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HPA Cilia section dataset

Do you want to explore primary cilia and their relationship to the cell on the spatial proteomics level?

Tired to get data sets without metadata that nobody understands? Looking for some more comprehensive information that what you get when you are just given a random folder of images withoiut labels? Don't worry: some of us got your back!

This growing document is going to guide you through all the aspects of the hpa cilia data set.

History and Authors

The data set was created in 2022-2025 within the Lundberg Lab as part of a large protein atlas mapping effort to add the primary cilia section in the Human Protein Atlas. This effort was spearheaded by Jan Hansen with many more contributors. The data set was ultimately analyzed and published in Cell as the following publication.

Hansen JN, Sun H, Kahnert K, Westenius E, Johannesson A, Villegas C, Le T, Tzavlaki K, Winsnes C, Pohjanen E, Mäkiniemi A, Fall J, Ballllosera Navarro F, Bäckström A, Lindskog C, Johansson F, von Feilitzen K, Delgado-Vega AM, Martinez Casals A, Mahdessian D, Uhlén M, Sheu SH, Lindstrand A, Axelsson U, Lundberg E. Intrinsic heterogeneity of primary cilia revealed through spatial proteomics. Cell. 2025. DOI: 10.1016/j.cell.2025.08.039 . PMID: 41005307.

Data analysis scripts used for this study and to generate part of the processed data are shared in this github repository: https://github.com/CellProfiling/HPA_Cilia_Study_Code.

Experimental details

See the paper.

Data

Available

In the hpa_cilia folder on the ell-vault you will find many subfolders that contain different versions of the data (processed files, segmentations etc.)

  • restructured_images: This folder contains the raw images after download from the hpa LIMS and being restructured so that images from the same stack are together and the planes are sorted.
  • combined: The raw images with additional channels containing segmentations created by Paul. Channel information:
    • C1: Cilia segmentation
    • C2: Basal Body segmentation
    • C3: Nuclei segmentation
    • C4: Protein of interest
    • C5: Cilia marker channel
    • C6: Basal body marker channel
    • C7: DNA/Nuclei channel
  • combined_max: Maximum projections of all combined image stacks.
  • analysis: This is results from a first run of SubCell on the images - done by Paul. It is very coarse for now and does not encompass the whole data set. We could consider rerunning SubCell for the whole data set and including it here.
  • analysis_ciliaBB: This folder contains all CiliaQ output files from profiling the cilia with the software CiliaQ. Ciliary morphology, intensity profiles etc. are available for all cilia.
  • CellCycle_Prediction: This folder contains data to train a cell cycle prediction model for RPTEC/TERT1 cells. See more details in the paper. The data was specifically generated for training the model. We succeeded only in training the GMNN model based on JNH038 data. The other data was then more used for validation.

There are other folders in this project related to specific analyses or individual experiments done for the publication. Please don't delete them and keep them in case one day we need to look up something for the publication.

Raw data

The raw data are stored on a hard drive in Sweden but they are no longer needed since all data has been processed into ome-tif files and stored in the LIMS of the Human Protein Atlas.