Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Whole Transcriptomic Sequencing of Metastatic Castration Resistant Prostate Cancer Samples

ABSTRACT: We report the gene expression profile of 8 metastatic castration resisistant prostate cancer samples analyzed by paired-end RNA-seq. We found evidence of extensive abnormal splicing as well as several novel fusion genes. Finally, we also observed several recurrent high-confidence somatic mutations. Paired-end RNA-seq by rRNA depletion

ORGANISM(S): Homo sapiens

SUBMITTER: Adam Sowalsky

PROVIDER: E-GEOD-50630 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer.

Sowalsky Adam G AG Xia Zheng Z Wang Liguo L Zhao Hao H Chen Shaoyong S Bubley Glenn J GJ Balk Steven P SP Li Wei W

Molecular cancer research : MCR 20140904 1

<h4>Unlabelled</h4>Men with metastatic prostate cancer who are treated with androgen deprivation therapies (ADT) usually relapse within 2 to 3 years with disease that is termed castration-resistant prostate cancer (CRPC). To identify the mechanism that drives these advanced tumors, paired-end RNA-sequencing (RNA-seq) was performed on a panel of CRPC bone marrow biopsy specimens. From this genome-wide approach, mutations were found in a series of genes with prostate cancer relevance, including AR ...[more]

PMID: 25189356

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Project description:Background RNA sequencing (RNA-seq) is a powerful technique for identifying and quantifying transcription and splicing events, both known and novel. However, given its recent development and the proliferation of library construction methods, understanding the bias it introduces is incomplete but critical to realizing its value. Results Here we present a method, in vitro transcription sequencing (IVT-seq), for identifying and assessing the technical biases in RNA-seq library generation and sequencing at scale. We created a pool of > 1000 in vitro transcribed (IVT) RNAs from a full-length human cDNA library and sequenced them with poly-A and total RNA-seq, the most common protocols. Because each cDNA is full length and we show IVT is incredibly processive, each base in each transcript should be equivalently represented. However, with common RNA-seq applications and platforms, we find ~50% of transcripts have > 2-fold and ~10% have > 10-fold differences in within-transcript sequence coverage. Strikingly, we also find > 6% of transcripts have regions of high, unpredictable sequencing coverage, where the same transcript varies dramatically in coverage between samples, confounding accurate determination of their expression. To get at causal factors, we used a combination of experimental and computational approaches to show that rRNA depletion is responsible for the most significant variability in coverage and that several sequence determinants also strongly influence representation. Conclusions In sum, these results show the utility of IVT-seq in promoting better understanding of bias introduced by RNA-seq and suggest caution in its interpretation. Furthermore, we find that rRNA-depletion is responsible for substantial, unappreciated biases in coverage. Perhaps most importantly, these coverage biases introduced during library preparation suggest exon level expression analysis may be inadvisable. 5 rRNA-depleted samples with duplicates, 1 polyA selected, 1 total RNA, and 1 plasmid library all without replicates.

Dataset Information

Whole Transcriptomic Sequencing of Metastatic Castration Resistant Prostate Cancer Samples

Publications

Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer.

Similar Datasets

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