biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsMarco MernbergerNextSeq 550RNA-seq of coding RNAHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-14099Since radiotherapy is the essential treatment of prostate cancer, this experiment aimed to elucidate the transcriptomic response of prostate cancer cells to irradiation by either conventional photons or alternatively carbon ions, focusing on DNA damage, DNA repair and androgen receptor signaling.biostudies-arrayexpressSample Treatment - LNCap and DU145 cells were treated by irradiations and LNCaP cells by addition of (5, 17)-17-hydroxy-androstane-3-one (di-hydro-testosterone; DHT) (20 nM) (Sigma-Aldrich). All treatments were performed in three independent triplicates with a calculated cell density of approximately 50% confluence at the time point of setup. For photon irradiation an X-RAD 320ix cabinet was used (X-ray unit (Precision X-Ray Inc, Denver, USA, 320 kV, 8 mA, filter: 0.5 mm Cu and 0.5 mm Al, dose rate 1 Gy/min). 12 C-irradiation was performed at the Marburg Ion-Beam Therapy Centre (MIT). Cells were irradiated with a horizontal beam of 114.5–129.5 MeV/n12 C-ions and positioned in the middle of a spread-out Bragg peak (SOBP) of 10–20 mm. Fields were applied using active scanning with a square of 324 cm2.Growth Protocol - Cells were cultured in accordance with the recommended conditions in RPMI full growth medium supplemented with fetal bovine serum.Nucleic Acid Extraction - RNA was isolated using the RNeasy Mini kit (Qiagen) and RNA quality was assessed using the Experion RNA StdSens Analysis Kit (Bio‐Rad).Sample Collection - The human prostate cancer cell lines LNCaP and DU145 were obtained and authenticated from the Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany LNCaP, DSMZ-ACC 256; DU145, DSMZ-ACC 261).Library Construction - RNAseq libraries were prepared from total RNA with the Lexogen QuantSeq 3'-mRNA Library Prep Kit FWD for Illumina (Lexogen, 015.24) in combination with the UMI Second Strand Synthesis Module for QuantSeq FWD (Illumina, Read 1) (Lexogen, 081.96) following the manufacturer's protocol. Quality of sequencing libraries was controlled on a Bioanalyzer 2100 using the Agilent High Sensitivity DNA Kit (Agilent).Sequencing - Pooled sequencing libraries were quantified with digital PCR (QuantStudio 3D, Thermo Fisher), sequenced on the NextSeq550 platform (Illumina) with 75 base single reads.OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesAndrea NistMatthias LauthFlorentine SubtilThomas PlaggeThorsten StieweAxel HegerleFabian EberleKatrin RothRainer HofmannUlrike TheissMarco MernbergerDinesh TiwariLilly MengenJörg HänzeRita Engenhart-CabillicfalseRNAseq of tumor cell lines LNCaP and DU145 irradiated by photons or carbon ionsSince radiotherapy is the essential treatment of prostate cancer, this experiment aimed to elucidate the transcriptomic response of prostate cancer cells to irradiation by either conventional photons or alternatively carbon ions, focusing on DNA damage, DNA repair and androgen receptor signaling.2025-07-07T00:00:00Z2024-05-23T09:29:14.68Z2024-05-23T09:29:14.68ZE-MTAB-14099ERP160496EFO_0002944EFO_0004170EFO_0003789EFO_0005518EFO_0003738EFO_0003969EFO_0004184