Transcriptomics

Dataset Information

298

Discovery of cis-spliced chimeric RNAs between adjacent genes in human prostate cells


ABSTRACT: Total RNA extracted from prostate cancer LNCaP cells transfected with siRNA against CTCF(siCTCF), or negative control siRNA (si-)were processed, and sequenced by two different companies using Illumina Hi-seq 2000 platform to generate RNA sequencing with two output sequences: paired-end 50bp and 101bp in read length. Nearly 100 million and 50 million raw reads were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and SOAPfuse software to detect fusion transcripts. Discovering fusion genes from siCTCF and si- in LNCaP cells.

ORGANISM(S): Homo sapiens  

SUBMITTER: Fujun Qin   Hui Li 

PROVIDER: E-GEOD-63487 | ArrayExpress | 2015-02-09

SECONDARY ACCESSION(S): GSE63487SRP050061PRJNA268024

REPOSITORIES: GEO, ArrayExpress, ENA

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Publications

Discovery of CTCF-sensitive Cis-spliced fusion RNAs between adjacent genes in human prostate cells.

Qin Fujun F   Song Zhenguo Z   Babiceanu Mihaela M   Song Yansu Y   Facemire Loryn L   Singh Ritambhara R   Adli Mazhar M   Li Hui H  

PLoS genetics 20150206 2


Genes or their encoded products are not expected to mingle with each other unless in some disease situations. In cancer, a frequent mechanism that can produce gene fusions is chromosomal rearrangement. However, recent discoveries of RNA trans-splicing and cis-splicing between adjacent genes (cis-SAGe) support for other mechanisms in generating fusion RNAs. In our transcriptome analyses of 28 prostate normal and cancer samples, 30% fusion RNAs on average are the transcripts that contain exons bel  ...[more]

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