CALIPERS: Cell cycle-aware live imaging for phenotyping experiments and regeneration studies

Abstract:

We introduce CALIPERS, a Fluorescence Ubiquitin Cell Cycle Indicator enabling cell cycle-aware phenotyping based on multiplexed live-cell imaging. We validate CALIPERS in three- and four-color reporter lines (HaCaT) and human induced pluripotent stem cells (WTC-11), co-expressing genetically encoded structural and functional fluorescent sensors. To exemplify the broad applications of CALIPERS, we show cell cycle-aware phenotyping in live-cell imaging applications ranging from proliferation and migration to cardiac-specific maturation and drug testing.

Code submission: https://github.com/alessandro-bertero/FUCCIplex.git

Dataset description:

This dataset includes all data and the additional files to recreate the sc-RNAseq analysis in our manuscript. The Rmd files include the Seurat QC pipeline to preprocess the counts data from cellranger (QC_Seurat_gitgub_polished.RmD) and the monocle pipeline to re-create the clusters and pseudotime analysis (monocle_github_polished.Rmd).

Data obtained from Cellranger 7.2 pipeline are also available here including all the 3 files, usually placed in the path "outs/count/filtered_feature_bc_matrix" by cellrancer. This includes: barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (alternatively the h5 file filtered_feature_bc_matrix.h5 can be loaded directly in Seurat v5).

We also added few RData files to recreate our graphs and follow our pipeline smoothly. 240111_seurat_before_clean.RData, 240111_seurat_clean.RData and 240111_seurat_processed.RData are the files created by the codes in QC_Seurat_gitgub_polished.RmD pipeline. Then, 240118_monocle_cds_clustered_proteincoding_PSEUDOTIME_clean_gene_info.RData is the file set created by the monocle_github_polished.Rmd pipeline.

We also suggest to use this pipeline within a docker container by pulling our docker image with R studio:

docker pull hedgelab/rstudio-hedgelab:latest