Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Project description:To further knowledge of piglet maturity, we have developed a microarray analysis to describe biological processes and to find candidate genes for key roles in piglet maturity. The objective was to identify which genes and biological processes are specifically involved in the difference between two extreme breeds: Large White (LW) and Meishan (MS). The LW breed is a selected breed known to show an increased rate of mortality at birth, while the MS breed presents more robust piglets at birth. MS and LW sows were inseminated with mixed semen (LW and MS) hence each litter was composed of pure fetuses (LW or MS) and crossed fetuses (LWMS from MS sows and MSLW from LW sows).
Project description:To further knowledge of piglet maturity, we have developed a microarray analysis to describe biological processes and to find candidate genes for key roles in piglet maturity. The objective was to identify which genes and biological processes are specifically involved in the difference between two extreme breeds: Large White (LW) and Meishan (MS). The LW breed is a selected breed known to show an increased rate of mortality at birth, while the MS breed presents more robust piglets at birth. MS and LW sows were inseminated with mixed semen (LW and MS) hence each litter was composed of pure fetuses (LW or MS) and crossed fetuses (LWMS from MS sows and MSLW from LW sows).
Project description:Purpose:The goal of this study was to enrich understanding of the reproductive difference Methods: Multiparous Canadian Large White cyclic sows were divided into two parts: high (H; total number of piglets born > 15.73) and low (L; total number of piglets born < 11.11) fecundity. Eight sows with similar parity from each part were chosen (n=16). Ovarian tissues were obtained on the 14 day (day 1 = first day of estrus) after estrus as in the luteal phase (L) and 20 day of the estrous cycle as in the follicular phase (F). Transcriptome profiling of ovarian tissues were generated by deep sequencing, in quadruplicate, using Illumina HiSeq X10 instrument. Results: Using an optimized data analysis workflow, we obtained the differentially expressed miRNAs between the high and low fecundity, with a fold change ≥1.5 and p value < 0.05. These results provide further insight into fecundity in pigs. Conclusions: Our study represents the first detailed analysis of ovary transcriptome. It will be significantly helpful to display a novel regulatory mechanism for further investigation of prolificacy in pigs.
2020-09-02 | GSE132307 | GEO
Project description:Whole-genome resequencing of Large White pig
Project description:n this study we had two primary aims: 1.) spatially define the transcriptional signatures of porcine maternal-fetal interface and 2.) develop and validate an organoid model which better recapitulated the porcine placenta. Using mid-gestation maternal-fetal interfaces of commercial landrace/large white composite gilts we performed spatial transcriptomics (n=4 interfaces) using Visium v1 spatial transcriptomics. We then went on to isolate trophoblast organoids from fresh-term placentas from crossbred sows consisting</p><p>655 of Yorkshire, Large White, and Landrace breeds. We then characterized the transcriptional profile of these organoids using bulk RNA-seq from 3 seperate lines using a standard Illumina library preparation. To characterize these organoids we performed single cell RNA-sequencing on 3 separate lines of swine trophoblast organoids using a standard 10x Genomics Single Cell 3' Gene Expression platform. All reads/samples were mapped to Sus scrofa v11.1.
Project description:In this study we had two primary aims: 1.) spatially define the transcriptional signatures of porcine maternal-fetal interface and 2.) develop and validate an organoid model which better recapitulated the porcine placenta. Using mid-gestation maternal-fetal interfaces of commercial landrace/large white composite gilts we performed spatial transcriptomics (n=4 interfaces) using Visium v1 spatial transcriptomics. We then went on to isolate trophoblast organoids from fresh-term placentas from crossbred sows consisting</p><p>655 of Yorkshire, Large White, and Landrace breeds. We then characterized the transcriptional profile of these organoids using bulk RNA-seq from 3 seperate lines using a standard Illumina library preparation. To characterize these organoids we performed single cell RNA-sequencing on 3 separate lines of swine trophoblast organoids using a standard 10x Genomics Single Cell 3' Gene Expression platform. All reads/samples were mapped to Sus scrofa v11.1.
Project description:Purpose:The goal of this study was to enrich understanding of the reproductive difference Methods:Multiparous Canadian Large White cyclic sows were divided into two parts: high (H; total number of piglets born > 15.73) and low (L; total number of piglets born < 11.11) fecundity. Eight sows with similar parity from each part were chosen (n=16). Ovarian tissues were obtained on the 14 day (day 1 = first day of estrus) after estrus as in the luteal phase (L) and 20 day of the estrous cycle as in the follicular phase (F). Transcriptome profiling of ovarian tissues were generated by deep sequencing, in quadruplicate, using Illumina HiSeq X10 instrument. Results: Using an optimized data analysis workflow, we obtained the differentially expressed RNAs between the high and low fecundity, with a fold change ≥1.5 and p value < 0.05. These results provide further insight into fecundity in pigs. Conclusions: Our study represents the first detailed analysis of ovary transcriptome. It will be significantly helpful to display a novel regulatory mechanism for further investigation of prolificacy in pigs.