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 are provided in the "Raw_FASTQ" folder. These can be demultiplexed using the barcode list provided in "expected_barcodes.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 files are provided in the folder "Processed_Files", compiled into one single file "Xpress.dgecounts.rds" or separated by count type "Smartseq3xpress_read/umicount_etc". The RDS file can be readily loaded into Seurat (free R package for analysis of single-cell RNAseq data). The "Xpress.gene_names.txt" file matches the gene IDs to gene names for zUMIs processing.