Agilent 2200 tapestation nucleic acid system

The Drop-seq libraries were prepared following a previously published protocol 30 . All the primers used in the library preparation are listed in Supplementary Table 2. The inDrops libraries were prepared using the following procedure: After completion of the microfluidics stage, the collection tubes were exposed to 6.5 J/cm 2 of a 365-nm UV lamp for 10 min to release photocleavable barcoding primers from the barcoding beads. Next, the collection tubes containing the UV-exposed emulsion were transferred to a reverse transcription reaction at 50 °C for 2 h followed by 15 Amplified libraries were purified using a 0.7X reaction volume of AMPure XP beads and eluted in 30 μl nuclease-free water. Aliquots of 15 μl of each resulting library were run in 2% agarose gels, and the desired 200-800 bp DNA library fragments were isolated using PureLink™ Quick Gel Extraction Kit (Invitrogen, cat #K210012). For the clonal barcoding library, we aimed for amplification of a band around 600 bp. Library quality was confirmed by Agilent 2200 TapeStation nucleic acid system (Agilent) using the Agilent High Sensitivity D1000 DS DNA kit. The resulting libraries had an average size of 350-550 bp (Supplementary Figure 7). Size-selected libraries were diluted to 4 nM and combined into a pool for paired-end, single index sequencing on the Illumina NextSeq 550 instrument,