Preprocessed h5ad files of scRNA-seq performed on atherosclerotic human carotid artery samples

Description of data

For single cell RNA sequencing of human carotid arteries, samples were harvested during CEA in our Department for Vascular and Endovascular Surgery. In total 17 plaques  were minced and digested using the Multi Tissue Dissociation Kit 2 (Miltenyi Biotech, 130-110-203) and the 37 C_Mulit_G program (GentleMACS Dissociator; Miltenyi Biotech, 130-093-235) according to the manufacturer's instructions. The cell suspension was cleaned up and finally resuspended in PBS + 0,04% BSA. Cells were loaded into a 10xGenomics microfluidics Chip G and encapsulated with barcoded oligo-dT-containing gel beads. Gel-Beads-in-emulsion (GEM) cleanup, cDNA amplification and 3´GeneExpression Library Construction was performed according to the manu-facturer´s instructions (CG000204 Rev D). Libraries from individual patient samples 1-10 (sequencing facility 1) were multiplexed into one lane before sequencing on an Illumina NovaSeq6000 instrument. One whole flow-cell was occupied and used for sequencing. This data has been deposited in NCBI's Gene Expression Omnibus and is accessible through GEO Series accession number GSE247238. Libraries from individual patient samples 11-17 (sequencing facility 2, GSE294291) were loaded on an Illumina NovaSeq with 2 × 150 paired-end kits and sequenced with Novogene (Martinsried, Germany). 

Description of files 

• GRCh38-p14-Gencode_v44_with_intron_final_data.h5ad: Anndata object containing final count matrix and metadata variables of scRNA-seq data used in study. 
• scRNA_data_column_descriptions.md: description of .obs columns in the Anndata object. 

Detailed description of preprocessing steps can be found in our manuscript.