library_construction_protocol: The inDrop™ System and single-cell RNA sequencing kit (1CellBio, Watertown MA) were used for single cell encapsulation.  Approximately 2,000 cells were co-encapsulated in 1-3 nL droplets with barcode-labeled hydrogel beads and reverse transcription/cell lysis reagents. Oligonucleotide primers with cell barcodes were released from the beads by an UV light exposure and reverse transcription was performed in the emulsion of droplets in oil.  Barcoded cDNA was released by breaking the droplets after reverse transcription and stored at -80°C. Library preparation was performed following the 1CellBio protocol version 2.3. The steps were as follows: second strand synthesis, in vitro transcription using T7 RNA polymerase, fragmentation of amplified RNA, reverse transcription, and PCR amplification. Size-selected libraries were sequenced on an Illumina HiSeq 2500 instrument using paired-end 2 x 50 base pairs.  Smart-Seq2 modified protocol