Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Amplicon sequencing of STING gene to validate CRISPR-Cas9 cut sites in PC9 cell line

ABSTRACT: Cells carrying lentiCRISPRv2 e.v. or lentiCRISPRv2 sgSTING were selected with puromycin before DNA was extracted to assess the genomic alterations at the target locus.

INSTRUMENT(S): Illumina NovaSeq 6000

ORGANISM(S): Homo sapiens

SUBMITTER: Johannes Braegelmann

PROVIDER: E-MTAB-10851 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Amplicon sequencing of STING gene to validate CRISPR-Cas9 cut sites in PC9 cell line

Project description:Amplicon sequencing of STING gene to validate CRISPR-Cas9 cut sites in PC9 cell line

| PRJEB46952 | ENA

Vec-STING LS-MS and US2 STING LS-MS

Project description:Since US2 causes STING to be degraded through ubiquitination, we aimed to find any ubiquitin enzymes that might be implicated in this action.

2024-08-09 | PXD053353 | Pride

Single-cell Gene Expression Flex analysis on cell line derived xenografts of PC9 cells treated with Osimertinib

Project description:The goal of the experiment is determine whether the mixing of human and mouse probe sets of the 10x Genomics Gene Expression Flex allows to profile cell line derived xenograft (CDX) samples. We profiled a CDX vehicle sample and a CDX sample after 10 days of treatment with Osimertinib at 25mg/kg.

2024-04-15 | E-MTAB-13963 | biostudies-arrayexpress

Single-cell Gene Expression Flex analysis on PC9 cells co-cultured with NIH-3T3 cells

Project description:The goal of the experiment is to determine whether it is feasible to use the 10x Genomics Gene Expression Flex solution in samples containing a mixture of human and mouse cells. First we tested how the presence of mouse cells impacted the data recovered by the use of the human whole trasnscriptome amplification (WTA) probe sets. Then we profiled a mixed species sample by using human and mouse probe sets in the same reaction. Finally, for samples with lower amounts of human cells we tried to correct the amount of cells recovered by the human and mouse probe sets by adjusting the amount of cells loaded from the respective hybridizations.

2024-04-15 | E-MTAB-13962 | biostudies-arrayexpress

Mass spectrometry analysis of proteins interacting with STING mutants

Project description:To investigate proteins interacting with STING mutants, HEK 293T cells were co-transfected with three STING mutant expression plasmids (human STING WT, STING delCTT (aa343-379 deletion), STING del6 (aa325-379 deletion) in a pcDNA3.1+ backbone) and either pcDNA-cGAS expression plasmid or control empty pcDNA plasmid. Lysed cells were then immunoprecipitated using sheep anti-STING or control sheep anti-IgG antibodies and protein G magnetic Dynabeads.

2024-02-19 | PXD038063 | Pride

Lymphopenia-induced T cell exhaustion in STING gain-of-function mouse model

Project description:STING gain-of-function (GOF) mutations lead to T cell lymphopenia, in the context of severe combined immunodeficiency (SCID) for STING GOF V154M mice. This T cell lymphopenia, which is of central origin, has been described as type I IFN independent and associated with dysfunctions of the rare mature T cells found in the periphery. To better describe the biological mechanisms of these dysfunctions, we performed a transcriptomic analysis by RNA-seq on sorted splenic CD4+ and CD8+ mature T cells from STING GOF mice. We highlighted an unexpected T cell exhaustion phenotype that could partly explain their dysfunctions. Acquired very early in life, but only once the peripheral environment is reached, the phenotype appeared to depend neither on type I IFNs, nor on the intrinsic activation of STING in T or stromal cells. Mechanistically, the few mature T cells reaching the periphery seem to be rapidly impacted by the lymphopenic environment through increased antigenic and IL-7 stimulations that could lead to their exhaustion. By using STING GOF long term-hematopoietic stem cells (LT-HSC) transplantations with supportive wild-type bone marrow (BM) cells, we prevented the T cell exhaustion of STING GOF T cells in the resulting non lymphopenic context. With the support of lymphopenic RAG1 hypomorphic mice developing the phenotype, our data uncover a lymphopenia-mediated T cell exhaustion mechanism in STING GOF mice, for which a synergistic effect of the mutation is also envisaged.

2024-01-07 | E-MTAB-13658 | biostudies-arrayexpress

3' UTR RNA-sequencing of humanized EGFR-mutant PC9 cell line xenografts treated with osimertinib/vehicle of RIG-I agonist IVT4/unspecific control IVT-GAC

Project description:Immunocompromised mice were inoculated with human lung adenocarcinoma cell line PC9 and with human PBMCs. Tumors were treated with osimertinib/vehicle of RIG-I agonist IVT4/unspecific control IVT-GAC to assess response.

2021-07-20 | E-MTAB-9891 | biostudies-arrayexpress

Analysis of gene expression change by gefitinib treatment in gefitinib sensitive PC9 and resistant PC9.

Project description:We established a gefitinib-resistant cell line (PC-9GR), by serial exposure of gefitinib to PC-9, an originally gefitinib-sensitive lung cancer cell line (PC-9na), for long period.We collected total RNA from both PC-9 and PC-9GR and examined mRNA expression profile, comprehensively. Gefitinib induced gene expression was measured in human lung cancer cell line was measured at 48 hours after exposure to 1uM Gefitinib.

2012-06-30 | E-GEOD-38302 | biostudies-arrayexpress

FADD is recruited to activated STING oligomers initiating caspase mediated NF-κB activation in Drosophila melanogaster

Project description:STING is an evolutionarily conserved key regulator of innate immunity. In mammals, STING activates two distinct signaling pathways, the IRF3 and the NF-κB pathways, which act in conjunction to drive antiviral immunity. While the molecular mechanism of STING-mediated IRF3 activation has been untangled by extensive work during the last decade, how STING activates NF-κB signaling remains poorly understood. The versatile FADD/Caspase 8 axis is widely used in various immune signaling pathways throughout the animal kingdom and here we show that this axis participates downstream of STING in the activation of the Drosophila NF-kB like transcription factor Relish. We provide a detailed structural model illustrating how FADD interacts with two separate STING dimers in the activated oligomerized form of STING, thus providing a molecular explanation for the signal-dependent recruitment of FADD. In the classic IMD signaling pathway, FADD interacts with IMD in a structural distinct but functional related manner, highlighting how the two pathways differentially utilize the adapter FADD.

2026-04-09 | PXD054811 | Pride

Sequence database choice significantly affects taxonomic and functional metaproteomic results in gut microbiota studies

Project description:Elucidating the role of gut microbiota in physiological and pathological processes has recently emerged as a key research aim in life sciences. In this respect, metaproteomics (the study of the whole protein complement of a microbial community) can provide a unique contribution by revealing which functions are actually being expressed by specific microbial taxa. However, its wide application to gut microbiota research has been hindered by challenges in data analysis, especially related to the choice of the proper sequence databases for protein identification. Here we present a systematic investigation of variables concerning database construction and annotation, and evaluate their impact on human and mouse gut metaproteomic results. We found that both publicly available and experimental metagenomic databases lead to the identification of unique peptide assortments, suggesting parallel database searches as a mean to gain more complete information. Taxonomic and functional results were revealed to be strongly database-dependent, especially when dealing with mouse samples. As a striking example, in mouse the Firmicutes/Bacteroidetes ratio varied up to 10-fold depending on the database used. Finally, we provide recommendations regarding metagenomic sequence processing aimed at maximizing gut metaproteome characterization, and contribute to identify an optimized pipeline for metaproteomic data analysis.

2016-10-10 | PXD004039 | Pride

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