Total RNA obtained from FACS-sorted cells was purified with the Absolutely RNA Nanoprep kit (Agilent), quantified with the NanoDrop spectrophotometer (Thermo Scientific) and measured for quality control by the Agilent Bioanalyzer. Samples with RIN (RNA integrity number) scores 8.8 and higher were further processed. 6ng starting material was reverse transcribed and amplified to 5-7µg cDNA with the RNA Ovation RNA-seq System V2 (NuGEN). 100ng of amplified cDNA was used to generate sequencing libraries with 56 unique barcoded adapters (Biological duplicates for 28 samples from K14-H2BGFP;Crabp1-GFP;Lef1-RFP, 7 populations from 4 zones) via the Ovation Ultralow DR Library System (NuGEN). Library concentration and quality was assessed by Qbit (invitrogen) and Bioanalyzer (Agilent).