biostudies-arrayexpressHan ZhangHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-15800RNA-immunoprecipitation sequencing (RIP-seq) was performed to identify the transcripts under the regulation of DEAD-box helicase 3 X-linked (DDX3X). The BPH1-derived Cancer Progression (BCaP) cell lines were used for RIP-seq. Input and RIP RNA from the androgen receptor low/negative castration-resistant prostate cancer (ARL/- CRPC) BCaPMT10 and non-tumorigenic BCaPNT1 cells were extracted using the RNease Mini Kit. Libraries were prepared using the KAPA RNA HyperPrep Kit and sequenced on an Illumina HiSeq 2500 platform.biostudies-arrayexpressSample Collection - A total of 8 × 10⁶ cells were lysed in 1 mL of non-denaturing lysis buffer (20 mM Tris-HCl, pH 7.5; 150 mM NaCl; 1.5 mM MgCl₂; and 0.25% NP-40) supplemented with 1× Halt protease and phosphatase inhibitor cocktail and divided for DDX3X pulldown assays. Protein concentrations were quantified to normalize input across cell lines, and each sample was adjusted to a final volume of 480 μL. An aliquot of 60 μL (1/8 of the total) from each sample was reserved for mRNA input normalization. Protein G Dynabeads, pre-bound to DDX3X or IgG control antibodies, were incubated with 480 μL of lysate for 4 h at 4 °C.Nucleic Acid Extraction - RNA from all samples, including input controls, was extracted using the RNeasy Mini Kit, and cDNA was synthesized from the isolated RNA for input and DDX3X RIP samples as described aboveGrowth Protocol - cells were cultured in RPMI 1640+L-glutamine medium, supplemented with 5% fetal bovine serum, 1% penicillin-streptomycin, and 0.2% Normocin, at 37℃, with 5% CO2.Sequencing - The cDNA was sequenced on an Illumina HiSeq 2500 platform at the University of Massachusetts–Boston CPCT Genomics Core FacilityLibrary Construction - Libraries were prepared using the KAPA RNA HyperPrep Kit following manufacture's instructionsOrganizationMINSEQE ScoreAssays and DataProcessed DataMAGE-TAB FilesData Transformation - The normalization efficiency of input samples was calculated and applied to the RIP samplesMetabolomicsUnknownTranscriptomicsGenomicsProteomicsIllumina HiSeq 2500n/aKAPA RNA HyperPrep KitRNeasy Mini KitRIP-seqHomo sapiensMolecular insights into DDX3X–AR mRNA regulation via non-canonical G-quadruplex in castration-resistant prostate cancerHan Zhang, Teresa Liu, Feixuan Wu, Avan Colah, Emily Ricke, Lingjun Li, Andrea Putnam, William RickeAnthony VeltriWilliam RickeJill MacoskaJordan VellkyHan ZhangfalseMolecular insights into DDX3X–mRNA regulation in castration-resistant prostate cancerRNA-immunoprecipitation sequencing (RIP-seq) was performed to identify the transcripts under the regulation of DEAD-box helicase 3 X-linked (DDX3X). The BPH1-derived Cancer Progression (BCaP) cell lines were used for RIP-seq. Input and RIP RNA from the androgen receptor low/negative castration-resistant prostate cancer (ARL/- CRPC) BCaPMT10 and non-tumorigenic BCaPNT1 cells were extracted using the RNease Mini Kit. Libraries were prepared using the KAPA RNA HyperPrep Kit and sequenced on an Illumina HiSeq 2500 platform.2026-04-17T00:00:00Z2026-04-17T01:02:04.134Z2025-10-20T13:58:20.337ZE-MTAB-15800ERP182520EFO_0002944EFO_0004170EFO_0003789EFO_0005310EFO_0005518EFO_0003816EFO_0004184