This file was generated on 2025-04-10 by Jana Rohe


A GENERAL INFORMATION

1. Title of the dataset:

	Microscopic analysis of human ASC-derived kidney organoids for polycystic kidney disease modelling

2. Brief description of the research project and its aims: 

	Polycystic kidney disease (PKD) is a genetic disorder and a major contributor to end-stage renal disease. Elucidating the cellular mechanisms underlying PKD necessitates three-dimensional 	models that accurately replicate cystogenesis in vitro. Existing organoid models frequently exhibit limited expression of adult kidney epithelial markers and lack standardized methods for 	cyst identification.

	This microscopy imaging data deposit supports our efforts to develop and characterize a model that more faithfully reflects adult kidney epithelium and provides a robust read-out for PKD 	research. We generated adult stem cell (ASC)-derived human kidney organoids (tubuloids) from patient tissue, and cultured them either in suspension or embedded in extracellular matrix 	(domes). This approach allowed us to compare organoid structure, cell polarity, cellular composition, and the representation of kidney epithelium during organoid development. Using 		pharmacological stimulation and tissue imaging, we demonstrate that these tubuloids reproducibly form cysts in vitro upon chronic cAMP signaling, making these data valuable for PKD 		investigation.
 
	Microscopy datasets (image and video files) of fixed and live tubuloids are presented, analyzed for cyst formation, expression of specific proteins of interest, and transduction 		efficiency.

3. Author Information
	A. Investigator Contact Information
		Name: Jana Rohe
		Institution: Institute of Pathology, University Hospital Bonn
		Address: Venusberg-Campus 1, Building 62, 53127 Bonn, Germany
		Email: Jana.Rohe@ukbonn.de

	B. Investigator Contact Information
		Name: Dr. Arsila Palliyulla Kariat Ashraf
		Institution: Institute of Innate Immunity, BMZ-II, University Hospital Bonn
		Address: Venusberg-Campus 1, Building B12, 53127 Bonn, Germany
		Email: arsilash@uni-bonn.de

	C. Project Supervisor (Principal Investigator) Contact Information
		Name: Prof. Dr. med. Marieta Ioana Toma
		Institution: Institute of Pathology, University Hospital Bonn
		Address: Venusberg-Campus 1, Building 62, 53127 Bonn, Germany
		Email: marieta.toma@ukbonn.de

	D. Project Supervisor (Principal Investigator) Contact Information
		Name: Prof. Dr. Dagmar Wachten
		Institution: Institute of Innate Immunity, BMZ-II, University Hospital Bonn
		Address: Venusberg-Campus 1, Building B12, 53127 Bonn, Germany
		Email: dwachten@uni-bonn.de 

	E. In case of questions related to this dataset, please contact:
		Name: Dr. Arsila Palliyulla Kariat Ashraf
		Institution: Institute of Innate Immunity, BMZ-II, University Hospital Bonn
		Address: Venusberg-Campus 1, Building B12, 53127 Bonn, Germany
		Email: arsilash@uni-bonn.de

4. Date of data collection: 

	2023-09-25 to 2025-10-28

5. Information about funding sources that supported the collection of the data: 

	The project associated with this dataset was supported by funds from the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation)
	under Germany’s Excellence Strategy – EXC2151 – Project-ID 390873048 (to D.W.), FOR5547 – Project-ID 503306912 (to D.W.), WA 3382/8-1 – Project-ID
	513767027, and a grant from the Else Kröner Fresenius Foundation (2021.EKFSE.53). Additionally, the research was funded internally by the 
	University of Bonn (to M.I.T.).

