Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

YTHDF2 regulates self non-coding RNA metabolism to control TLR3 activation in Inflammation

ABSTRACT: To elucidate the roles of YTHDF2 in the UV response in Human Keratinocyte (HaCaT) cells, the YTHDF2 interactome was analyzed through immunoprecipitation using a YTHDF2-specific antibody. Control IgG served as a negative control in this study. The cells were treated with UVB at 20 mJ/cm², and one hour post-treatment, alterations in the binding partners interacting with YTHDF2, along with their post-translational modifications, were analyzed using proteomics.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Skin Epidermis

DISEASE(S): Disease Free

SUBMITTER: Seungwon Yang

LAB HEAD: Yu-Ying He

PROVIDER: PXD059422 | Pride | 2025-09-10

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	MSB49087Band_01__F165182_.MGF	Mgf
	MSB49087Band_01__F165182_.dta	Other
	MSB49087Band_01__F165182_.mzid.gz	Mzid
	MSB49087Band_01__F165182_.mzid_MSB49087Band_01__F165182_.MGF	Mzid
	MSB49087Band_02__F165184_.MGF	Mgf

Items per page:

1 - 5 of 125

Similar Datasets

LC-MS/MS of HNE-apoE3 and HNE-apoE4

Project description:The overall goal of our study is to understand the effect of HNE modification on the structure and function of apolipoprotein E3 (apoE3) and apoE4, which play a critical role in brain cholesterol homeostasis. Immunoblots indicated HNE modification of recombinant apoE3 and apoE4 with a major band at ~36 kDa, while LC-MS/MS analysis revealed modification of H140 and H299 in both, and additionally at C112 in apoE3.

2024-08-09 | PXD038105 | Pride

Mass spectrometry-based analysis of LRBA phosphorylation

Project description:Vasopressin/cAMP/protein kinase A (PKA) signaling phosphorylates AQP2 water channels in renal collecting ducts to reabsorb water from urine for the prevention of further water loss. Lipopolysaccharide-responsive and beige-like anchor protein (LRBA) mediates vasopressin-induced AQP2 phosphorylation; therefore LRBA is essential for urinary concentration. LRBA is identified as the PKA substrates in a mouse cortical collecting duct principal cell line (mpkCCDcl4) whose phosphorylation levels are nearly perfectly correlated with those of AQP2. Although mouse LRBA contains several consensus PKA phosphorylation sites, their phosphorylation status in response to vasopressin remain unknown. Post-translational modification analysis revealed that RRDS1607 and RRIS2189 were phosphorylated by vasopressin.

2022-07-23 | PXD033859 | Pride

cAMP/PKA signaling phosphorylates LRBA in renal collecting duct

Project description:Vasopressin/cAMP/protein kinase A (PKA)/aquaporin-2 (AQP2) water channels signaling in the kidneys is a canonical pathway that determines AQP2 activity in response to body fluid balance. AQP2 phosphorylation by PKA increases water reabsorption from urine for the prevention of further water loss. We used several activators of cAMP/PKA signaling as screening tools to generate various phosphorylation patterns of PKA substrates and AQP2 in a mouse cortical collecting duct principal cell line (mpkCCDcl4). We next quantified phosphorylation levels of PKA substrates and AQP2 after western blot analysis using a phospho-PKA substrates antibody. Finally, we screen for PKA substrates whose phosphorylation levels were well correlated with those of AQP2. Immunoprecipitation with a phospho-PKA substrates antibody followed by mass spectrometry analysis revealed that the leading candidate in this assay proved to be a lipopolysaccharide-responsive and beige-like anchor protein (LRBA). Phosphorylation levels of LRBA was nearly perfectly correlated with those of AQP2.

2022-07-23 | PXD033852 | Pride

Transcription profiling of human A549 lung adenocarcinoma cell line time Course of TGF-beta treatment

Project description:Time Course of TGF-beta treatment of A549 lung adenocarcinoma cell line on Affymetrix HG_U133_plus_2 arrays; triplicate experiments. The goal of the experiment is to profile temporal gene expression changes during TGF-beta-induced epithelial-mesenchymal transition (EMT). During EMT cancer cells loose their epithelial specifc proteins and gain mesenchymal proteins to acquire migratory and invasive phenotype essential for metastasis. Human A549 lung adenocarcinoma cell line was treated with 5 ng/mL TGF-beta for 0, 0.5, 1, 2, 4, 8, 16, 24, and 72 h to induce EMT. The experiment was repeated 3 times. Samples were assayed using Affymetrix HG_U133_plus_2 arrays with 54675 probe-sets, using standard techniques. We provide the raw .CEL files and a supplementary Excel spreadsheet with log-transformed data and selected results from a statistical analysis. Experiment Overall Design: Human A549 lung adenocarcinoma cell line was treated with 5 ng/mL TGF-beta for 0, 0.5, 1, 2, 4, 8, 16, 24, and 72 h. The experiment was repeated 3 times. Samples were assayed using Affymetrix HG_U133_plus_2 arrays with 54675 probe-sets, using standard techniques. The 2 h sample of the third experiment was not run on an array due to poor RNA, so that only 26 arrays were run.

2009-09-15 | E-GEOD-17708 | biostudies-arrayexpress

Transcription profiling of rat A7r5 vascular smooth muscle cells over-expressing glucose transporter

Project description:Hypothesis: Overexpression of the GLUT1 facilitative glucose transporter, in A7r5 vascular smooth muscle cells, is sufficient and/or necessary to induce alterations in gene expression which influence apoptosis, growth, and proliferation. Experiment Overall Design: Scientific Approach: A7r5 rat embryonic vascular smooth muscle cells (VSMCs) (ATCC, CRL-1444) were infected for 72 hours with adenoviral vectors containing human GLUT1 or empty vector controls at a multiplicity of infection of 10 (MOI of 1 = 100 particles/cell) and grown in both high glucose (25mM) and low glucose (5.5mM) media. The human GLUT1 cDNA adenoviral vector and empty vector controls were a gift from Dr Arno Kumagai (University of Michigan). Total RNA was isolated using TRIzol (Invitrogen Life Technologies, Carlsbad, CA), followed by extraction with phenol/chloroform until the interface was clear. Total RNA was further purified using Qiagen RNeasy Mini Kit (Qiagen 74106). Immunoblot analysis was conducted to confirm GLUT1 overexpression at the time of Total RNA isolation (72 hours post-infection) for each condition. Experiment Overall Design: Number of chips: Total RNA was isolated from each of 2 conditions (control cells in low glucose (5.5mM), and GLUT1 overexpressing cells in low glucose), on three separate days and pooled to obtain one sample for each condition. In total we submitted two samples.

2009-11-07 | E-GEOD-15713 | biostudies-arrayexpress

The miRNA microarray data after UVB exposure to human keratinocyte HaCaT cells

Project description:UVB plays a key role in inflammation and DNA damage in human skin. Human keratinocyte HaCaT cells were utilized to determine the up- and down-regulated miRNA after UVB exposure. We used microarrays to identify the miRNA affected after UVB (15 mJ/cm^2) exposure to HaCaT cells

2020-03-23 | GSE142534 | GEO

Differentially expressed genes in wt and Nrf3-ko mouse keratinocytes before and after 24 h 100 mJ/cm2 UVB irradiation

Project description:We identified a pro-apoptotic function of Nrf3 in keratinocytes after UVB irradiation. To determine the underlying mechanism of action we wanted to compare the transcriptome of wt and Nrf3-ko mouse keratinocytes before and after 24 h 100 mJ/cm2 UVB irradiation

2023-10-09 | GSE226792 | GEO

Proteomics of poly(ADP-ribosyl)ation uncovers a role for HIRA in the chromatin adaptation at ALT telomeres

Project description:The synthesis of poly(ADP-ribose) (PAR) reconfigures the local environment and recruits repair complexes to damaged chromatin. The degradation of PAR by PARG is essential for progression and completion of DNA repair. Here, we show that inhibition of PARG disrupts homology-directed repair (HDR) mechanisms that underpin alternative telomere lengthening (ALT). By proteomics, we uncovered a novel role for PARylation in regulating the chromatin assembly factor, HIRA in ALT cancer cells. We show that HIRA is enriched at telomeres during G2 phase and is indispensable for histone H3.3 deposition and telomere DNA synthesis. Depletion of HIRA elicits systemic death of ALT cancer cells was mitigated by re-expression of ATRX protein that is frequently inactivated in ALT tumors. We propose that PARylation enables HIRA to fulfill its essential role in the adaptive response due to ATRX deficiency that pervades ALT cancers.

2020-10-12 | PXD020243 | Pride

GSK3B shRNA in Panc-1 xenografts

Project description:The Panc-1 human pancreatic cancer line (ATCC) was constructed to stably express control or GSK3B shRNA. Control or GSK3B shRNA expressing Panc-1 cells were implanted subcutaneously into the flanks of 3-5 week old, female, athymic nude mice. Tumors were grown to at least 250mm3. Tumor tissue was microdissected for further analysis. We compared control shRNA (n=4) to GSK3B shRNA (n=3) Panc-1 xenografts. The array data with simple statistical calculations are also provided in a supplementary Excel workbook, with probe-set annotation that we used at the time (users may want newer annotation). We compared xenografts of Panc-1 (Human pancreatic carcinoma cell line, grown in mice) stably expressing GSK3B shRNA (n=3) to similar xenografts with control shRNA (n=4). Xenografts were grown in the flanks of female, athymic nude mice until they reached at least 250mm3. Tumor tissue was microdissected for further analysis. mRNA abundance assays were performed using Affymetrix HG_U133_plus_2 arrays, with 54675 probe-sets.

2014-01-09 | E-GEOD-35351 | biostudies-arrayexpress

Microsatellite stable (n=38) and instable-high (n=13) human colorectal tumors assayed with Affymetrix HuGeneFL arrays.

Project description:mRNA assays were performed on 51 samples of human colorectal tumors using Affymetrix HuGeneFL arrays containing 7129 probe-sets. We compared 38 microsatelite stable (MSS) tumors with 13 microsatellite instable-high (MSI) tumors to form a list of genes differing between the two types. In order to identify molecular signatures characterizing MSI tumors, we examined only MSI-high cancers and not MSI-low ones. Keywords: disease state analysis Human samples of 38 microsatellie stable and 13 microsatellite instable-high colorectal tumors, each from a separate patient, had mRNA assays performed using Affymetrix HuGeneFL arrays, with 7129 probe-sets. A supplementary Excel file (Colon_HuFL_logs.xls) is attached below that gives the log-transformed probe-set values. It also gives the p-values from T-tests comparing these values between MSS and MSI samples, as well as an estimated average fold-difference, for which the mathematical functions are explicitly given.

2009-04-10 | E-GEOD-11543 | 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