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RNAseq data to study PRPF6 regulated splice forms in colon cancer cell lines

Alternative splicing plays critical roles in differentiation, development, and cancer (Pettigrew et al., 2008; Chen and Manley, 2009). The recent identification of specific spliceosome inhibitors has generated interest in the therapeutic potential of targeting this cellular process (van Alphen et al., 2009). Using an integrated genomic approach, we have identified PRPF6, an RNA binding component of the pre-mRNA spliceosome, as an essential driver of oncogenesis in colon cancer. Importantly, PRPF6 is both amplified and overexpressed in colon cancer, and only colon cancer cells with high PRPF6 levels are sensitive to its loss. Our data clearly point to an important role for PRPF6 in colon cancer growth and suggest that a better understanding of its role in alternative splicing in colon cancer is warranted. To determine the specific alternative splice forms that PRPF6 regulates in colon cancer, we plan three experiments: 1. The first involves knocking down expression of PRPF6 in two different cancer cell lines with 3 different siRNAs, and then completing RNA-seq to determine the gene expression changes that occur relative to a non-targeting control siRNA. Because of the role for PRPF6 in pre-mRNA splicing, we especially want to quantify the changes in splice-specific forms of all genes genome-wide to identify genes whose splicing is altered upon PRPF6 knockdown. 2. The second involves immunoprecipitating PRPF6 from two different cancer cell lines and isolating any RNA that is bound to PRPF6, since PRPF6 is an RNA-binding protein. We then want to carry out RNA-seq to identify which RNA molecules co-immunoprecipitated with PRPF6. This will help us determine possible functions for PRPF6 in regulating colon cancer growth. 3. The third involves overexpressing PRPF6 in cell lines and then carrying out RNA-seq to identify any changes in splice-specific gene expression. This will allow us to determine whether increased PRPF6 expression is sufficient to drive alternative splicing changes.

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Studies are experimental investigations of a particular phenomenon, e.g., case-control studies on a particular trait or cancer research projects reporting matching cancer normal genomes from patients.

Study ID Study Title Study Type
EGAS00001000761 Other

This table displays only public information pertaining to the files in the dataset. If you wish to access this dataset, please submit a request. If you already have access to these data files, please consult the download documentation.

ID File Type Size Located in
EGAF00000512770 fastq.gz 3.1 GB
EGAF00000512771 fastq.gz 3.2 GB
EGAF00000512772 fastq.gz 4.0 GB
EGAF00000512773 fastq.gz 4.1 GB
EGAF00000512774 fastq.gz 4.6 GB
EGAF00000512775 fastq.gz 4.7 GB
EGAF00000512776 fastq.gz 3.1 GB
EGAF00000512777 fastq.gz 3.1 GB
EGAF00000512778 fastq.gz 4.8 GB
EGAF00000512779 fastq.gz 4.9 GB
EGAF00000512780 fastq.gz 3.2 GB
EGAF00000512781 fastq.gz 3.2 GB
EGAF00000512782 fastq.gz 7.9 GB
EGAF00000512783 fastq.gz 7.9 GB
EGAF00000512784 fastq.gz 4.5 GB
EGAF00000512785 fastq.gz 4.6 GB
EGAF00000512786 fastq.gz 3.9 GB
EGAF00000512787 fastq.gz 4.0 GB
EGAF00000512788 fastq.gz 3.5 GB
EGAF00000512789 fastq.gz 3.6 GB
EGAF00000512790 fastq.gz 9.4 GB
EGAF00000512791 fastq.gz 9.4 GB
EGAF00000512792 fastq.gz 4.1 GB
EGAF00000512793 fastq.gz 4.3 GB
EGAF00000512794 fastq.gz 6.1 GB
EGAF00000512795 fastq.gz 6.3 GB
EGAF00000512796 fastq.gz 5.6 GB
EGAF00000512797 fastq.gz 5.7 GB
EGAF00000512798 fastq.gz 7.4 GB
EGAF00000512799 fastq.gz 7.5 GB
EGAF00000512800 fastq.gz 6.7 GB
EGAF00000512801 fastq.gz 6.8 GB
EGAF00000512802 fastq.gz 3.6 GB
EGAF00000512803 fastq.gz 3.7 GB
EGAF00000512804 fastq.gz 3.6 GB
EGAF00000512805 fastq.gz 3.7 GB
EGAF00000512806 fastq.gz 2.3 GB
EGAF00000512807 fastq.gz 2.3 GB
EGAF00000512808 fastq.gz 1.5 GB
EGAF00000512809 fastq.gz 1.5 GB
EGAF00000512810 fastq.gz 6.3 GB
EGAF00000512811 fastq.gz 6.4 GB
EGAF00000512812 fastq.gz 4.5 GB
EGAF00000512813 fastq.gz 4.6 GB
EGAF00000512814 fastq.gz 5.3 GB
EGAF00000512815 fastq.gz 5.4 GB
EGAF00000512816 fastq.gz 3.5 GB
EGAF00000512817 fastq.gz 3.6 GB
EGAF00000512818 fastq.gz 4.1 GB
EGAF00000512819 fastq.gz 4.2 GB
EGAF00000512820 fastq.gz 8.4 GB
EGAF00000512821 fastq.gz 8.5 GB
EGAF00000512822 fastq.gz 4.2 GB
EGAF00000512823 fastq.gz 4.2 GB
EGAF00000512824 fastq.gz 9.4 GB
EGAF00000512825 fastq.gz 9.6 GB
EGAF00000512826 fastq.gz 3.2 GB
EGAF00000512827 fastq.gz 3.3 GB
EGAF00000512828 fastq.gz 3.0 GB
EGAF00000512829 fastq.gz 3.1 GB
EGAF00000512830 fastq.gz 5.7 GB
EGAF00000512831 fastq.gz 5.7 GB
EGAF00000512832 fastq.gz 4.3 GB
EGAF00000512833 fastq.gz 4.3 GB
EGAF00000512834 fastq.gz 3.6 GB
EGAF00000512835 fastq.gz 3.6 GB
EGAF00000512836 fastq.gz 4.0 GB
EGAF00000512837 fastq.gz 4.1 GB
68 Files (327.3 GB)