6. Language of the dataset:

	English

7. Geographic location of data collection: 

	Bonn, Germany

B DATA & FILE OVERVIEW

1. File List: 
	
	1: Rohe-Ashraf-et-al-2025-BMC_Figure-1_Dome-and-Suspension-Tubuloids:
		Bright field microscopy images of tubuloids from dome and suspension culture in passages (P) 0 to 5.
	2: Rohe-Ashraf-et-al-2025-BMC_Figure-2_Immunohistochemistry
		Bright field microscopy images of dome and suspension tubuloids in P1 and P3, stained for Cytokeratin 7 (CK7),
		CK19, and PAX8. And bright field microscopy Images of dome and Suspension organoids in P1 and P3, stained with GATA3, CDH1, and CD13.
	3: Rohe-Ashraf-et-al-2025-BMC_Figure-3_Immunohistochemistry
		Bright field microscopy images of dome and suspension tubuloids in P1 and P3 (or P4), stained for CD24, TACSTD2, ATP1A1, or CDH16.
	4: Rohe-Ashraf-et-al-2025-BMC_Figure-4_Cyst-Induction
		Bright field microscopy images of Forskolin, DMSO or untreated dome and suspension tubuloids used for the 
		quantification of cyst induction.
	5: Rohe-Ashraf-et-al-2025-BMC_Figure-5_Immunostaining
		Immunofluorescence images of Forskolin, DMSO or untreated dome and suspension tubuloids used for the quantification of tubuloid 
		epithelial width and ciliary length.
	6: Rohe-Ashraf-et-al-2025-BMC_Figure-S1_Dome-and-Suspension-culture_MIB1
		Bright field microscopy images of live dome tubuloids in P6 to 8 and primary human kidney cells immediately 
		cultured in suspension after tissue dissociation. 
		Microscopy images and slide scans of fixed dome and suspension tubuloids in P1, stained for MIB1.
	7: Rohe-Ashraf-et-al-2025-BMC_Figure-S3B_GATA3-quantification
		Microscopy images and slide scans of fixed dome and suspension tubuloids in P1 and P4, stained for GATA3 and used for quantification.
	8: Rohe-Ashraf-et-al-2025-BMC_Figure-S5_Transduction
		Immunofluorescence images of rAAV2/8-CMV-EGFP transduced dome and suspension tubuloids at P3D10. 
	9: Rohe-Ashraf-et-al-2025-BMC_Live-cell imaging
		Phase-contrast and fluorescent microscopy images of live suspension tubuloids at P3, stained with Calcein-AM.

2. Are there multiple versions of the dataset?

	No

3. Relationship between files <when relevant>: 

	All files within a folder were used in one figure. Images not shown in the publication were used to aquire data for 
	statistical analysis.

4. Additional related data collected that was not included in the current data package: 

	Bulk RNA-Sequencing data from P3, 4, and 5 dome and suspension tubuloids from four donors can be found at: DOI

C SHARING/ACCESS INFORMATION

1. Was data derived from another source?
	
	No

2. Licenses/restrictions placed on the data: 

	CC-BY-4.0 (https://creativecommons.org/licenses/by/4.0/)

3. Links to publications that cite or use the data: 
IsSupplemenTo:
	Rohe, J., Ashraf, A.P.K., Kehl, M. et al. Modelling kidney cystogenesis using human kidney tubuloid cultures. BMC Mol and Cell Biol 27, 26 (2026). https://doi.org/10.1186/s12860-026-00591-x

4. Links to other publicly accessible locations of the data: 

	DOI:

5. Links/relationships to ancillary datasets: 

	DOI:

D METHODOLOGICAL INFORMATION

1. Description of methods used for collection/generation of data: 

	Human kidney tubuloids were generated, treated and stained according to the protocols as published in: DOI

	1: Rohe-Ashraf-et-al-2025-BMC_Figure-1_Dome-and-Suspension-Tubuloids:
		Microscopy images were taken with a Leica DM IRB inverted research microscope in combination with a 
		Nikon DS-U3 Digital Sight Camera Control Unit + Microscope camera at magnification 5x and 10x, bright field.
	2: Rohe-Ashraf-et-al-2025-BMC_Figure-2_Immunohistochemistry
		Microscopy images were taken with a KEYENCE BZ-X Microscope and the BZ-PF40LP Plan Fluorite 40X LD PH 
		lens at 40x magnification. PNG images are segments from 40x slide scans taken with a Leica Aperio GT 450 DX 
		digital pathology scanner.
	3: Rohe-Ashraf-et-al-2025-BMC_Figure-3_Immunohistochemistry
		Images were taken as described above (Rohe-Ashraf-et-al-2025-BMC_Figure-2_Immunohistochemistry).
	4: Rohe-Ashraf-et-al-2025-BMC_Figure-4_Cyst-Induction
		Microscopy images were taken with a Leica DM IRB inverted research microscope in combination with a 
		Nikon DS-U3 Digital Sight Camera Control Unit + Microscope camera at magnification 5x, bright field.
	5: Rohe-Ashraf-et-al-2025-BMC_Figure-5_Immunostaining
		Immunofluorescence images were taken with the Leica Stellaris 8 confocal microscope with a 40x multi-immersion objective with applied 
		glycerol immersion.
	6: Rohe-Ashraf-et-al-2025-BMC_Figure-S1_Dome-and-Suspension-culture_MIB1
		Microscopy images were taken with a Leica DM IRB inverted research microscope as described at magnification 
		20x and 40x.
	7: Rohe-Ashraf-et-al-2025-BMC_Figure-S3B_GATA3-quantification
		Microscopy images were taken with a KEYENCE BZ-X Microscope and the BZ-PF40LP Plan Fluorite 40X LD PH 
		lense at 40x magnification. PNG images are segments from 40x slide scans taken with a Leica Aperio GT 450 DX 
		digital pathology scanner.
	8: Rohe-Ashraf-et-al-2025-BMC_Figure-S5_Transduction
		Immunofluorescence images of rAAV2/8-CMV-EGFP transduced dome and suspension organoids were taken with the Leica Stellaris 8 confocal microscope with a 63x water-immersion 			objective.
	9: Rohe-Ashraf-et-al-2025-BMC_Live-cell imaging
		Phase-contrast and fluorescent microscopy images were captured using the Sartorius IncuCyte® S3 Live-Cell Analysis with the 4x objective.

