biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsJeffrey WangNAIllumina NovaSeq XRNA-seq of coding RNAHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16091The purpose of this experiment is to identify cellular processes that are associated with cellular expression of oncRNAs, which are cancer-emergent non-coding, small RNAs. To test this, we compared the transcriptomes of our breast cancer cells lines (MDA-MB-231 and HCC-LM2) overexpressing oncRNA.ch7.29 or oncRNA.ch17.67 relative to respective controls. Cell lines were transduced with shctrl, oncRNA.ch7.29, or oncRNA.ch17.67 under the control of a U6 promoter. RNA was extracted from the cell lines and used as input for mRNA-seq library construction.biostudies-arrayexpressLibrary Construction - 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).Sample Collection - 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).Nucleic Acid Extraction - RNA was extracted extracted using the Zymo Research Quick-RNA Microprep Kit (cat#R1051), following manufacturer's instructions.Sequencing - mRNA-seq libraries were pooled and sequenced on 1 lane of NovaSeqX 100x6x0x0 at the UCSF Center for Advanced Technology (CAT).OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesJeffrey WangfalseSystematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic driversThe purpose of this experiment is to identify cellular processes that are associated with cellular expression of oncRNAs, which are cancer-emergent non-coding, small RNAs. To test this, we compared the transcriptomes of our breast cancer cells lines (MDA-MB-231 and HCC-LM2) overexpressing oncRNA.ch7.29 or oncRNA.ch17.67 relative to respective controls. Cell lines were transduced with shctrl, oncRNA.ch7.29, or oncRNA.ch17.67 under the control of a U6 promoter. RNA was extracted from the cell lines and used as input for mRNA-seq library construction.2025-11-23T00:00:00Z2026-06-16T17:40:27.534Z2025-11-11T15:51:06.461ZE-MTAB-16091ERP184215EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184