Pig whole-body with embedded organs using automatic workflow for inserting the organs
Ontology highlight
ABSTRACT: In this workspace, we have the automatic workflow and configuration files for inserting organs needed to produce the pig whole-body scaffold with embedded organs for the SPARC project.
Project description:In this workspace, we have the automatic workflow and configuration files for inserting organs needed to produce the human whole-body scaffold with embedded organs for the SPARC project.
Project description:In this workspace, we have the automatic workflow and configuration files for inserting organs needed to produce the rat whole-body scaffold with embedded organs for the SPARC project.
Project description:In this workspace, we have the workflow and configuration files needed to produce the mouse whole-body scaffold with embedded organs for the SPARC project.
Project description:In this workspace, we have the workflow and configuration files needed to produce the human whole-body scaffold with nerves centrelines and embedded organs for the SPARC project.
Project description:By leveraging single-cell/nuclei RNA sequencing, we generate the first single-cell transcriptome atlas of over 200,000 pig cells from 20 tissues/organs.
Project description:By leveraging single-cell/nuclei RNA sequencing, we generate the first single-cell transcriptome atlas of over 200,000 pig cells from 20 tissues/organs, as well as cultured ECs
Project description:Tissue sample acquisition is a limiting step in many studies. There are many thousands of formalin fixed paraffin embedded archival blocks collected around the world, but in contrast relatively few fresh frozen samples in tumor banks. Once samples are fixed in formalin the RNA is degraded and traditional methods for gene expression profiling are not suitable. In this study we have evaluated the whole genome DASL assay from Illumina to perform transcriptomic analysis from archived breast tumor tissue fixed in formalin paraffin embedded blocks. We profiled 76 familial breast tumors from cases carrying a BRCA1, BRCA2 or ATM mutation, or from non-BRCA1/2 families. We found that replicate samples correlated well with each other (r2=0.9-0.98). In 12/15 cases, the matched formalin-fixed and frozen samples predicted the same tumor molecular subtypes with confidence. These results demonstrate that the whole genome DASL assay is a valuable tool to profile degraded RNA from archival FFPE material. This assay will enable transcriptomic analysis of a large number of archival samples that are stored in pathology archives around the globe and consequently will have the potential to improve our understanding and characterisation of many diseases.
Project description:Artificial selection has resulted in animal breeds with extreme phenotypes. As an organism is made up of many different tissues and organs, each with its own genetic programme, it is pertinent to ask what are the relative contributions of breed or sex when assessed across tissues. Are all tissues equally affected by breed or sex? How relevant is tissue in terms of total transcriptome variability? Experiment Overall Design: In order to gain insight on these issues, we have microarrayed 16 different tissues hybridization on Affymetrix microarrays from four animals of the extreme pig breeds Large White and Iberian, two males and two females