Single cells were collected directly (one cell/well) in to wells containing 10X lysis buffer (Clontech) plus Protector RNAse inhibitor (Roche). The RNA in each well was primed with oligo dT primer that incorporates a unique 10 basepair barcode and Takara's SMART Sequence to the 3'ends  and reverse transcribed (RT) to yield cDNA using SMARTScribe RT enzyme (Takara) and a template switching oligo to incorporate the SMART sequence to 5'-ends. cDNAs from each well/96-well plate was combined, purified, and amplified for 16 cylces using an oligo for the SMART sequence. Full-length cDNAs were sheared and cDNAs blunt-ended, an A base added to the 3'-ends and Illumina sequencing adapters ligated to these ends.  Ligated fragments were then amplified for 16 cycles using standard i7 indexing primer and P5 primer that binds only to the 3' ends of the cDNAs containing SMART sequences and barcodes.  Fragments were sequenced on an Illumina HiSeq-2500 using paired reads extending 26 bases for read one to read cell barcodes, and 98 bases for read two for mRNA data.  Each plate was represented by a unique index and each well is represented by unique barcode.
GEO Accession
GSM4377514