Single-cell RNA sequencing (scRNAseq) sample preparationWT and Clec1a mice were infected intracheally with E. coli and lungs were recovered and dissociated at day 1, 3 or 7 post-infection. The obtained cell suspension was FACS-sorted for CD45+, CD45+Ly6G- and CD45-CD31+ cell populations (BD FACS ARIA, BD Biosciences). Then, in order to reduce the predominant neutrophil population and to enrich in endothelial cells for scRNAseq experiments, purified cells were mixed with as follow (6·105 CD45+ Ly6G- cells, 3·105 CD45+ cells and 105 CD45- CD31+ cells). ScRNAseq library preparation and sequencingCells were incubated with TotalSeq barcoded-antibodies for each sample, in order to identify the origin of the cell after the RNA library creation. Around 16000 cells per reaction were then processed with a 10X Chromium Next Controller following the 3’ V3 protocol. RNA libraries were then prepared with the Chromium Single Cell 3′ Library and Gel Bead Kit v2 (PN-120267) and Chromium Next GEM Single Cell 3′ Library and Gel Bead Kit v3.1 (PN-1000121) (10X Genomics). Libraries were then sequenced with an Illumina NovaSeq 6000. scRNAseq data analysisSequenced data underwent the Cellranger-7.2.0 pipeline, in order to perform sample demultiplexing, sequence alignment, barcode processing and unique molecular identity (UMI) counting. Filtered matrixes were processed and cells containing more than 5% of mitochondrial genes were cut off. Dataset integration, and clustering was performed using the Seurat package (v4.4.0). The uploaded data correspond to the seurat objects containing the integrated datasets (with cell annotation and clustering), for primary and secondary infection (alldata.Primary and alldata.secondary). Furthermore, filtered matrixes used to generate these Seurat objects (Primary Infection scRNAseq Filtered Matrix Part 1-3, Secondary Infection scRNAseq Filtered Matrix) were provided.