PXD029718 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Proteome analysis of kidney organoid cells 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_08:04:37.099.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD029718 |
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 |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2021-11-12 06:14:32 | ID requested | |
⏵ 1 | 2023-05-12 08:04:37 | announced | |
Publication List
Keyword List
submitter keyword: TNFalpha, cytokine, shotgun LC MS/MS,Human kidney organoids, TNFa |
Contact List
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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
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[ - ]
- PRIDE
- PXD029718
- Label: PRIDE project
- Name: Proteome analysis of kidney organoid cells during TNFa stimulation