Project description:LNCaP cells were transfected with 3 different REST siRNAs Transcriptomics analysis was performed to compare gene expression changes induced by REST knockdown
Project description:LNCaP cells were transfected with 3 different REST siRNAs Transcriptomics analysis was performed to compare gene expression changes induced by REST knockdown Genome-wide transcriptomic analysis of LNCaP cells transfected with REST siRNA
Project description:RNA immunoprecipitation coupled with next generation sequencing (RIP-seq) was used to map the HNRNPL-RNA interactome in LNCaP cells.
Project description:LNCaP prostate cancer cells were stimulated with the synthetic androgen R1881. RNA-sequencing was performed to identify changes induced by enzalutamide treatment on the transcriptome level.
Project description:Libraries of single-stranded oligodeoxynucleotides (ssODNs) can be enriched for sequences that specifically bind molecules on naïve complex biological samples like cells or tissues. Depending on the enrichment strategy, the ssODNs can identify molecules specifically associated with a defined biological condition, for example a pathological phenotype, and thus are potentially useful for biomarker discovery. We performed ADAPT, a variant of SELEX, on exosomes secreted by VCaP prostate cancer cells. A library of ~1011 ssODNs was enriched for those that bind to VCaP exosomes and discriminate them from exosomes derived from LNCaP prostate cancer cells. Next-generation sequencing (NGS) identified the best discriminating ssODNs, nine of which were resynthesized and their discriminatory ability confirmed by qPCR. Affinity purification with one of the sequences (Sequence 7) combined with LC-MS/MS identified its molecular target complex, whereof most proteins are part of or associated with the multiprotein ESCRT complex participating in exosome biogenesis. Within this complex, YBX1 was identified as the directly bound target protein. ADAPT thus is able to differentiate exosomes from cancer cell subtypes from the same lineage. The composition of ESCRT complexes in exosomes from VCaP versus LNCaP cells might constitute a discriminatory element between these prostate cancer subtypes.
Project description:The goal of this study was to use NGS RNAseq deep-sequencing in order to characterize the complement of polyadenylated mRNAs and lncRNAs expressed in LNCaP, a prostate cancer cell line. RNA-seq data were processed as aggregates of the two biological replicates to increase resulting transcriptome coverage. Trimmed reads were mapped with TopHat v.2.0.12 and Bowtie v.2.2.3, and a custom GTF file to guide transcriptome assembly. This custom GTF file was built by using the human transcriptome annotation GTF file downloaded from Ensembl Project web-site (http://www.ensembl.org/) and modified to include all lncRNAs reported in Cabili et al, Genes & Development 2011. polyA+ RNA profiles of LNCaP prostate cancer cell line grown in culture for 48 h in the absence of androgen were generated by paired-end deep sequencing, in duplicate, using Illumina HiSeq2000.
