CD40–TRAF6 inhibition reduces chronic inflammation but does not affect infarct size of left ventricular function following myocardial infarction in mice

scRNAseq dataset to the publication ...

Data processing:

Isolated cardiac immune cells were stained against CD45 (Biolegend, 103116) and one specific TotalSeq Hashtag (Biolegend, TotalSeq™-A0301 - 306) in MACS-Buffer (Miltenyi biotech, 130-091-221) for 15 min at room temperature. Cell viability and cell number were assessed via DAPI staining while sorting. Cell sorting was performed on a MoFlo XDP (Beckman Coulter). In total, cells from 6 different mice were pooled in one sequencing run, which were to be characterized via different hashtags. A total amount of 40,000 cells were used as input for the single-cell droplet libraries generated on a 10× Chromium Controller system utilizing the Chromium Single Cell 3 Reagent Kit v3 according to manufacturer’s instructions. Sequencing was carried out on a NetxSeq550 system (Illumina Inc. San Diego, CA, USA) with a mean sequencing depth of ~50,000 reads/cell and 5,000 reads/hashtag. The experiment was performed twice. Raw sequencing data were processed using the 10× Genomics CellRanger software (v6.0.0). Raw BCL-files were demultiplexed and processed to Fastq-files using the CellRanger mkfastq pipeline. Alignment of reads to the mm10 genome and UMI counting was performed via the CellRanger count pipeline to generate a gene-barcode matrix.