This file was generated on 2025-03-10 by Karl, Rudolfo


A GENERAL INFORMATION

1. Title of the dataset: Microscopy images of renal macrophages in the tissue environment and in 3D cultures

2. Brief description of the research project and its aims: Microscopy images (confocal, brightfield) shown in the publication. We present here the unedited raw images in a .tif or .jpg format. The images are supplementary information for the various figures shown in the paper "Renal tissue-resident macrophages promote cystogenesis in early polycystic kidney disease".

3. Author Information

	A. Investigator Contact Information
		Name: Karl, Rudolfo
		Institution: University of Bonn
		Address: BMZ-II, Building 12, Room 2G.420,University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
		Email: rudi.karl@uni-bonn.de

	B. Project Supervisor (Principal Investigator) Contact Information
		Name: Wachten, Dagmar
		Institution: University of Bonn
		Address: BMZ-II, Building 12, Room 2G.420,University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
		Email: dwachten@uni-bonn.de

	C. In case of questions related to this dataset, please contact:
		Name: Karl, Rudolfo
		Institution: University of Bonn
		Address: BMZ-II, Building 12, Room 2G.420,University Hospital Bonn, University of Bonn, Venusberg Campus 1, 53127 Bonn, Germany
		Email: rudi.karl@uni-bonn.de

4. Date of data collection: 2023-01-01 - 2024-12-31

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

6. Language of the dataset: English


B DATA & FILE OVERVIEW

1. File List:

Explanation of naming conventions:

FigureNumber_TypeofImage(Brightfield=BF, Immunofluorescence=IF, Histology=H)_GenotypeOfMouse(PKD1+/+=WT, PKD1RC/RC=RC)_AgeOfMouse_ConditionOf3Dculture(Light=L, Forskolin=F, Dark=D)

Figure2_H_RC_12w.jpg
Figure2_H_WT_12w.jpg
Figure2_H_RC_24w.jpg
Figure2_H_WT_24w.jpg
Figure2_H_WT_4w.jpg
Figure2_H_RC_4w.jpg
Figure2_H_RC_6w.jpg
Figure2_H_WT_6w.jpg
Figure2_IF_RC_24w.tif
Figure2_IF_RC_24w[02-28].tif
Figure2_IF_WT_24w.tif
Figure2_IF_WT_24w[01-21].tif
Figure2_IF_RC_6w.tif
Figure2_IF_RC_6w[02-23].tif
Figure2_IF_WT_6w.tif
Figure2_IF_WT_6w[02-22].tif
Figure4_BF_RC_ciliabPAC_D.tif
Figure4_BF_RC_ciliabPAC_F.tif
Figure4_BF_RC_ciliabPAC_L.tif
Figure4_BF_WT_ciliabPAC_D.tif
Figure4_BF_WT_ciliabPAC_F.tif
Figure4_BF_WT_ciliabPAC_L.tif
Figure4_IF_ciliabPAC_24w_F.tif
Figure4_IF_ciliabPAC_24w_L.tif
Figure4_IF_WT_24w_D.tif
FigureS5_BF_ciliabPAC_D.tif
FigureS5_BF_ciliabPAC_F.tif
FigureS5_BF_ciliabPAC_L.tif

2. Are there multiple versions of the dataset? no

3. Relationship between files: Files are grouped by figure in the publication and further by age and genotype of the mouse the cells are originating from.

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: https://doi.org/10.1242/jcs.263992


D METHODOLOGICAL INFORMATION

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

Organism: Mus Musculus

Biological entity: Stained cryosections of murine kidneys AND unstained/stained 3D culture gels

Description: renal kidneys after cryopreservation AND collagen/matrigel 3D mono- and co-cultures of renal epithelial cells (mIMCD-3) and primary renal macrophages

Intrinsic variables: renal epithelial cells: mIMCD-3 WT, mIMCD-3 cilia-bPAC; mice: Pkd1 +/+, Pkd1 RC/RC

Extrinsic variables: 3D culture: Forskolin, Light, Dark/DMSO

Experimental variables: Images vary by genotype of the mouse, are of the mouse and treatment of the 3D culture

Imaging_method: confocal microscopy (for fluorescent images), brightfield microscopy (for histology images)

Imaging instrument: Stemi 508 (Zeiss) for 3D culture brightfield images; AxioScan.Z1 widefield microscope for histology images; Leica Stellaris 8 for immunofluorescence images

Image acquisition_parameters: Z-stacks (1 µm step size) of fluorescently stained 3D cultures and kidney cryosections were taken on a confocal microscope with 20x and 40x multi-immersion objective with applied glycerol immersion, respectively. 

2. Methods for processing the data: 

Images were acquired using the Leica Las-X software in a .lif format. Images were then converted into OME.tif file. Images contain further metadata regarding the exact microscope setup.  No further image processing was applied to the images featured in this dataset.

3. Instrument- and/or software-specific information needed to interpret the data: 

As files are in a .tif and .jpeg format, so no specialized software is needed to access them. To access the metadata imbedded in the images, a text editor or image analysis program (e.g. FIJI) is needed.

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

Karl, Rudolfo
Palliyulla Kariat Ashra, Arsila

5. Describe any quality-assurance procedures performed on the data: None of the channels were oversaturated when acquiring the images.


E DATA-SPECIFIC INFORMATION FOR:

DataGroup: Figure2_H
1. Z-Stack: false

2. Channel information: RGB image, no channels

3. Stain: H&E staining

4. Spatial Information: <µm per pixel in x/y/z direction>

DataGroup: Figure2_IF
1. Z-Stack: true

2. Channel information: Channel1: DAPI, Channel2: CDH16 (Rhodamin), Channel3: ARL13b - AF647, Channel4: F4/80 - AF488

3. Stain: Immunofluorescence staining

4. Spatial Information: 2.6374 pixels per micron, 1 µm steps per stack

DataGroup: Figure4_BF
1. Z-Stack: false

2. Channel information: RGB image, no channels

3. Stain: No staining

4. Spatial Information: 2.2727 pixels per micron

DataGroup: Figure4_IF
1. Z-Stack: true

2. Channel information: Channel1: DAPI, Channel2: bPAC (mCHerry), Channel3: ARL13b - AF647, Channel4: F4/80 - AF488

3. Stain: Immunofluorescence staining

4. Spatial Information: 2.6414 pixels per micron, 1 µm steps per stack

DataGroup: FigureS5_BF
1. Z-Stack: false

2. Channel information: RGB image, no channels

3. Stain: No staining

4. Spatial Information: 4.5455 pixels per micron