR5+ tumour cells. Selective ablation of LGR5+ CSCs in LGR5-iCaspase9 knock-in organoids leads to tumour regression, followed by tumour regrowth driven by re-emerging LGR5+ CSCs. KRT20 knock-in reporter marks differentiated cancer cells that constantly diminish in tumour tissues, while reverting to LGR5+ CSCs and contributing to tumour regrowth after LGR5+ CSC ablation. We also show that combined chemotherapy potentiates LGR5+ CSCs targeting. These data provide insights into the plasticity of CSCs and their potential as a therapeutic target in human colorectal cancer.

2017-03-30 | GSE83513 | GEO

RNA sequencing of mouse dendritic cells in Aire-reporter strain

Project description:Bulk RNA-seq analysis of mouse dendritic cells (DCs) in Aire-reporter strain (AGF-KI: human AIRE and GFP-Flag tag knock-in). Aire+ DCs and Aire- DCs were isolated from lymph nodes and bone marrow, using Aire-sufficient (+/KI) and Aire-deficient background (-/KI).

2023-01-05 | GSE211006 | GEO

cGAS maintains basal antiviral state

Project description:Upon recognition of aberrantly located DNA, the innate immune sensor cGAS activates STING/IRF-3-driven antiviral responses. Here we characterized the ability of a specific variant of the cGAS-encoding gene MB21D1, rs610913, to alter cGAS-mediated DNA sensing and viral infection. rs610913 is a frequent G>T polymorphism resulting in a P261H exchange in the cGAS protein. Data from the International Collaboration for the Genomics of HIV suggested that rs610913 nominally associates with HIV-1 acquisition in vivo. Molecular modeling of cGAS(P261H) hinted towards the possibility for an additional binding site for a potential cellular co-factor in cGAS dimers. However, cGAS(WT) or cGAS(P261H)-reconstituted THP-1 cGAS KO cells shared steady-state expression of interferon-stimulated genes (ISGs), as opposed to cells expressing the enzymatically inactive cGAS(G212A/S213A). Accordingly, cGAS(WT) and cGAS(P261H) cells were less susceptible to lentiviral transduction and infection with HIV-1, HSV-1, and Chikungunya virus as compared to cGAS KO- or cGAS(G212A/S213A) cells. Upon DNA challenge, innate immune activation appeared to be mildly reduced upon expression of cGAS(P261H) compared to cGAS(WT). Finally, DNA challenge of PBMCs from donors homozygously expressing rs610913 provoked a trend towards a slightly reduced type I IFN response as compared to PBMCs from GG donors. Taken together, the steady-state activity of cGAS maintains a base-line antiviral state rendering cells more refractory to ISG-sensitive viral infections. rs610913 failed to grossly differ phenotypically from the wild-type gene, suggesting that cGAS(P261H) and wild-type cGAS share a similar ability to sense viral infections in vivo.

2022-05-25 | GSE203334 | GEO

RNAseq of GFP-sorted cells (Low-GFP vs. High-GFP, GFP-fed vs GFP+fed)

Project description:RNAseq of GFP-sorted cells (Low-GFP vs. High-GFP, GFP-fed vs GFP+fed)

| PRJNA544322 | ENA

Expression data from Flt3L-derived bone marrow dendritic cells from WT or Clec9agfp/gfp mice treated or not with dead cells

Project description:DNGR-1 (CLEC9A) is expressed in CD8-like dendritic cells (DCs) and detects a ligand exposed on necrotic cells. We have characterized the transcripts that are induced in cultures of Flt3L-derived bone-marrow-derived WT or DNGR1-deficient DCs upon incubation with dead cells. Microarray analysis of the transcriptome of DNGR-1-deficient and WT DCs cultured with dead cells failed to reveal any DNGR-1-dependence in the transcriptional response to dead cells. Flt3L-BMDC from WT or DNGR-1-deficient (Clec9a gfp/gfp) mice were left untreated or were cultured for 5 hours with UV-treated dead cells at a 1:2 ratio. CD24hi CD11blow B220- CD8Î±+-like DC were purified by cell sorting and RNA was extracted. There were 3 replicates for each of the four experimental conditions.

2012-04-30 | E-GEOD-36435 | 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