Genentech Data Access Committee

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This DAC controls 45 datasets

Dataset ID	Description	Technology	Samples
EGAD00001000214	Whole genome sequencing of colon samples	Illumina HiSeq 2000	11
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
EGAD00001000221	Whole genome sequencing of SCLC tumor/normal samples	Illumina HiSeq 2000	4
EGAD00001000222	Exome capture sequencing of SCLC tumor/normal pairs and cell lines	Illumina HiSeq 2000	103
EGAD00001000223	RNA sequencing of SCLC tumor/normal sample pairs and cell lines	Illumina HiSeq 2000	79
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
EGAD00001000815	Exome-seq, RNA-Seq, SNP array profiling of gastric tumor samples.	Illumina HiSeq 2000	102
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
EGAD00001000885	Exome read sequences for 30 tumor-normal pairs for the study "Diverse modes of genomic alterations in Hepatocellular Carcinoma".	Illumina HiSeq 2000	60
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
EGAD00001001013	RNAseq and exome sequencing data of gastric cancer cell lines.	Illumina HiSeq 2000	30
EGAD00001001034	Whole genome data (Complete genomics platform) for the study EGAS00001000824		24
EGAD00001001057	RNA-seq from normal human tissues (2 x 75 bp)	Illumina HiSeq 2000	3
EGAD00001001104	MMP-seq tumor samples, UDG treated (FASTQ)	Illumina MiSeq	16
EGAD00001001107	MMP-seq cell lines (FASTQ)	Illumina Genome Analyzer IIx	154
EGAD00001001108	MMP-seq tumor samples (FASTQ)	Illumina Genome Analyzer IIx	218
EGAD00001001862	RNA-seq of PDXs	Illumina HiSeq 2000	12
EGAD00001001863	Exome data of PDX models.	Illumina HiSeq 2500	4
EGAD00001001922	RNA-seq from normal human tissues (2 x 250 bp)	Illumina HiSeq 2000	14
EGAD00001002243	RNA-seq data for clinical samples	Illumina HiSeq 2500	2
EGAD00001002244	WGS data for cell lines and clinical samples	Illumina HiSeq 2500	4
EGAD00001003443	Massively parallel nanowell-based single-cell gene expression profiling	Illumina HiSeq 2500	14
EGAD00001003550	Cell line exome sequencing	Illumina HiSeq 2500	176
EGAD00001004351	ERBB2/HER2 transmembrane and juxtamembrane domain mutations in cancer. Exome sequencing of tumor and matched blood and 2 blood samples from relatives.	Illumina HiSeq 2500	4
EGAD00001005057	None	Illumina HiSeq 4000	6
EGAD00001005187	RNA was isolated from purified human CD8 cells that were incubated with anti-HER2/CD3 TDB in the presence of SK-BR-3 cells. Sequencing libraries were generated and submitted for transcriptome profiling by high-throughput sequencing. Experiments were performed in triplicates for anti-HER2/CD3 TDB treatment and control. This Dataset is associated with the following ArrayExpress Experiment: E-MTAB-8211 - The effect of anti-HER2/CD3 TDB on transcription in human CD8 T cells (bulk)	Illumina HiSeq 4000	6
EGAD00001005188	Single-cell RNA-seq libraries were generated from human PBMCs that were incubated with anti-HER2/CD3 TDB in the presence of KPL-4 cells. This dataset is linked with the following ArrayExpress Experiment: E-MTAB-8212 - The effect of anti-HER2/CD3 TDB on transcription in human PBMCs (single-cell)	Illumina HiSeq 4000	4
EGAD00001005464	Single-cell RNA-seq of tumor-infiltrating lymphocytes from 14 cancer patients before treatment, taken from tumor, normal adjacent tissue, and peripheral blood. Dataset consists of paired-end FASTQ files, including replicate libraries and runs.	Illumina HiSeq 4000	45
EGAD00001005465	Single-cell TCR-seq of tumor-infiltrating lymphocytes from 14 cancer patients before treatment, taken from tumor, normal adjacent tissue, and peripheral blood. Dataset consists of paired-end FASTQ files, including replicate libraries and runs.	Illumina HiSeq 2500	88
EGAD00001007061	Amplicon seqeuencing of (1) wildtype IPC298 cell line grown for 3-4 weeks with DMSO, amplified for ARAF exon 11 (2) IPC298 cells treated for 3-4 weeks with 10uM belvarafenib, isolated colony 9, amplified for ARAF exon 11 (3) MelJuso cell line grown with DMSO, amplified for ARAF exon 11	Illumina HiSeq 4000	3
