Data

Description	Links
Genome Browser Tracks	GRCm38, all samples, fully customizable: UCSC Track Hub
Datasets	All raw & count data: GEO SuperSeries GSE263763 available upon study publication RNA-seq time-series (Figure 1, 2, 3) raw & count data: GEO Series GSE263759 available upon study publication ATAC-seq time-series (Figure 1, 2, 3) raw & count data: GEO Series GSE263758 available upon study publication Proof-of-concept CROP-seq KO15 screen (Figure 4) raw & count data: GEO Series GSE263760 available upon study publication Upscaled CROP-seq KO150 screen (Figure 5, 6) raw & count data: GEO Series GSE263761 available upon study publication The access token for reviewers is specified in the manuscript.
Supplemental Tables	Table S1 (related to Figures 1, 2, and S2): Details of the RNA-seq time series including sample annotations and quality metrics; differential gene expression and enrichment analysis results for each stimulus and time point; and clustering of temporal gene expression profiles with enrichment analyses for each stimulus. (XLSX) Table S2 (related to Figures 1, 2, and S2): Details of the ATAC-seq time series including sample annotations and quality metrics; annotated consensus regions; differential chromatin accessibility and enrichment analyses for each stimulus and time point; and clustering of temporal chromatin profiles with enrichment analyses for each stimulus. (XLSX) Table S3 (related to Figures 3, S4, and S5): Integrative analysis of the RNA-seq and ATAC-seq profiles (including identification of divergent genes); clustering of the temporal profiles of divergent genes; enrichment analysis for temporal clusters of divergent genes; and transcription factor binding site enrichment analysis. (XLSX) Table S4 (related to Figures 4, S6, S7 and S8): Details of the proof-of-concept CROP-seq screen (KO15) including single-cell annotations, quality metrics, and Mixscape results, as well as differential gene expression and enrichment analyses for the knockout effects within each time point. (XLSX) Table S5 (related to Figures 5, 6, S9-12): Details of the upscaled CROP-seq screen (KO150) including single-cell annotations, quality metrics, and Mixscape results; differential gene expression and enrichment analyses for the knockout effects within each time point; average cross-prediction probabilities and STRING interaction scores for each time point; joint analysis and cross-prediction probabilities across time points; and enrichment analyses of knockout perturbation signatures in temporal clusters of divergent genes of Listeria treatment. (XLSX) Table S6 (related to Figures 4 and 5): Experimental details of the combined CROP-seq and CITE-seq assay, including target genes, oligonucleotide sequences (primers, gBlocks, guide RNA libraries), and antibodies. (XLSX)
Source Code	Data processing and analysis workflows RNA-seq processing: Snakemake workflow rna-seq-star-deseq2 ATAC-seq processing: Ultimate ATAC-seq Data Processing, Quantification & Annotation Pipeline Genome track visualization: Genome Browser Track Visualization Workflow Enrichment analysis: Genomic Region & Gene Set Enrichment Analysis & Visualization Workflow for Human and Mouse Genomes Unsupervised analysis: Unsupervised Analysis Workflow Data analysis Source code and software specifications are publicly avilable on GitHub We generalized and expanded most of these analyses to Snakemake workflows in an effort to augment multi-omics research by streamlining bioinformatics analyses into modules and recipes. For more details and instructions check out the project's repository here: MrBiomics.

Citation

Peter Traxler*, Stephan Reichl*, Lukas Folkman, Lisa Shaw, Victoria Fife, Amelie Nemc, Djurdja Pasajlic, Anna Kusienicka, Daniele Barreca, Nikolaus Fortelny, André F. Rendeiro, Florian Halbritter, Wolfgang Weninger, Thomas Decker, Matthias Farlik^#, and Christoph Bock^{#^}.
Integrated time series analysis and high-content CRISPR screening delineates the dynamics of macrophage immune regulation. 2025 (In revision)

* These authors contributed equally
^# Senior author
^{^} Lead contact
Correspondence: cbock@cemm.oeaw.ac.at (C.B.)