Chrono-atlas of cell-type-specific daily gene expression rhythms in the regenerating colon

This dataset accompanies the manuscript "Chrono-atlas of cell-type specific daily gene expression rhythms in the regenerating colon" (Carmona-Alcocer, Gobet et al.).

Single-cell RNA-seq (10x Genomics Flex) was performed on mouse colon tissue collected at four Zeitgeber times (ZT01, ZT07, ZT13, ZT19) across three conditions: undamaged (control) distal colon, regenerating distal colon (day 17 post-DSS), and regenerating proximal colon (day 17 post-DSS). Per2-Luciferase mice (B6.129S6-Per2tm1Jt/J) were used, with both sexes represented (n=2 per time point).

Files included:

raw_h5/ : Raw Cell Ranger output (feature-barcode matrices in h5 format) for each sample.

cellbender/ : CellBender-corrected count matrices (h5 format) after ambient RNA removal, with default parameters and expected cell count of 5,000 per sample.

annotated_dataset.rds : Final integrated Seurat object containing all samples after quality control, DoubletFinder doublet removal, RPCA integration, cell type annotation (29 cell types across 9 broad categories), and metadata including condition, region, sex, Zeitgeber time, and cell type labels.

Preprocessing summary:

Alignment: Cell Ranger multi (v7.0.1) to GRCm39

Ambient RNA removal: CellBender (remove-background)

Doublet removal: DoubletFinder (4% expected rate, homotypic adjustment)

QC filters: 300-15,000 UMIs, 300-5,000 genes, <7.5% mitochondrial reads

Integration: Reciprocal PCA (rPCA) with 3,000 highly variable genes

Clustering: Leiden algorithm

Cell type annotation: canonical markers with subclustering for ISC/TA, fibroblast, and SMC populations

Associated resources:

Raw sequencing reads: European Nucleotide Archive, accession PRJEB102541

Analysis code: https://github.com/naef-lab/colon-chrono-atlas