DAC

Genentech Data Access Committee

Dac ID Contact Person Email Access Information
EGAC00001000055 Frederic de-Sauvage gDAC-d [at] gene [dot] com No additional information is available

This DAC controls 30 datasets:

Dataset ID Description Technology Samples
EGAD00001000215 RNA sequencing of colon tumor/normal sample pairs Illumina HiSeq 2000; 139
EGAD00001000216 Exome capture sequencing of colon tumor/normal pairs Illumina HiSeq 2000; 144
EGAD00001000214 Whole genome sequencing of colon samples Illumina HiSeq 2000; 11
EGAD00001001863 Exome data of PDX models. Illumina HiSeq 2500; 4
EGAD00001001862 RNA-seq of PDXs Illumina HiSeq 2000; 12
EGAD00001000223 RNA sequencing of SCLC tumor/normal sample pairs and cell lines Illumina HiSeq 2000; 79
EGAD00001000222 Exome capture sequencing of SCLC tumor/normal pairs and cell lines Illumina HiSeq 2000; 103
EGAD00001000221 Whole genome sequencing of SCLC tumor/normal samples Illumina HiSeq 2000; 4
EGAD00001000886 RNA-Sequencing data (raw read sequences) for 23 samples, from 12 patients, for the study "Diverse modes of genomic alterations in Hepatocellular Carcinoma" Illumina HiSeq 2000; 23
EGAD00001000885 Exome read sequences for 30 tumor-normal pairs for the study "Diverse modes of genomic alterations in Hepatocellular Carcinoma". Illumina HiSeq 2000; 60
EGAD00001000817 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. Illumina HiSeq 2000; 34
EGAD00001000815 Exome-seq, RNA-Seq, SNP array profiling of gastric tumor samples. Illumina HiSeq 2000; 102
EGAD00010000622 SNP array data for gastric cancer cell lines unknown 30
EGAD00001001034 Whole genome data (Complete genomics platform) for the study EGAS00001000824 24
EGAD00001001108 MMP-seq tumor samples (FASTQ) Illumina Genome Analyzer IIx; 218
EGAD00001001104 MMP-seq tumor samples, UDG treated (FASTQ) Illumina MiSeq; 16
EGAD00001001107 MMP-seq cell lines (FASTQ) Illumina Genome Analyzer IIx; 154
EGAD00001001057 RNA-seq from normal human tissues (2 x 75 bp) Illumina HiSeq 2000; 3
EGAD00001001922 RNA-seq from normal human tissues (2 x 250 bp) Illumina HiSeq 2000; 14
EGAD00001002243 RNA-seq data for patient samples Illumina HiSeq 2500; 2
EGAD00001002244 WGS data for cell lines and patient samples Illumina HiSeq 2500; 4
EGAD00001000725 This dataset contains RNA sequencing data for 675 cancer cell lines. RNA libraries were made with the TruSeq RNA Sample Preparation kit (Illumina) according to the manufacturer protocol. The libraries were sequenced on an Illumnia HiSeq 2000 Illumina HiSeq 2000; 675
EGAD00010000951 SNP array data for 668 cancer cell lines Illumina 2.5M 668
EGAD00001001013 RNAseq and exome sequencing data of gastric cancer cell lines. Illumina HiSeq 2000; 30
EGAD00010000278 SCLC matched normal genotypes Illumina_2.5M 51
EGAD00010000276 SCLC tumor genotypes Illumina_2.5M 56
EGAD00010000274 Colon matched tumour samples Illumina_2.5M 74
EGAD00010000272 Colon tumour samples Illumina_2.5M 75
EGAD00001003443 Massively parallel nanowell-based single-cell gene expression profiling Illumina HiSeq 2500;ILLUMINA 14
EGAD00001003550 Cell line exome sequencing Illumina HiSeq 2500;ILLUMINA 176