PXD029696

PXD029696 is an original dataset announced via ProteomeXchange.

Title	Proteomic analysis of kidney organoid supernatant during TNFa stimulation
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 after treatment of organoids with 5ng/mL TNFalpha for 24h and 48h compared with vehicle control (VC). Incubation of organoids (day 25 of differentiation) with TNFalpha led to an activation of NFkappaB signaling, and, interestingly, secretion of cytokines and complement components, alongside with extracellular matrix components. Interestingly, this signaling system directly links inflammatory signaling, production of cytokines and complement; and production of extracellular matrix. Thus, we provide a repository of kidney organoid proteins that revealed the potential to model pathophysiological pathways beyond genetic diseases. Organoids were grown according to the Freedman protocol (Freedman, Brooks et al. 2015, Czerniecki, Cruz et al. 2018). The IPSCs were differentiated for a three-week period until first spheroids from. We started TNFa stimulation at day 25, with the 24h stimulation ending on day 26 and the 48h stimulation ending on day 27. We chose day 25 because it lies centrally in the day 21 to day 29 window, where we observe reproducible spheroids with limited off-target differentiation of organoids, which becomes an issue after day 29.
HostingRepository	PRIDE
AnnounceDate	2023-05-12
AnnouncementXML	Submission_2023-05-12_07:56:59.298.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD029696
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	FatihDemir
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Exploris 480

Revision	Datetime	Status	ChangeLog Entry
0	2021-11-12 05:46:29	ID requested
⏵ 1	2023-05-12 07:56:59	announced

10.6019/PXD029696;

submitter keyword: TNFalpha, cytokine, shotgun LC MS/MS,Human kidney organoids, TNFa

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. PXD029696
     1. Label: PRIDE project
     2. Name: Proteomic analysis of kidney organoid supernatant during TNFa stimulation