library_construction_protocol: BCBM T347-Ctrl and T347-RET+ cells (n =3) were collected, RNA was extracted using Qiagen RNeasy Kit (Qiagen; #74104), following manufacturer instructions. Poly-A containing mRNA molecules were purified using poly-T oligoattached magnetic beads. Following purification, the mRNA was fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H and subsequent ligation of the adapter. The products were purified and enriched with PCR amplification. PCR yield was quantified by Qubit and samples were pooled together to make a single strand DNA circle (ssDNA circle), which gave the final library.  DNA nanoballs (DNBs) were generated with the ssDNA circle by rolling circle replication (RCR) to enlarge the fluorescent signals at the sequencing process. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 100 bp were read through on the DNBseq platform. The DNBseq platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using Combinational Probe-Anchor Synthesis Sequencing Method.