Data set for a validated open-source multi-solver fourth generation composite femur model

Contains Abaqus, Ansys and FEBio validated models of fourth generation composite femurs and the output results as well as the experimental data for validation ** The condition for use of these models is that the following publication is cited: ** A.R.MacLeod, H.Rose, H.S.Gill, A Validated Open-Source Multi-Solver Fourth Generation Composite Femur Model, Journal of Biomechanical Engineering, 2016 The files contained in this directory are for the composite femur model F10 discussed in the publication. All models are for the converged 0.75 mm mesh size detailed in the publication. The ABAQUS input file: F10_ABAQUS.inp The ANSYS input file: F10_ANSYS.ans The FEBIO geometry and main input files: F10_FEBIO_GEOM.feb F10_FEBIO_MAIN.feb The predicted equivalent strains for each of the models is given is the 'Results' files: Results_F10_Abaqus.txt Results_F10_Ansys.txt Results_F10_FEBio.txt In these files, rows 1-4 represent strain gauge locations 1-4. There are 11 load increments for each location: 0 to 500 N in 50 N increments. The experimental results are also provided in an identical format: Results_F10_EXPERIMENTAL_STRAINS.tx

Gene expression analysis of subpopulations of mouse embryonic stem cells sorted based on Id1 and Nanog expression

Overall design: Id1-Venus Nanog-tagRFP (IVNR) reporter mouse ES cells cultured in LIF+FCS were sorted into Nanog-tagRFP-high, Id1-Venus-high, or double low subpopulations. Unsorted IVNR cells cultured in LIF+FCS, as well as Id1-Venus (Id1V) reporter ES cells cultured in 2i and in 2i+LIF were included as controls. All samples were collected in duplicate. Total 12 samples. Experiment type: Expression profiling by array.Analysis of gene expression in sorted subpopulations of mouse embryonic stem cells. We set out to investigate whether expression of Id1 in Nanog-low cells affected the expression of pluripotency factors and signalling molecules.Malaguti M, Lowell S, 2018, Gene expression analysis of subpopulations of mouse embryonic stem cells sorted based on Id1 and Nanog expression, Gene Expression Omnibus, https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE10822

Dataset for Sox10 contributes to the balance of fate choice in dorsal root ganglion progenitors

The development of functional peripheral ganglia requires a balance of specification of both neuronal and glial components. In the developing dorsal root ganglia (DRGs), these components form from partially-restricted bipotent neuroglial precursors derived from the neural crest. Work in mouse and chick has identified several factors, including Delta/Notch signaling, required for specification of a balance of these components. We have previously shown in zebrafish that the Sry-related HMG domain transcription factor, Sox10, plays an unexpected, but crucial, role in sensory neuron fate specification in vivo. In the same study we described a novel Sox10 mutant allele, sox10baz1, in which sensory neuron numbers are elevated above those of wild-types. Here we investigate the origin of this neurogenic phenotype. We demonstrate that the supernumerary neurons are sensory neurons, and that enteric and sympathetic neurons are almost absent just as in classical sox10 null alleles; peripheral glial development is also severely abrogated in a manner similar to other sox10 mutant alleles. Examination of proliferation and apoptosis in the developing DRG reveals very low levels of both processes in wild-type and sox10baz1, excluding changes in the balance of these as an explanation for the overproduction of sensory neurons. Using chemical inhibition of Delta-Notch-Notch signaling we demonstrate that in embryonic zebrafish, as in mouse and chick, lateral inhibition during the phase of trunk DRG development is required to achieve a balance between glial and neuronal numbers. Importantly, however, we show that this mechanism is insufficient to explain quantitative aspects of the baz1 phenotype. The Sox10(baz1) protein shows a single amino acid substitution in the DNA binding HMG domain; structural analysis indicates that this change is likely to result in reduced flexibility in the HMG domain, consistent with sequence-specific modification of Sox10 binding to DNA. Unlike other Sox10 mutant proteins, Sox10(baz1) retains an ability to drive neurogenin1 transcription. We show that overexpression of neurogenin1 is sufficient to produce supernumerary DRG sensory neurons in a wild-type background, and can rescue the sensory neuron phenotype of sox10 morphants in a manner closely resembling the baz1 phenotype. We conclude that an imbalance of neuronal and glial fate specification results from the Sox10(baz1) protein’s unique ability to drive sensory neuron specification whilst failing to drive glial development. The sox10baz1 phenotype reveals for the first time that a Notch-dependent lateral inhibition mechanism is not sufficient to fully explain the balance of neurons and glia in the developing DRGs, and that a second Sox10-dependent mechanism is necessary. Sox10 is thus a key transcription factor in achieving the balance of sensory neuronal and glial fates

Somatic Cell Nuclear Transfer (Cloning) Efficiency

Cloning by nuclear transfer from adult somatic cells is a remarkable demonstration of developmental plasticity. When a nucleus is placed in oocyte cytoplasm, the changes in chromatin structure that govern differentiation can be reversed, and the nucleus can be made to control development to term. The overall efficiency of cloning is typically between 0 and 3 % (number of live offspring as a percentage of the number of nuclear transfer embryos), irrespective of the species, the donor cell type or technique. However, this is the cumulative result of losses at each stage of the cloning process. The tables in the PDF provide a summary of the data for each report published by the Data Creators on somatic cell (fetal to adult cells) nuclear transfer up until the time of its compilation, in July 2002. Where the appropriate data was made available, the table provides cloning efficiency for each major stage of the process.Wilmut, Ian; Paterson, LA. (2015). Somatic Cell Nuclear Transfer (Cloning) Efficiency, 2002 [dataset]. University of Edinburgh. Roslin Institute. http://dx.doi.org/10.7488/ds/312

