Here we provide the processed bulk mRNA-sequencing data of murine bone marrow-derived macrophages treated with bile acid-loaded apoptotic hepatocytes or DMSO-loaded apoptotic hepatocytes from two biological replicates. The two uploaded files are specified below:

samples_aH.csv: Sample metadata table for the four bulk RNA-seq libraries included in this source data file. Each row corresponds to one sequencing library and contains the following columns: mouse (biological replicate identifier; WT1 and WT2 are two independent wild-type mice), treatment1 (primary treatment; "aH" denotes apoptotic hepatocytes), treatment2(secondary treatment applied on top of treatment1; either DMSO vehicle control or TLCA, taurolithocholic acid; which were loaded on the hepatocytes prior to inducing apoptosis), condition (combined treatment label used as the column header in the counts matrix), and batch (sequencing batch; all four libraries shown here were processed in batch1).
counts_aH.txt: Raw gene-level read count matrix for the same four libraries, in tab-delimited format. Rows correspond to genes and columns correspond to samples. Column headers (WT1_aH_DMSO, WT2_aH_DMSO, WT1_aH_TLCA, WT2_aH_TLCA) match the mouse and condition fields in samples_aH.csv and follow the convention <mouse>_<treatment1>_<treatment2>. Values are unnormalized integer read counts obtained from HISAT2 alignment to the mouse reference genome GRCm38.p6 followed by gene-level quantification with featureCounts (Subread package) using the NCBI RefSeq annotation (assembly accession GCF_000001635.26), counted in paired-end mode on exon features summarized per gene_id, with multi-mapping and ambiguously assigned reads excluded. These raw counts are the direct input to the differential expression analysis (via DESeq2) reported in Figure 3B.