PXD025054

PXD025054 is an original dataset announced via ProteomeXchange.

Title	LC-MSMS study of hiPSC-derived β-like cells in different 3D Eevironments
Description	In this project hiPSC-derived β-like cells were studied in two different 3D enviromnets; size-adjusted cell aggregates (using Aggrewell™ plates) and inside alginate capsules. The hiPSC derived from a patient with maturity-onset diabetes of the young 1 (MODY1), which is a monogenic diabetes form, caused by a mutation in the HNF4A gene. We also generated and included a CRISPR/cas9 corrected isogenic control line. Human islets were also included as positive control. In the data analysis we compared to proteome of the cells in 3D environments compared to the frat 2D enviromnet. We found HNF4A mutation specific effects with both distinct 3D environments, where the cells are challenged differentially in term of oxygen, nutrient supply and cell-to-cell contact. We identified HNF4A mutation-specific phenotypes, including a unique proteome signature suggesting metabolic changes in the alginate bead environment, and mutation-specific cellular phenotypes and a unique proteome signature in the aggregation environment.
HostingRepository	PRIDE
AnnounceDate	2022-05-20
AnnouncementXML	Submission_2022-05-19_22:30:08.600.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Yngvild Bjoerlykke
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2021-03-29 02:45:08	ID requested
⏵ 1	2022-05-19 22:30:09	announced

Carrasco M, Wang C, S, ø, viknes AM, Bj, ø, rlykke Y, Abadpour S, Paulo JA, Tjora E, Nj, ø, lstad P, Ghabayen J, Nermoen I, Lyssenko V, Chera S, Ghila LM, Vaudel M, Scholz H, R, æ, der H, -Like Cells. Diabetes, 71(4):862-869(2022) [pubmed]

submitter keyword: NF4A, CRISPR/cas9, MODY1, hiPSC, β-cell differentiation, alginate encapsulation, cell aggregates, global proteomics, TMT quantification

Helge Raeder
contact affiliation	University of Bergen, Department of Clinical Medicine, Norway
contact email	Helge.Rader@uib.no
lab head
Yngvild Bjoerlykke
contact affiliation	University of Bergen
contact email	yngvild.bjorlykke@gmail.com
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/2022/05/PXD025054

PRIDE project URI

• PRIDE
  1. PXD025054
     1. Label: PRIDE project
     2. Name: LC-MSMS study of hiPSC-derived β-like cells in different 3D Eevironments