Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Mass spectrometric analysis of YTHDF3 in HepG2 cells

ABSTRACT: Comparative proteomic analysis was conducted via YTHDF3 co-immunoprecipitation and LC-MS/MS in control (shNC) and A3-knockdown (shA3) HepG2 cells to identify differentially associated proteins.

ORGANISM(S): Homo Sapiens

SUBMITTER: Yingmin Wu

PROVIDER: PXD070136 | iProX | Thu Oct 30 00:00:00 GMT 2025

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Similar Datasets

HepG2 TP53BP2-knockdown

Project description:HepG2 TP53BP2-knockdown

| PRJNA854656 | ENA

HepG2 HepAD38 TP53BP2-knockdown

Project description:HepG2 HepAD38 TP53BP2-knockdown

| PRJNA854649 | ENA

Chip-chip from HepG2 cells and HepG2 cells with slug overexpression

Project description:The transcription factor slug represses genes with E-box and then activates cancer stem cell related pathway: Wnt, Notch and Hedgehog pathway. Chromatin immunoprecipitation (ChIP) of slug by ChIP-on-chip analysis demonstrated that slug indirectly activates cancer stem cell related pathway and thus promotes vasculogenic mimicry formation. Comparison of HepG2-control in regular culture, HepG2-slug in regular culture and HepG2-slug on Matrigel.

2012-09-21 | E-GEOD-41027 | biostudies-arrayexpress

Effect of ZFP740 knockdown on HepG2 cells

Project description:Effect of ZFP740 knockdown on HepG2 cells

| PRJNA1117433 | ENA

Chromatin immunoprecipitation of human HepG2 cells SREBP-1 and RNA polII in HepG2 on ENCODE arrays

Project description:Chromatin immunoprecipitation of SREBP-1 and RNA polII in HepG2 with detection on ENCODE arrays.

2009-02-16 | E-TABM-530 | biostudies-arrayexpress

TMT-proteomics of AUF1 knockdown in HepG2 cell

Project description:HepG2 cells is knockdown with siAUF1 or siNC, total cellular proteins were extracted with SDT buffer and quantified. The protein samples underwent FASH enzymatic digestion and TMT labeling, followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis.

2024-01-24 | PXD048822 |

Proteomics of HEPG2 cells following FTO overexpression and knockdown

Project description:Proteomics of HEPG2 cells following FTO overexpression and knockdown. Data accompany our paper entitled “Dynamic Regulation of N6,2′-O-dimethyladenosine (m6Am) in Obesity” scheduled for publication in Nature Communications, 2021

2021-10-27 | PXD029268 | Pride

Using RNA-Seq to create sample-specific proteomic databases that enable mass spectrometric discovery of splice junction peptides

Project description:Many new alternative splice forms have been detected at the transcript level using next generation sequencing (NGS) methods, especially RNA-Seq, but it is not known how many of these transcripts are being translated. Leveraging the unprecedented capabilities of NGS, we collected RNA-Seq and proteomics data from the same cell population (Jurkat cells) and created a bioinformatics pipeline that builds customized databases for the discovery of novel splice-junction peptides. Results: Eighty million paired-end Illumina reads and ~500,000 tandem mass spectra were used to identify 12,873 transcripts (19,320 including isoforms) and 6,810 proteins. We developed a bioinformatics workflow to retrieve high-confidence, novel splice junction sequences from the RNA data, translate these sequences into the analogous polypeptide sequence, and create a customized splice junction database for MS searching.

2013-05-17 | GSE45428 | GEO

Multilayered-proteomics analysis of insulin signaling in insulin sensitive and resistant HepG2 IGF1R KO cell line

Project description:This is a mass spectrometry (MS)-based proteomics dataset, generated to study insulin signaling in a hepatocellular cell model (HepG2 insulin-like growth factor knock-down), at the IR interactome, phos-phoproteome, and proteome level. To induce insulin sensitivity and resistance in HepG2 IGF1R KO cells, the following protocol, established based on a previously published study by Dall’Agnese et al. (https://doi.org/10.1038/s41467-022-35176-7), was used. The day after cell seeding, culture medium was changed to serum-free low glucose DMEM for 48 hours. Following the serum washout, cells were treated for 48 hours in low glucose DMEM with 1.25 % HSA (human serum albumin) and either a phys-iologic level of 0.1 nM insulin and a pathologic level of 3 nM insulin, to make the cells either sensitive or resistant to insulin. Insulin sensitive and resistant HepG2 IGF1R KO cells, were subjected to an insulin wash-out over 35 minutes, with 7 media exchanges. Afterwards, the cells were stimulated for 5 minutes with varying insulin concentrations (0, 0.1, 3, or 100 nM) in low glucose DMEM with 1.25% HSA. Note that 0.1 nM is named 100 pM in the files. We performed 5 biological independent experiments, which were used to study the IR interactome, phosphoproteome, and a reference single-shot proteome. These cells were lysed in a co-immunoprecipitation (IP)-lysis buffer, preserving protein-interactions. Additional-ly, we generated SDS-based label-free DIA-MS single-shot proteome dataset, from four independent experiments of the insulin sensitive and resistant HepG2 IGF1R KO cells, directly after the insulin-resistance inducing procedure.

2025-05-06 | PXD047011 | Pride

Expression analysis of HepG2, HepG2-slug and HepG2-slug on Matrigel

Project description:Investigation of whole genome gene expression level changes in hepatocellular carcinoma cell line hepG2 in regular culture, hepG2-slug in regular culture and hepG2-slug on Matrigel. Whole genome gene expression level changes have been compared in hepatocellular carcinoma cell line hepG2 in regular culture, hepG2-slug in regular culture and hepG2-slug on Matrigel. Roche NimbleGen micro-array analysis was employed to assess global genome expression in HepG2 in regular culture, HepG2-slug in regular culture and HepG2-slug on Matrigel. The results demonstrated that the up-regulated genes and the down-regulated genes increased significantly when HepG2-slug cells with VM forming ablity were cultured on Matrigel and formed VM.

2012-09-21 | E-GEOD-41026 | 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