title: GSM5657785: NCIH104_OCT11_sg2; Homo sapiens; RNA-Seq
library_construction_protocol: Total RNA was extracted using TRIzol following the standard protocol; cells were fixed with 1% formaldehyde for 10 minutes and quenched with glycine following standard protocol (see method in paper) for ChIP-Seq. polyA RNA was selected and fragmented with NEBNext Poly (A) mRNA Magnetic isolation  module (NEB #E7350) and the library was prepared with NEBNext Ultra II RNA Library Prep kit for  Illumina (NEB #E7770) with 2 ug RNA according to the manufacturer's protocol. For single cell RNA-seq, cell suspensions were stained for viability with Sytox blue (ThermoFisher S34857) and sorted on a Sony  SH800S (Sony Biotechnology Inc, San Jose, CA) using a 100 μm chip (Catalog #LE-C3110) in “Ultra  Purity” mode. Sorted cells were washed and resuspended in PBS containing 0.04% BSA. An aliquot  was stained with ViaStain AOPI (Nexcelom #CS2-0106-5mL) and counted using a Countess FL II  automated cell. Up to 12,000 cells were loaded per lane on 10X Chromium microfluidic chips. Single  cell capture, barcoding, and library preparation were performed using the 10X Chromium chemistry,  using the NextGEM Single-Cell 3' Library Kit v3.1 (1000121; 10X Genomics). ChIP-seq library was prepared using the NEBNext Ultra II DNA Library Prep Kit  for Illumina (E7645) following manufacturer's protocol with AMPure XP beads (Beckman, A63881)  with no size selection.