EGAD00001007062	Whole Exome Sequencing of Belvarafenib resistant IPC-298 clones after treatment for 3-4 weeks with 10uM belvarafenib	Illumina HiSeq 4000	6
EGAD00001007872	To QC the TraCe-seq strategy, single-cell RNA-seq libraries were generated from a variety of human cancer cell lines transduced with the TraCe-seq library to validate the TraCe-seq strategy. Specifically, 5 different cell lines (PC9, MCF-10A, MDA-MB-231, NCI-H358, and NCI-H1373) were each transduced with a unique TraCe-seq barcode. The transduced cells were selected with puromycin only, dissociated to single cell suspensions, and then mixed together. The complex mixture of the 5 cell lines was profiled by 10X scRNA-seq. Furthermore, transduced NCI-H1373 cells were sorted by FACS to enrich for the top 50% of eGFP positive cells, and sorted cells were cultured briefly and used to construct scRNA-seq libraries and profiled by 10x scRNA-seq. To carry out the full TraCe-seq experiment, ~600 PC9 cells carrying unique TraCe-seq barcodes were expanded over 12 doublings to establish the barcoded population. A subset of the barcoded PC9 population was used to generate scRNA-seq libraries and profiled by 10x scRNA-seq prior to treatment to establish a baseline transcription profile for each barcoded clone. The rest of the cells were then treated for four days with 1 µM erlotinib, 1 µM GNE-069, or 1 µM GNE-104 respectively. scRNA-seq libraries were then generated form the treated cells and profiled by 10x scRNA-seq.	Illumina HiSeq 4000	6
EGAD00001008384	RNA Sequencing upon shRNA mediated depletion of RAF kinases or treatment with Cobimetinib (GDC-0973, 250nM, 6hrs) or with pan RAFi (AZ-628, 10uM, 6hrs)	Illumina HiSeq 2500	24
EGAD00001008722	Engineered Human Primary T Cell transcriptome study	Illumina NovaSeq 6000	45
EGAD00001008731	Although cross-species transcriptional analysis has been generated for DCs, transcriptomic conservation between mouse and human FRCs at single-cell resolution has been unclear. To test whether GREM1+ FRCs might also play a role in DC homeostasis in humans, we performed scRNA-seq of CD45–PDPN+ stromal cells, as well as CD45+CD11c+ immune cells from healthy human LNs of three human donors. Data was generated using the 10x platform.	Illumina HiSeq 4000	6
EGAD00001009176	We sorted CD45-CD44+CD90+ stromal cells from multiple tumor types and performed bulk RNA-sequencing.	Illumina HiSeq 2500	171
EGAD00001010895	transcriptome analysis of NK cells sorted from PBMCs at baseline and after addition of a CD20 (B cell)-targeted T cell dependent bispecific antibody (TDB)	Illumina NovaSeq 6000	1
EGAD00001011041	PC-9 cells were barcoded following protocol from Chang et al. Nature Biotech. 2021, which does not affect downstream analysis. PC-9 cells were trypsinized into single-cell suspensions and processed using Chromium Single Cell Gene Expression 3’ Library and Gel Bead Kit V2.0 following the manufacturer’s instructions (10X Genomics). Cells were counted and checked for viability using Vi-CELL XR cell counter (Beckman Coulter), and then injected into microfluidic chips to form Gel Beads-in-Emulsion (GEMs) in the 10X Chromium instrument. Reverse transcription was performed on the GEMs, and RT products were purified and amplified. Expression libraries were made from the cDNA and profiled using the Bioanalyzer High Sensitivity DNA kit (Agilent Technologies) and quantified with Kapa Library Quantification Kit (Kapa Biosystems). Illumina HiSeq2500 (Illumina) was used to sequence the libraries.	Illumina HiSeq 4000	1
EGAD00010000272	Colon tumour samples	Illumina_2.5M	75
EGAD00010000274	Colon matched tumour samples	Illumina_2.5M	74
EGAD00010000276	SCLC tumor genotypes	Illumina_2.5M	56
EGAD00010000278	SCLC matched normal genotypes	Illumina_2.5M	51
EGAD00010000622	SNP array data for gastric cancer cell lines		30
EGAD00010000951	SNP array data for 668 cancer cell lines	Illumina 2.5M	668