Project description:Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing
Project description:Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing
Project description:Cancer Genome Scanning in Plasma: Detection of Tumor-Associated Copy Number Aberrations, Single-Nucleotide Variants, and Tumoral Heterogeneity by Massively Parallel Sequencing
Project description:We applied a massively parallel reporter assay (MPRA) in lymphoblastoid cells to functionally evaluate 49,256 allelic pairs, representing 30,893 genetic variants in high, local linkage disequilibrium for 744 independent cis-expression quantitative trait loci (eQTLs) assessed for colocalization across 114 traits.
Project description:In order to support our research of bladder cancer in human genome, we conducted massively parallel pyrosequencing of mRNAs (RNA-Seq) using normal, paracancerouse and cancerous human bladder tissues. We obtained a total of 30.0 million read pairs from normal, 33.1 million read pairs from paracancerous and 36.5 million read pairs from cancerous. The RNA-Seq data derived from the sample illustrated the differencially expression genes among normal, paracancerous and cancerous bladder tissues of human.
Project description:In order to support our research of bladder cancer in human genome, we conducted massively parallel pyrosequencing of mRNAs (RNA-Seq) using normal, paracancerouse and cancerous human bladder tissues. We obtained a total of 30.0 million read pairs from normal, 33.1 million read pairs from paracancerous and 36.5 million read pairs from cancerous. The RNA-Seq data derived from the sample illustrated the differencially expression genes among normal, paracancerous and cancerous bladder tissues of human. 3 samples examined: normal tissue, paracancerous tissue, cancerous tissue.
Project description:Forkhead box A2 (FOXA2) is a critical regulator of endometrial gland development in mice. In the adult mouse uterus, FOXA2 is expressed solely in the GE cells of the endometrium. Conditional deletion of Foxa2 after birth in the uterus, using the progesterone receptor Cre mouse (PgrCre), impeded gland development, thereby rendering the adult mouse infertile due to defects in blastocyst implantation stemming from a lack of endometrial glands and their secretions. As a first step to begin understanding the FOXA2 function in the endometrial glands of the uterus, genome-wide investigation of in vivo FOXA2 and RNA polymerase II (POL2) binding target regions in the neonatal and adult uterus was determined by chromatin immunoprecipitation followed by massively parallel sequencing (ChIP-Seq). In order to determine the transcriptional regulatory networks mediating FOXA2 regulation of endometrial gland development and function, chromatin immunoprecipitation and massively parallel sequencing (ChIP-Seq) was used to create a genome-wide profile of in vivo FOXA2-binding sites in the developing (PD 12) and adult (DOPP 2.5 and 3.5) mouse uterus.
Project description:Purpose: Determine the change in expression of genes in AR deficient CD8 T cells Methods: C57Bl/6J splenocytes were isolated, total CD8 T cells magnetically enriched and electroporated with non-targeting gRNA or AR-specific gRNAs. Cells were stimulated with aCD3/28 for three days before isolating RNA and library prep. Sequencing was performed by the Massively Parallel Sequencing Shared Resource (MPSSR) at OHSU. Results: AR regulated genes in mouse CD8 T cells.
