High-content cell imaging (Blood Cell Painting)

The same subset of individuals that were analyzed for single-cell transcriptomics and immune profiling were also analyzed for high-content imaging, in FinnGen EA5. The high-content cell imaging was done in collaboration with FIMM's cell imaging facility (HCA), and the project itself in collaboration with Finnish Red Cross Blood Service.

Blood Cell Painting (BCP) is a project where single cells from 390 healthy blood donors were imaged (Opera Phenix high-content microscope), single-cell features were extracted from the images, and genetic analyses were done for these features. Features were extracted using BIAS from Single-Cell Technologies. The Blood Cell Painting preprint with more details and results (Högel-Starck et al. 2024) can be found here: https://www.biorxiv.org/content/10.1101/2024.05.17.594648v2

The README files and both raw and processed feature-level data can be found in:

/finngen/library-red/EA5/cell_painting/

BCP_EA5_1.0 refers to the pilot phase of the project for 99 donors, and BCP_EA5_2.0 contains the entirety of data from all 390 donors selected for the project.

Sample timestamps: In case a sample timestamp is needed for the blood donor's data (i.e., when was the sample collected), you can use the files below to screen for your samples.

• /finngen/library-red/EA5/omics_metadata/20250204_EA5_Plasma_Metadata_All.csv

• /finngen/library-red/EA5/omics_metadata/20250204_EA5_Plasma_Metadata_Readme.md