RNA-seq: DP and PFi cells in  GM, OM and OMSW
Cells  were homogenized by centrifugation through Qiashredders (Qiagen, 79654), and  total RNA was isolated using a commercially available kit as per the  manufacturers instructions (Qiagen, RNeasy Plus Micro kit, 74034). Quantitationw as performed with Qubit RNA  high sensitivity assay (ThermoFisher, Q32852), and RIN was assessed using  Agilent Bioanalyzer. All samples had RIN >9. cDNA library construction was performed at Oxford  Genomics (Oxford, United Kingdom) using the Smart-seq2 library preparation  protocol and libraries were sequenced using 75bp paired-end-reads on 2 lanes  of an Illunmia HiSeq 4000 instrument.  Libraries QC was performed using FASTQC and reads were trimmed using  Flexbar, fastq files were aligned to hg19 using HiSAT2 with defualt  parameters, SAM files were converted to BAM using SAMTOOLS and BAMs for each lane were merged with  PICARD.