title: Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers
design: Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers
library_construction_protocol: All cells were cultured in a 37°C 5% CO2 humidified incubator. MDA-MB-231 cells were cultured in Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% FBS, glucose (2 g/L), L-glutamine (2 mM), 25 mM HEPES, penicillin (100 units/mL), streptomycin (100 μg/mL) and amphotericin B (1 μg/mL) (Gibco). HCC1806-LM2 (HCC-LM2) cells were grown in Roswell Park Memorial Institute-1640 medium supplemented with 10% FCS, l-glutamine (2 mM), sodium pyruvate (1 mM), penicillin (100 U ml−1), streptomycin (100 μg ml−1) and amphotericin (1 μg ml−1). RNA was extracted extracted using the Zymo Research Quick-RNA Microprep Kit (cat#R1051), following manufacturer's instructions. mRNA-seq libraries were constructed from 100-200 ng RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD according to the manufacturer's instructions (Lexogen, Cat. #015).