DiMN (Exp 3) - ALS and Control (unaffected) diMN cell lines differentiated from iPS cell lines using a short and direct differeintiation protocol - RNA-seq
Ontology highlight
ABSTRACT: Total RNA-Seq was carried out on rRNA depleted RNA obtained from motor neuron lines generated from subject induced pluripotent stem cell (iPSC) lines. The iPSC lines were derived from 11 ALS and 4 Control (unaffected) individuals, in duplicate.
SUBMITTER: Jie Wu, Malcolm Casale, Ryan Lim, Jennifer Stocksdale
Project description:DIA proteomics was carried out on total protein obtained from motor neuron lines generated from subject induced pluripotent stem cell (iPSC) lines. The iPSC lines were derived from 11 ALS and 4 Control (unaffected) individuals, in duplicate.
Project description:DIA proteomics was carried out on total protein obtained from motor neuron lines generated from subject induced pluripotent stem cell (iPSC) lines. The iPSC lines were derived from 11 ALS and 4 Control (unaffected) individuals, in duplicate.
Project description:Reprogramming somatic cells to induced pluripotent stem cells (iPSCs) sets their identity back to an embryonic age. This presents a fundamental hurdle for modeling late-onset disorders using iPSC-derived cells. We therefore developed a strategy to induce age-like features in multiple iPSC-derived lineages and tested its impact on modeling Parkinson’s disease (PD). We first describe markers that predict fibroblast donor age and observed the loss of these age-related markers following iPSC induction and re-differentiation into fibroblasts. Remarkably, age-related markers were readily induced in iPSC-derived fibroblasts or neurons following exposure to progerin including dopamine neuron-specific phenotypes such as neuromelanin accumulation. Induced aging in PD-iPSC-derived dopamine neurons revealed disease phenotypes requiring both aging and genetic susceptibility such as frank dendrite degeneration, progressive loss of tyrosine-hydroxylase expression and enlarged mitochondria or Lewy body-precursor inclusions. Our study presents a strategy for inducing age-related cellular properties and enables the modeling of late-onset disease features. Induced pluripotent stem cell-derived midbrain dopamine neurons from a young and old donor overexpressing either GFP or Progerin.
Project description:Total RNA-Seq was carried out on rRNA depleted RNA obtained from motor neuron lines generated from subject induced pluripotent stem cell (iPSC) lines. The iPSC lines were derived from 4 ALS, 3 SMA and 3 Control (unaffected) individuals, in duplicate.
Project description:Induced pluripotent stem cells (iPSCs) harbor great promise for in vitro generation of disease-relevant cell types, such as mesodiencephalic dopaminergic (mdDA) neurons involved in Parkinson’s disease. Although iPSC-derived midbrain DA neurons have been generated, detailed genetic and epigenetic characterization of such neurons is still lacking. The goal of this study is to examine the authenticity of iPSC-derived DA neurons obtained by established protocols. We FACS-purified mdDA (Pitx3gfp/+) neurons derived from mouse iPSCs and primary mdDA (Pitx3gfp/+) neurons to analyze and compare their genetic and epigenetic features. Although iPSC-derived DA neurons largely adopt characteristics of their in-vivo counterparts, relevant deviations in global gene expression and DNA methylation were found. Hypermethylated genes, mainly involved in neurodevelopment and basic neuronal functions, consequently showed reduced expression levels. Such abnormalities should be addressed as they might affect unambiguous long-term functionality and hamper the potential of iPSC-derived DA neurons for in-vitro disease modeling or cell-based therapy. RRBS methylation maps were generated for iPSCs cells, dopaminergic neurons derived from iPSCs and primary mesodiencephalic dopaminergic neurons
Project description:Spinal Muscular Atrophy (SMA) is an autosomal recessive motor neuron disease and is the second most common genetic disorder leading to death in childhood. Motoneurons derived from induced pluripotent stem cells (iPSC) obtained by reprogramming SMA patient and his healthy father fibroblasts, and genetically corrected SMA-iPSC obtained converting SMN2 into SMN1 with target gene correction (TGC), were used to study gene expression and splicing events linked to pathogenetic mechanisms. Microarray technology was used to assess the global gene expression profile as well as splicing events of iPS-derived motorneurons from SMA patient, unaffected father and TGC-treated cells. The microarray data derived from three different groups: SMA patient, healty father and treated SMA patient's cells. Each population consists of three RNA profiling cell samples.
Project description:Understanding evolutionary mechanisms underlying expansion and reorganization of the human brain represents an important aspect in analyzing the emergence of cognitive abilities typical of our species. Comparative analyses of neuronal phenotypes in closest living relatives (Pan troglodytes; the common chimpanzee) can shed the light into changes in neuronal morphology compared to the last common ancestor (LCA), opening possibilities for analyses of the timing of their appearance, and the role of evolutionary mechanisms favoring a particular type of information processing in humans. Here, we use induced pluripotent stem cell (iPSC) technology to model neural progenitor cell migration and early development of cortical pyramidal neurons in humans and chimpanzees. In addition, we provide morphological characterization of the early stages of neuronal development in human and chimpanzee transplanted cells, and examine the role of developmental mechanisms previously proposed for the evolutionary expansions of the human brain on the early development of pyramidal neurons in the two species. The strategy proposed here lay down the basis for further comparative analysis between human and non-human primates and opens new avenues for understanding cognitive capability and neurological disease susceptibility differences between species. PolyA RNA-Seq profiling of neural progenitor cells (NPCs) and neurons differentiated from human and chimpanzee iPSCs.
Project description:Human iPSCs were differentiated towards an induced-SMC (iSMC) phenotype in a 10-day protocol. Proteomics was performed throughout the entire differentiation time course to provide a robust, well-defined starting and ending cell population. Proteomics data verified iPSC differentiation to iSMCs. Proteomics comparison with primary human SMCs showed a high correlation with iSMCs. After iSMC differentiation, we initiated calcification in the iSMCs by culturing the cells in osteogenic media for 17 days.
Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a submission of mass-spectrometry analyses from 6 induced pluripotent stem cell lines generated by the HipSci project.
Project description:The Human Induced Pluripotent Stem Cells Initiative (HipSci) is generating a large, high-quality reference panel of human IPSC lines. This is a pilot submission of mass-spectrometry analyses from 18 induced pluripotent stem cell lines generated by the HipSci project. This submission includes also data for two embryonic stem cell lines, and one reference sample comprising a mixture of 42 IPSC lines. Associated BioSamples accessions: <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2397999">SAMEA2397999</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398167">SAMEA2398167</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398916">SAMEA2398916</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2397948"> SAMEA2397948 </a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2399112">SAMEA2399112</a>,<a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2399257">SAMEA2399257</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398553">SAMEA2398553</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398821">SAMEA2398821</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398316">SAMEA2398316</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2469778">SAMEA2469778</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2399037">SAMEA2399037</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398656">SAMEA2398656</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398428">SAMEA2398428</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2469777">SAMEA2469777</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2397959">SAMEA2397959</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398442">SAMEA2398442</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398024">SAMEA2398024</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA2398450">SAMEA2398450</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA3402864">SAMEA3402864</a>, <a href="http://www.ebi.ac.uk/biosamples/sample/SAMEA3110364">SAMEA3110364</a>