Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

HepG2 cell APOBEC3B-AcGFP anti-AcGFP-IP DIA analysis

ABSTRACT: APOBEC3B-AcGFP expressing HepG2 or AcGFP expressing HepG2 plated on 10 cm dishes were stimulated with Act D (1 µM), MNNG (50 µM) for 3 h. The cells were washed with PBS three times and lysed with RIPA buffer containing protease inhibitor cocktail. The protein amounts of cell lysates were measure in BCA protein assay. 0.1 mL of the cell lysate (5 mg/mL) were added with 4 µL of Anti GFP (VHH), GFP-Trap Magnetic Agarose and rotated for 1 h at 4˚C. The obtained data were analyzed using DIA-NN 1.8.1. Proteins with both precursor FDR and protein FDR of 1% were identified and quantification values were calculated.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Yohei Saito

PROVIDER: PXD058962 | JPOST Repository | Thu Dec 18 00:00:00 GMT 2025

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	KK2016-1_N12.raw	Raw
	KK2016-2_Ac-Control.raw	Raw
	KK2016.tsv	Tabular
	KK2133-1_Ac.raw	Raw
	KK2133-2_Mn.raw	Raw

Items per page:

1 - 5 of 7

Similar Datasets

Data in support of Gold micro-particles for knee osteoarthritisGold micro-particles for knee osteoarthritis

Project description:This study investigated the effect of intraarticular gold micro particle implants for the treatment of pain and inflammation in KOA. The present open, exploratory, proof-of-concept study investigated whether intraarticular gold ions could act as a KOA treatment option through modulation of inflammatory mediators, pain sensitivity, and central pain mechanisms. The primary aim of this study were 1) to measure the effect on pain and function after intra-articular injection of 20 mg gold microparticles > 20 µm into the KOA joint using the patient’s synovial fluid (SF) as a carrier and 2) measure associated possible proteomic changes in the SF and serum.

2022-12-03 | PXD030746 | Pride

Toxicoproteomics reveals an effect of Clozapine on autophagy in human liver spheroids

Project description:Clozapine is an atypical antipsychotic drug for treatment-resistant schizophrenia. Its side effects, including liver enzyme abnormalities, experienced by many patients preclude a more common use as a first-line therapy of schizophrenia. Toxicoproteomics approaches have been demonstrated to effectively guide the identification of toxicological mechanisms. Here, to further our understanding of Clozapine's molecular effects we performed a Data-independent Acquisition (DIA)-based quantitative proteomics investigation of Clozapine-treated human liver spheroid cultures. In total, we quantified 4,479 proteins across five treatment groups (vehicle, 15 µM, 30 µM, 60 µM Clozapine, and 10 ng/mL TNFa + IL-1a). 60 µM Clozapine treatment yielded 36 differentially expressed proteins (fdr < 0.05). Gene-set enrichment analysis indicated perturbation of several gene-sets, which included interferon gamma signaling (e.g., IFNGR1) and prominently autophagy related processes (e.g., upregulation of SQSTM1, MAP1LC3B/LC3B2, GABARAPL2, and NCOA4). Clozapine's effects on autophagy were confirmed using conventional SQSTM1 and LC3B markers by targeted mass-spectrometry and Western Blot.

2022-12-09 | PXD034257 | Pride

miRNA34 expression in SW480 cells

Project description:SW480 were stably transfected with an episomal plasmid expressing GFP and miRNA34 from a bidirectional doxycyclin regulatable promoter (Bornkamm et al Nucleic Acids Res. 2005 Sep 7;33(16)). Polyclonal cell lines were obtained by selection with Hygromycin at 350ug/ml for 10 days. The cell llnes identified as GFP only express GFP, whereas the cell lines identified as miRNA34a express both GFP and miRNA34 under doxycyclin control. For the present experiment, cells were treated with 1ug/ml Docycyclin for 72h. Cells were harvested and total RNA was isolated using Trizol (Invitrogen). After RNA cleanup (RNeasy, Qiagen) Affymetrix 133 Plus 2.0 micorarrays were hybridized using standard techniques. Keywords: Cell line transfection

2007-08-20 | GSE7678 | GEO

Mass spectrometry analysis of the impact of replication stress upon phosphorylation and protein interaction of human RIF1 protein

Project description:Wild-type or S2265A version of GFP-RIF1 protein (isoform 1) was over-expressed in Flp-In-T-REx cells (Watts et al. 2020. eLife 9:e58020) and immunopurified using GFP-Trap magnetic agarose beads. Proteins were subjected to on-beads trypsin digestion and resulting peptides were analysed by mass spectrometry for protein identification/quantification and identification of phosphorylated residues. Raw MS file names and descriptions: IP_RIF1_A.raw = GFP-RIF1-L immunoprecipitated from cells without aphidicolin treatment. IP_RIF1_B.raw = GFP-RIF1-L immunoprecipitated from cells treated with 1 µM aphidicolin for 24 hr before harvesting. IP_RIF1_C.raw = GFP-RIF1-L (S2265A) immunoprecipitated from cells treated with 1 µM aphidicolin for 24 hr before harvesting.

