Human 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 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 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 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:In this workspace we have the files needed to produce the rat whole-body scaffold with SPARC priority embedded organs for the SPARC project.
Project description:Our knowledge about the molecular regulation of zebrafish gonad development and function is very limited. This study aims to identify gonad-expressed genes in zebrafish and to analyze their expression in various organs. Using our custom ÂGonad Uniclone Microarray v1, we performed a total of 32 hybridizations, using eight target organs with four biological replicates each. The target organs consisted of adult ovary and testis; the brain, kidney and rest-of-body (ie. whole body except the three organs listed earlier) from both male and female zebrafish, were used as controls. For simplicity, rest of body will be regarded as an organ. All targets were hybridized against a pooled common reference consisting of equal amounts of targets from all dissected organs from a single adult male and a single adult female.
Project description:In this workspace, we have the workflow and configuration files needed to produce the 3D human whole-body scaffold with embedded organs and integrated musculoskeletal and vasculature systems for the SPARC project.
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:Aims of the project is the identification of soluble chemosensory proteins in the olfactory organs of the honeybee mite Varroa destructor. Different families of soluble proteins acting as carriers for odorants have been identified in hexapods, while very limited information is available for other terrestrial Arthropoda. In mites and ticks olfactory organs are located on the distal part of the forelegs and on the capitulum appendages. These two body tagmata and the second pair of legs as control, have been dissected out of phoretics and reproductives Varroa destructor females and protein extracts have been analysed through shotgun proteomics. Protein identification and relative quantification (Label-free quantification, LFQ) has been performed using MaxQuant (version 1.5.8.3). Among the proteins more abundant in appendages bearing chemosensory organs, considering as a model hexapoda soluble olfactory proteins, we have searched for small secreted proteins whose structure include a hydrophobic binding pocket.
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. RNA was extracted from FFPE Familial breast tumours and analysed using the WG-DASL assay for Illumina.