2. Methods for processing the data: 
	
	Bright field microscopy images (TIF) are unprocessed, raw data. Segments from whole slide scans were exported as PNGs 
	with QuPath-0.5.1 (Bankhead, P. et al. QuPath: Open source software for digital pathology image analysis. Scientific Reports (2017). 
	https://doi.org/10.1038/s41598-017-17204-5)

3. Instrument- and/or software-specific information needed to interpret the data: 
	
	Not applicable

4. People involved in sample collection, processing, analysis and/or submission: 

	Jana Rohe1, Arsila Palliyulla Kariat Ashraf2, Jörg Ellinger3, Melina Kehl1, Xenia Thielmann1, Glen Kristiansen1, Marieta Ioana Toma1, Dagmar Wachten2

	1Institute of Pathology, University Hospital Bonn (UKB), Medical Faculty, University of Bonn, Bonn, Germany
	2Institute of Innate Immunity, Biophysical Imaging, Medical Faculty, University of Bonn, Bonn, Germany
	3Department of Urology and Pediatric Urology, University Hospital Bonn (UKB), Medical Faculty, University of Bonn, Bonn, Germany


5. Describe any quality-assurance procedures performed on the data: 

	Not applicable

6. Standards and calibration information: 

	Not applicable

7. Environmental/experimental conditions: 

	Domes: 		Tubuloids grown in collagen droplets
	Suspension: 	Tubuloids grown in without extracellular matrix in ultra low attachment-plates for cell culture, generated from dissociated dome tubuloids.

	Forskolin: 	Dome or suspension tubuloids treated with 10 µM Forskolin.
	DMSO:		Dome or suspension tubuloids treated with DMSO control.
	Media: 		Untreated dome or suspension tubuloids.

	rAAV2/8-CMV-EGFP: Dome or Suspension tubuloids transduced with rAAV2/8-CMV-EGFP at passage 3 day 0.

	Time of treatment as indicated in file name.


E
DATA-SPECIFIC INFORMATION FOR: Rohe-Ashraf-et-al-2025-BMC_Figure-1_Dome-and-Suspension-Tubuloids

1. Units of measurement used:
	µm
2. Specialized formats or other abbreviations used: 
	PXDY:   Passage (P) number 'X' and culture day (D) number 'Y'
	BF:     Bright-field
3. File name description: 
	Date of data collection_Type of sample_Number of passage and culture day_Type of tubuloid culture_Type of image acquisition technique_Magnification 

DATA-SPECIFIC INFORMATION FOR: Rohe-Ashraf-et-al-2025-BMC_Figure-2_Immunohistochemistry

1. Units of measurement used:
	µm
2. Specialized formats or other abbreviations used: 
	CD13:	Alanyl aminopeptidase, Aminopeptidase N	
	CDH1: 	Cadherin-1, E-Cadherin
	CK7: 	Cytokeratin 7
	CK19:	Cytokeratin 19
	GATA3:	GATA binding protein 3
	PAX8:	Paired box protein 8
	PXDY:   Passage (P) number 'X' and culture day (D) number 'Y' 
	DAB:    3,3'-diaminobenzidine
3. File name description: 
	Date of data collection_Type of sample_Number of passage and culture day_Type of tubuloid culture_Type of antigen-type of immunodetection technique_Magnification  

DATA-SPECIFIC INFORMATION FOR: Rohe-Ashraf-et-al-2025-BMC_Figure-3_Immunohistochemistry

1. Units of measurement used:
	µm	
2. Specialized formats or other abbreviations used: 
	ATP1A1:	ATPase Na+/K+ transporting subunit alpha 1
	CD24:	Signal transducer CD24, cluster of differentiation 24	
	CDH16:	Cadherin 16, Kidney-specific cadherin	
	TACSTD2:tumor-associated calcium signal transducer 2, TROP2
	PXDY:   Passage (P) number 'X' and culture day (D) number 'Y' 
	DAB:    3,3'-diaminobenzidine
3. File name description: 
	Date of data collection_Type of sample_Number of passage and culture day_Type of tubuloid culture_Type of antigen-type of immunodetection technique_Magnification  

DATA-SPECIFIC INFORMATION FOR: Rohe-Ashraf-et-al-2025-BMC_Figure-4_Cyst-Induction

