Mouse BMDC E3-ligase Perturb-seq (GSE327057), reprocessed: counts and per-perturbation differential expression

Cell x gene counts and per-perturbation differential expression for the Geiger-Schuller et al. E3-ligase Perturb-seq screen in mouse bone-marrow-derived dendritic cells (GEO GSE327057; LPS 3 h; 1,130 E3-ligase and partner targets, 3 guides each, plus non-targeting and cutting controls). The data were reprocessed from FASTQ with STARsolo (STAR 2.7.11b; GRCm39, GENCODE M39; GeneFull counts; EmptyDrops_CR) for 45 of the 46 screen channels. Contents: geiger_bmdc_e3_genefull_counts.h5ad: 504,303 cells x 78,348 genes, raw GeneFull UMI counts, per-cell metadata and per-cell guide UMIs; guide assignments were recomputed. per_target_de_long.tsv.gz and per_target_de_matrices.h5: edgeR quasi-likelihood results for each of the 1,130 targets against non-targeting controls (channel-paired pseudobulks, design ~ channel + condition) on a fixed set of 2,300 genes, with FDR within target and across all targets. per_target_summary.tsv, genes.tsv and guides.tsv. Calibration files from 100 non-targeting pseudo-targets: calibration_ntc_pseudotargets.tsv and empirical_fdr_global_calls.tsv; genes with a null false-positive rate of at least 15% are flagged. cutting_control_de.tsv.gz. The model reproduces the published WDR82 to Zeb2os result exactly. README.md describes every file, the reprocessing, guide assignment, the DE model and calibration. MD5SUMS.txt lists checksums. Please cite the original screen when using these data: Geiger-Schuller et al., bioRxiv (2023), https://doi.org/10.1101/2023.01.23.525198, and GEO GSE327057. Results can be browsed gene by gene in the single-cell gene browser (https://github.com/ericmalekos/single-cell-gene-browser).