2022-04-14 | PXD032015 | Pride

Real-time quantitative PCR analysis of human EBV-B cells during UPR

Project description:Human B cells were isolated from peripheral blood from one healthy donor and two patients with Common Variable Immunodeficiency (CVID) and were immortalized by infection with Epstein Barr virus (EBV) in vitro. Immortalized EBV-B cells (in biological triplicates) were treated twelve different ways for 4 hours: 1.untreated control, 2. Thapsigargin (Tg) 1 µM, 3. Tunicamycin (Tm) 10 µg/ml, 4. 4-phenylbutyrate (4-PBA) 1 mM, 5. Tg 1 µM plus 4-PBA 1 mM, 6. Tm 10 µg/ml plus 4-PBA 1 mM, 7. Dimethyl sulfoxide (DMSO) 1 mM, 8. Tg 1 µM plus DMSO 1 mM, 9. Tm 10 µg/ml plus DMSO 1 mM, 10. Tauroursodeoxycholic acid (TUDCA) 5 mM, 11. Tg 1 µM plus TUDCA 5 mM, and 12. Tm 10 µg/ml plus TUDCA 5 mM. We used Applied Biosystems TaqMan OpenArray Real-Time PCR System (Thermo Scientific) to quantitate gene expression of relevant genes from the cells (in technical triplicates).

2020-01-19 | GSE126201 | GEO

Fatty Acid Binding Protein 5 is a Novel Target in Multiple Myeloma

Project description:To identify protein changes in human myeloma cancer cells resulting from FABP inhibition, we treated GFP+/Luc+MM.1S cells with the single inhibitors (50 µM BMS309405 or 50 µM SBFI-26) or the combination (50 µM of each) for 48 hour, isolated total cell proteins, and performed a mass spectrometry-based proteomic analysis.

2023-01-12 | PXD032829 | Pride

Comparison of expression profiles of Ba/F3 cells transduced with human CALR or human CALR + Type 1 mutation (hCALR-del52) by RNA-seq

Project description:Murine Ba/F3 cells were transduced with retroviral vectors (pMSCV-IRES-GFP) expressing hCALR or hCALR-del52 and treated with 1ng/ml interleukin-3 (IL-3). RNA-seq was performed in triplicates, with on average 109 M reads per group (36 M reads per replicate).

2016-01-29 | GSE62822 | GEO

RIPK3 negatively regulates the (CXCL4+TLR8)-induced IFN response while promoting NLRP3 inflammasome activation in human monocytes

Project description:To investigate the function of RIPK3 in regulation of IFN response and inflammatory response in human monocytes stimulated with CXCL4 and TLR8, We blocks (CXCL4 + TLR8)-induced pyroptosis and RIPK3 activation using necrosulfonamide (NSA, 5 µM) and GSK'872 (10 µM) and measure gene expression genome-wide with RNA-seq.

2023-04-30 | GSE201909 | GEO

Toxicoproteomics reveals an effect of Clozapine on autophagy in human liver spheroids

Project description:Clozapine is an atypical antipsychotic drug used to treat treatment-resistant schizophrenia. Its side effects, including liver enzyme abnormalities, experienced by many patients preclude its more common use as a first-line therapy for schizophrenia. Toxicoproteomic approaches have been demonstrated to effectively guide the identification of toxicological mechanisms. Here, to further our understanding of the molecular effects of clozapine, we performed a data-independent acquisition (DIA)-based quantitative proteomics investigation of clozapine-treated human liver spheroid cultures. In total, we quantified 4,479 proteins across the five treatment groups (vehicle; 15 µM, 30 µM, and 60 µM clozapine; and 10 ng/mL TNFα + IL-1β). Clozapine (60 µM) treatment yielded 36 differentially expressed proteins (FDR < 0.05). Gene-set enrichment analysis indicated perturbation of several gene sets, including interferon gamma signaling (e.g., interferon gamma receptor 1) and prominent autophagy-related processes (e.g., upregulation of sequestosome-1 (SQSTM1), MAP1LC3B/LC3B2, GABARAPL2, and nuclear receptor coactivator 4). The effects of clozapine on autophagy were confirmed by targeted mass spectrometry and western blotting using conventional SQSTM1 and LC3B markers. Combined with prior literature, our work suggests a broad contribution of autophagy to both the therapeutic and side effects of clozapine. Overall, this study demonstrates how proteomics can contribute to the elucidation of physiological and toxicological mechanisms of drugs.

2022-12-13 | PXD038007 | Pride

Spatial confinement induces reciprocating migration of epidermal keratinocytes and forms triphasic epithelia

Project description:Epithelial cells undergo epithelial-mesenchymal transition (EMT) during migration and regain their epithelial phenotype in the post-migration phase (mesenchymal-epithelial transition; MET). Keratinocytes (KCs), skin epithelial cells, placed on a microporous membrane migrated through 3.0 µm or larger micropores. Live imaging of immortalized HaCaT KCs which stably express green fluorescent protein (GFP)-labelled LifeAct (LifeAct-HaCaTs) revealed that KCs moved in a reciprocating manner with actin-rich filopodia-like structures of KCs extending into and out of the 3.0 µm micropores. HaCaT KCs cultured on 3.0 µm pored-membranes upregurated the genes associated with tissue development and cell differenciation compared with on 0.4 µm-pored membranes. These results demonstrate that KCs migrate through confined spaces in a reciprocating manner, which might help form triphasic epithelia, recapitulating wound healing processes.

2025-02-18 | GSE282553 | 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