An ongoing role for Wnt signaling in differentiating melanocytes in vivo

The accompanying files contain the original data files or code for the studies in the following paper in PCMR: An ongoing role for Wnt signaling in differentiating melanocytes in vivo. Laura Vibert1, Gerardo Aquino2, Ines Gehring3, Tatiana Subkhankulova1, Thomas F. Schilling3, Andrea Rocco2 and Robert N. Kelsh1 Correspondence: Robert Kelsh email: [email protected] 1Developmental Biology Programme, Department of Biology and Biochemistry and Centre for Regenerative Medicine, Claverton Down, University of Bath, Bath, BA2 7AY, UK 2Department of Microbial and Cellular Sciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK 3Developmental and Cell Biology School of Biological Sciences, University of California, Irvine, 4109, Natural Sciences II, Irvine, CA 92697-2300, USA Please note that all original numerical datasets are included and listed by reference to the original figure in Vibert et al

Mar2019 ImageXpress backup

The ImageXpress MicroXl platform is a high content instrument from Molecular Devices. Incorporation of a large sensor scientific CMOS camera together with LED solid light source provides enhanced optical sensitivity and image quality over standard high content systems. New MetaXpressTM software solutions such as a “Digital Confocal Option” and “Custom Module Editor” provides increased capability and flexibility to customize image analysis routines for quantification of defined phenotypes. The AcuityXpressTM software facilitates quality control assessment across multiple plates and tissue slides and incorporates multivariate statistical and similarity profiling tools to exploit multiparametric phenotypic data. The ImageXpress platform represents a fully equipped high content solution integrated with plate handling robotics (PAA Scara 4 robot), barcode reader and an extensive image-informatics suite (MetaXpressTM and AcuityXpressTM software) that stream-lines; complex high-content analysis routines; data analysis; image storage and review

Feb2019 ImageXpress backup

The ImageXpress MicroXl platform is a high content instrument from Molecular Devices. Incorporation of a large sensor scientific CMOS camera together with LED solid light source provides enhanced optical sensitivity and image quality over standard high content systems. New MetaXpressTM software solutions such as a “Digital Confocal Option” and “Custom Module Editor” provides increased capability and flexibility to customize image analysis routines for quantification of defined phenotypes. The AcuityXpressTM software facilitates quality control assessment across multiple plates and tissue slides and incorporates multivariate statistical and similarity profiling tools to exploit multiparametric phenotypic data. The ImageXpress platform represents a fully equipped high content solution integrated with plate handling robotics (PAA Scara 4 robot), barcode reader and an extensive image-informatics suite (MetaXpressTM and AcuityXpressTM software) that stream-lines; complex high-content analysis routines; data analysis; image storage and review

Dec2016 ImageXpress backup

## Access ## This dataset is held in the Edinburgh DataVault, directly accessible only to authorised University of Edinburgh users.The ImageXpress MicroXl platform is a high content instrument from Molecular Devices. Incorporation of a large sensor scientific CMOS camera together with LED solid light source provides enhanced optical sensitivity and image quality over standard high content systems. New MetaXpressTM software solutions such as a “Digital Confocal Option” and “Custom Module Editor” provides increased capability and flexibility to customize image analysis routines for quantification of defined phenotypes. The AcuityXpressTM software facilitates quality control assessment across multiple plates and tissue slides and incorporates multivariate statistical and similarity profiling tools to exploit multiparametric phenotypic data. The ImageXpress platform represents a fully equipped high content solution integrated with plate handling robotics (PAA Scara 4 robot), barcode reader and an extensive image-informatics suite (MetaXpressTM and AcuityXpressTM software) that stream-lines; complex high-content analysis routines; data analysis; image storage and review

Jul2017 ImageXpress backup

The ImageXpress MicroXl platform is a high content instrument from Molecular Devices. Incorporation of a large sensor scientific CMOS camera together with LED solid light source provides enhanced optical sensitivity and image quality over standard high content systems. New MetaXpressTM software solutions such as a “Digital Confocal Option” and “Custom Module Editor” provides increased capability and flexibility to customize image analysis routines for quantification of defined phenotypes. The AcuityXpressTM software facilitates quality control assessment across multiple plates and tissue slides and incorporates multivariate statistical and similarity profiling tools to exploit multiparametric phenotypic data. The ImageXpress platform represents a fully equipped high content solution integrated with plate handling robotics (PAA Scara 4 robot), barcode reader and an extensive image-informatics suite (MetaXpressTM and AcuityXpressTM software) that stream-lines; complex high-content analysis routines; data analysis; image storage and review

Jun2019 ImageXpress backup

The ImageXpress MicroXl platform is a high content instrument from Molecular Devices. Incorporation of a large sensor scientific CMOS camera together with LED solid light source provides enhanced optical sensitivity and image quality over standard high content systems. New MetaXpressTM software solutions such as a “Digital Confocal Option” and “Custom Module Editor” provides increased capability and flexibility to customize image analysis routines for quantification of defined phenotypes. The AcuityXpressTM software facilitates quality control assessment across multiple plates and tissue slides and incorporates multivariate statistical and similarity profiling tools to exploit multiparametric phenotypic data. The ImageXpress platform represents a fully equipped high content solution integrated with plate handling robotics (PAA Scara 4 robot), barcode reader and an extensive image-informatics suite (MetaXpressTM and AcuityXpressTM software) that stream-lines; complex high-content analysis routines; data analysis; image storage and review