The cell metadata for this experiment are provided in "ss3_PE.metadata.txt".

Raw, multiplexed FASTQ files containing nucleotide base sequences and respective quality scores, as well as zUMIs-processed files, are provided in the "Raw_FASTQ_files" and specifically in the file SS3_2021_PMEHL.tar.gz. These can be demultiplexed using the barcode list provided in "index_name.txt". 

In our analysis, the FASTQ demultiplexing was performed with the zUMIs pipeline to generate a processed count matrix separated by samples and gene names. These are provided in the folder "Processed_Files", and in the file "ss3_PE.dgecounts.rds". The RDS file can be readily loaded into Seurat (free R package for analysis of single-cell RNAseq data). The "ss3_PE.gene_names.txt" file matches the gene IDs to gene names for zUMIs processing.