PXD047707-1

PXD047707 is an original dataset announced via ProteomeXchange.

Title	Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression
Description	In this study we examine the impact of cell confluency on gene expression. We focused on Argonaute (AGO) protein dynamics and associated gene and protein expression in HEK293, A375, and SHSY5Y cell lines. As a consequence of cell confluency, AGO2 protein translocates into the nucleus. Therefore, we generated transcriptomic data using RNA sequencing to compare gene expression in subconfluent versus confluent cells, which highlighted significant alterations in gene regulation patterns directly corresponding to changes in cell density. Our study also encompasses miRNA profiling data obtained through small RNA sequencing, revealing miRNA expressional changes dependent on cellular confluency, as well as cellular localization. Finally, we derived proteomic data from mass spectrometry analyses following AGO1-4 immunoprecipitation, providing a comprehensive view of AGO interactome in both nuclear and cytoplasmic compartments under varying confluency. These datasets offer a detailed exploration of the cellular and molecular dynamics, influenced by cell confluency, presenting a valuable resource for further research in cellular biology, particularly in understanding the basic mechanisms of cell density in cancer cells.
HostingRepository	PRIDE
AnnounceDate	2024-04-18
AnnouncementXML	Submission_2024-04-18_03:46:34.779.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Johannes Fuchs
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	TMT6plex-126 reporter+balance reagent acylated residue; monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2023-12-11 06:02:57	ID requested
⏵ 1	2024-04-18 03:46:35	announced
2	2024-10-22 06:36:35	announced	2024-10-22: Updated project metadata.

Dataset with its publication pending

submitter keyword: cell density,cell confluence, PAR-CLIP, RNA interference, mass spectrometry, gene regulation, RNA sequencing

Aishe Sarshad
contact affiliation	Department of Medical Biochemistry and Cell biology Sahlgrenska Academy University of Gothenburg
contact email	aishe.sarshad@gu.se
lab head
Johannes Fuchs
contact affiliation	Gothenburg University
contact email	johannes.fuchs@gu.se
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2024/04/PXD047707

PRIDE project URI

• PRIDE
  1. PXD047707
     1. Label: PRIDE project
     2. Name: Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression