Retinal pigment epithelial cell maturation

Subset that includes image data

General information

• Title: Maturation-dependent changes in complement production and complement C3 processing in retinal pigment epithelium cells
• Authors: Juliane Schikora¹, Aaron Dort¹, Antonia Nickel¹, Jasmin Bergert¹, Stella Y. Schayan-Araghi¹, Pratiti Banerjee¹, Hannah N. Wolf¹, Helen May-Simera² and Diana Pauly¹
• Affiliations: ¹Experimental Ophthalmology, University Marburg, Marburg, Germany; ²Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany

Repository overview

This subset of the repository contains the image data of the study in zip folders. This includes several replicates of the recorded 16-bit stacks as tif-files of the immunostainings that can be opened using Fiji. It further contains summary images as jpg-files used for image analysis. And it includes Fiji macros used for the analysis.

During the study Fiji (imageJ) version 1.54f was used (Schindelin, J., Arganda-Carreras, I., Frise, E., Kaynig, V., Longair, M., Pietzsch, T., Preibisch, S., Rueden, C., Saalfeld, S., Schmid, B., Tinevez, J.-Y., White, D. J., Hartenstein, V., Eliceiri, K., Tomancak, P., & Cardona, A. (2012). Fiji: an open-source platform for biological-image analysis. Nature Methods, 9(7), 676–682. https://doi.org/10.1038/nmeth.2019).

The following Fiji macros are included in this subset:

• Generation_summary_images.ijm: This macro is for the generation of merged and single channel stacks. Use this with the tif files inlcuded in the Immature_vs_mature folder and the Treatment folder of this image data subset.
• Image_analysis_ARPE-19_NA.ijm: This macro is for the measurement of nuclei area in ARPE-19 cells. Use this with the jpg files of the CellType “ARPE-19” and the Variable “NA” inlcuded in the Image_analysis folder of this image data subset.
• Image_analysis_iPSC-RPE_NA.ijm: This macro is for the measurement of nuclei area in iPSC-RPE cells. Use this with the jpg files of the CellType “iPSC-RPE” and the Variable “NA” in the Image_analysis folder of this image data subset.
• Image_analysis_CA.ijm: This macro is for the measurement of cell area in ARPE-19 and iPSC-RPE cells. Use this with the jpg files of the Variable “CA” inlcuded in the Image_analysis folder of this image data subset.
• Image_analysis_GT335-A.ijm: This macro is for the measurement of GT335 ciliary area in ARPE-19 and iPSC-RPE cells. Use this with the jpg files of the Variable “GT335-A” inlcuded in the Image_analysis folder of this image data subset.

Experiments were conducted with two cell types, ARPE-19 (adult retinal pigment epithelial cell line) and induced pluripotent stem cell-derived RPE (iPSC-RPE) cells. ARPE-19 and iPSC-RPE cells were each grouped into four condition categories:

• Immature: Cells with an immature, RPE-unspecific phenotype
• Mature: Cells with a mature, RPE-specific phenotype
• Treated: Cells that were treated with 10 ng/mL TGF-Beta1
• Control: Untreated cells

This subsets includes three folders:

• Immature_vs_mature.zip: The image data of immature and mature ARPE-19 and iPSC-RPE cells.
• Treatment.zip: The image data of treated and control ARPE-19 and iPSC-RPE cells.
• Image_analysis.zip: The image data used to conduct image analysis.

Data collection structure (current subset marked in bold letters)

/ Data collection: Retinal pigment epithelial cell maturation
├── /Analytical data
│ └── /README1.md.html
│ └── /Codebook.md.html
│ └── /Transcript_expression_analysis.csv
│ └── /Multiplex_immunoassay.csv
│ └── /Multiplex_immunoassay_validation.csv
│ └── /Enzyme_linked_immunosorbent_assay.csv
│ └── /Image_analysis.csv
│ └── /Transepithelial_resistance.csv
├── /Image data
│ └── /README2.md.html
│ └── /Codebook.md.html
│ ├── /Immature_vs_mature.zip
│ ├── /Treatment.zip
│ ├── /Image_analysis.zip
│ └── /Generation_summary_images.ijm
│ └── /Image_analysis_ARPE-19_NA.ijm
│ └── /Image_analysis_CA.ijm
│ └── /Image_analysis_GT335-A.ijm
│ └── /Image_analysis_iPSC-RPE_NA.ijm
├── /Video data
│ └── /README3.md.html
│ └── /Codebook.md.html
│ └── /[Variable(s)]_video.mp4
│ └── /Video_generation.ijm
├── /Western blot data
│ └── /README4.md.html
│ └── /Codebook.md.html
│ ├── /Immature_vs_mature.zip
│ ├── /Treatment.zip
│ ├── /Specificity_controls.zip

Description of tif/jpg-files

Each tif/jpg-file name follows the conventions:

[CellType]_[Condition]_[Variable(s)]_[ReplicateNumber].tif
[CellType]_[Condition]_[Variable(s)]_[ReplicateNumber].jpg