library_construction_protocol: Cells from 3D culture were spin down and the total RNA were prepared using RNAeasy kit from Qiagen. The poly-A containing RNA transcripts were enriched from one microgram of total RNA for each sample using oligo-dT bead, further fragmented and converted to cDNA and Illumina sequencing library using PrepX RNA-seq library kit on the automated Apollo 324TM NGS Library Prep System (Clontech, CA).  Different DNA barcodes were attached to each library.  The RNA-seq libraries were examined on Agilent Bioanalyzer DNA High Sensitivity chips for size distribution, quantified by Qubit fluorometer (Invitrogen, CA), and pooled at equal molar amount. The library pools were denatured and sequenced on Illumina HiSeq 6000 SP 100nt Lane v1.5 as paired-end according to manufacturer's protocol.