PXD029716

PXD029716 is an original dataset announced via ProteomeXchange.

Title	LC MS/MS of kidney organoids during differentiation from day 21 to 29
Description	Kidney organoids are a valuable and innovative model to understand genetic diseases, kidney development and transcriptomic dynamics. However, their proteome has not been analyzed so far. Here, we analyzed the organoid proteome trajectory during differentiation. Genes involved in podocytopathies and cystic kidney diseases were abundantly expressed on protein level, distinguishing organoids from almost every available cell culture model. On their pathway to terminal differentiation, organoids developed increased deposition of extracellular matrix. Single cell transcriptomic analysis suggests that most changes locate to podocytes and early podocyte progenitors. This matrix deposition is different from commonly used animal models of glomerular disease. We grew organoids from two independent batches according to the Freedman protocol, and performed proteomic profiling (Freedman, Brooks et al. 2015, Czerniecki, Cruz et al. 2018). The IPSCs were differentiated for a three-week period until first spheroids from. From day 21 of the culture they were used in our experiments up until day 29, where off-target differentiation of organoids becomes an issue.
HostingRepository	PRIDE
AnnounceDate	2023-05-12
AnnouncementXML	Submission_2023-05-12_07:47:25.252.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	FatihDemir
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Q Exactive HF

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-12 06:08:00	ID requested
⏵ 1	2023-05-12 07:47:25	announced

Dataset with its publication pending

submitter keyword: shotgun LC MS/MS, differentiation, maturation,Human kidney organoids

Markus M.Rinschen
contact affiliation	Aarhus University Department of Biomedicine DK-8000 Aarhus C
contact email	rinschen@biomed.au.dk
lab head
FatihDemir
contact affiliation	Aarhus University Department of Biomedicine Markus Rinschen Lab
contact email	fatih.demir@biomed.au.dk
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD029716
     1. Label: PRIDE project
     2. Name: LC MS/MS of kidney organoids during differentiation from day 21 to 29