1. Units of measurement used:
	µm
2. Specialized formats or other abbreviations used: 
	PXDY:   Passage (P) number 'X' and culture day (D) number 'Y'
	DMSO:   Dimethyl Sulfoxide
	h:      hour
	BF:     Bright-field
3. File name description: 
	Date of data collection_Number of kidney_Number of passage and culture day_Type of tubuloid culture_Type of treatment_Annotation of technical replicate (A/B/C)_Time of image acquisition_Type of image 	acquisition technique_Magnification 

DATA-SPECIFIC INFORMATION FOR: Rohe-Ashraf-et-al-2025-BMC_Figure-5_Immunostaining

1. Units of measurement used:
	µm
2. Specialized formats or other abbreviations used: 
	PXDY:   Passage (P) number 'X' and culture day (D) number 'Y'
	ARL13B:	ADP-ribosylation factor-like protein 13B
	DAPI:	4′,6-Diamidin-2-phenylindol
	DMSO:	Dimethyl Sulfoxide
	EGFP: 	enhanced green fluorescent protein
	ZO-1:	Zonula Occludens-1
	AF488:  Alexa Fluor 488
	AF647:  Alexa Fluor 647
3. File name description: 
	Date of data collection_Number of kidney_Number of passage and culture day_Type of tubuloid culture type_Type of treatment_Annotation of technical replicate (A/B/C)_Number of field of view_Type of antigens 	and dyes (first listed antigen stained with specific primary and secondary antibody = channel 2; second listed antigen stained with specific primary and secondary antibody = channel 3; third listed dye = 	channel 1)_Magnification 

DATA-SPECIFIC INFORMATION FOR: Rohe-Ashraf-et-al-2025-BMC_Figure-S1_Dome-and-Suspension-culture_MIB1

1. Units of measurement used:
	µm
2. Specialized formats or other abbreviations used: 
	PXDY:   Passage (P) number 'X' and culture day (D) number 'Y'
	MIB1:   Monoclonal antibody against marker of proliferation Kiel 67 (Ki-67) Protein
	DAB:    3,3'-diaminobenzidine
3. File name description: 
	Date of data collection_Type of sample_Number of kidney_Number of passage and culture day_Type of tubuloid culture_Type of antigen-type of immunodetection technique_Annotation of technical replicate (A/	B/C)_Magnification   

DATA-SPECIFIC INFORMATION FOR: Rohe-Ashraf-et-al-2025-BMC_Figure-S3B_GATA3-quantification

1. Units of measurement used:
	µm
2. Specialized formats or other abbreviations used: 
	PXDY:   Passage (P) number 'X' and culture day (D) number 'Y'
	GATA3:	GATA binding protein 3
	DAB:    3,3'-diaminobenzidine
3. File name description: 
	Date of data collection_Type of sample_Number of kidney_Number of passage and culture day_Type of tubuloid culture_Type of antigen-type of immunodetection technique_Annotation of technical replicate (A/	B/C)_Magnification 

DATA-SPECIFIC INFORMATION FOR: Rohe-Ashraf-et-al-2025-BMC_Figure-S5_Transduction

1. Units of measurement used:
	µm
2. Specialized formats or other abbreviations used:
	PXDY:   	 Passage (P) number 'X' and culture day (D) number 'Y'
	ARL13B:		 ADP-ribosylation factor-like protein 13B
	EGFP: 		 enhanced green fluorescent protein
 	rAAV2/8-CMV-EGFP:recombinant adeno-associated Virus, serotype 2/8, Cytomegalovirus promoter, enhanced green fluorescent Protein
	ZO-1:		 Zonula Occludens-1
	DAPI:	         4′,6-Diamidin-2-phenylindol
	AF488:  	 Alexa Fluor 488
	AF647:  	 Alexa Fluor 647
3. File name description: 
	Date of data collection_Number of kidney_Number of passage and culture day_Type of tubuloid culture_Type of treatment_Annotation of technical replicate (A/B/C)_Number of field of view_Type of antigens 	and dyes (first listed antigen stained with specific primary and secondary antibody = channel 2; second listed antigen stained with specific primary and secondary antibody = channel 3; third listed dye = 	channel 1)_Magnification  		

DATA-SPECIFIC INFORMATION FOR: Rohe-Ashraf-et-al-2025-BMC_Live-cell-imaging

1. Units of measurement used:
	µm
2. Specialized formats or other abbreviations used:
	PX:   		Passage (P) number 'X'
	DMSO:		Dimethyl sulfoxide
	Calcein-AM:	Acetoxymethly ester of calcein, a cell permeable dye that can be used to assess cell viability.
3. File name description: 
	Date of data collection_Type of imaging_Type of sample_Number of passage_Type of tubuloid culture_Type of treatment_Type of dye_Type of image acquisition technique_Magnification