a) Setup of the Drop-seq workflow used as part of CROP-seq. b) Bioanalyzer trace of a typical cDNA library prepared with CROP-seq. c) Electropherogram of a sequencing-ready CROP-seq library after tagmentation. d) Doublet estimates based on a HEK293T (human) / 3T3 (mouse) mixing experiment across all detected cells and transcripts (without filtering). e) Percent of detected genes aligning to the human and mouse transcriptomes (filtered for cells with more than 500 detected genes). f) PCR duplication rates based on unique molecular identifiers (UMIs) in the HEK293T (human) / 3T3 (mouse) mixing experiment. g) Distribution of the distance of read mapping positions to the 3′end of gene models (blue line) and their cumulative sum (red line). h) Detailed performance statistics for twelve CROP-seq experiments. Green and orange labels indicate different batches of Drop-seq beads, where batch 1 suffered from production problems affecting the cell barcodes, which have been bioinformatically corrected to improve the data quality of the affected samples.