amplification were performed using the parameters described by Picelli et al51. The quality of the cDNA library was checked using a High-Sensitivity DNA chip (Agilent Bioanalyzer). Libraries were prepared using the Nextera XT library prep kit (96 index primers, Illumina). Because the Nextera XT kit is very sensitive to the concentration of cDNA, we screened pre-amplified cDNA libraries from all plates using the Qubit dsDNA HS Assay kit and used 125 pg cDNA from each positive well to further process the tagmentation and indexing. Twelve additional PCR cycles were performed to further enrich for pre-amplified tagmented DNA. The quality of the tagmented library was checked using the High-Sensitivity Bioanalyzer chip. The final pooled library was diluted to 2 nM using the elution buffer (Qiagen), and 10 pM was loaded on an Illumina HiSeq 2500 instrument for sequencing. Libraries were sequenced to obtain 50 bp single end reads (TruSeq Rapid kit, Illumina) with 8 additional cycles for indexing. On average, we obtained 2 million pass filter reads per single cell (Extended Data Fig. 6c). We considered a gene expressed if there were at least 10 reads detected for that gene. Cells that expressed more than 1,000 genes and <10% mitochondrial RNAs
