Bulk RNAseq data from WT and Clec1a KO purified splenic cDC1 stimulated in vitro with IFNβ, Necrotic cells or E. coli.

Purified cDC1 stimulationSpleens and mesenteric lymph nodes from WT and Clec1a KO mice were recovered and underwent mechanical and enzymatic dissociation. The resulting cell suspension was then enriched in cDC1 cells. Purified cDC1 cells were then sorted with by FACS (based on the expression of CD11c, MHCII and XCR1) using a Cytek Aurora spectral flow cytometer. Purified cDC1 were then plated in flat-bottom 96-well plates and stimulated with E. coli (MOI = 10), MCA-OVA UV-treated cells (ratio 1:10) or recombinant mouse IFNβ (1000 U/ml) for 6h. mini-bulk RNAseq library preparation and sequencingTreated cDC1 were resuspended in 4 technical replicates per condition (n=6 mice per genotype) at a concentration of 1250 cells/uL directly in lysis buffer containing 0.16uL 10% Triton X-100, 0.08 uL RNAse Out (40U/uL) and 3.75 uL RNAse DNAse free water. 5000 cells /well (= 4uL cell suspension /well) were then immediately loaded on a 96-plate using an OT-2 library prep robot (Opentrons). 1uL barcoded RT-primers with universal adapters, well-specific barcodes, and unique molecular identifiers were then added to the wells and incubated at 72°C for 3 min before reverse transcription. Barcoded complementary DNAs from multiple samples were then pooled, amplified, and tagmented using a transposon fragmentation approach which enriches for 3′ ends of complementary DNA. A library of 350 to 800 bp was run on a 100-cycle 1.5B flow cell on the NOVAseq X-plus series at the Genomics Antlantic platform (Nantes) facility (Nantes). An average of 5 million 75 bp single-end reads were obtained for each sample. Samples were demultiplexed and aligned to the GRCm38 (mm10) genome using the DGE bioinformatics pipeline. Post-sequencing, data demultiplexing was performed using Illumina bcl2fastq. The resulting FASTQ files were analyzed using the 3’ Sequencing RNA Profiling (SRP) pipeline (Charpentier et al., 2021, DOI : 10.21203/RS.3.PEX-1336/V1). RNAseq data analysisDifferential gene expression (DGE) analysis was performed by using the DESeq2 package (v1.46.0). Provided data The data provided correspond to the dds object obtained with the DESeq2 R package containing the RNAseq data (cDC1_Stim_RNAseq_DGEseq_DDS) as well as DGE results in .xlsx format (mBulk_DEG_results).