The Drop-seq and 10x sequencing data were processed using the standard pipeline (Drop-seq core computational protocol V1.2, http://mccarrolllab.com/dropseq/) with minor modifications. For Drop-seq Read1, bases 1 to 12 were tagged with cell-barcode “XC,” and bases 13 to 20 were tagged with UMI “XM.” For 10x Read1, bases 1 to 16 were tagged with cell barcode XC, and bases 17 to 26 were tagged with UMI XM. Read2 was trimmed at the 5′ end to remove any adaptor sequence, and the 3′ end was trimmed to remove poly(A) sequences of length six or more and then aligned to human (hg38) genome reference using STAR aligner (STAR_2.5.1a), allowing no more than three mismatches. Gene expression matrix was then generated using the “MIN_BC_READ_THRESHOLD=2” option to retain UMIs with two or more reads.

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