Project description:<p>To determine IL-17-induced global transcriptome changes in midbrain neurons derived from induced pluripotent stem cells (iPSC) from three sporadic Parkinson's disease (PD) patients and three age- and sex-machted controls, deep RNA sequencing (RNA-Seq) of IL-17-treated and untreated PD and control iPSC-dderived midbrain neurons was performed. Total RNA was isolated from untreated and IL-17-treated cells with the TruSeq RNA Sample Preparation Kit v2 (Illumina). RNA libraries were quantified using the KAPA SYBR FAST ABI Prism Library Quantification Kit (Kapa Biosystems) and cluster generation was performed on the cBot with the TruSeq SR Cluster Kit v3 (Illumina). The sequencing run was performed on a HiSeq 1000 instrument (Illumina) using the indexed, 50 cycles single read (SR) protocol and the TruSeq SBS v3 Kit (Illumina). Image analysis and base calling resulted in .bcl files that were then converted into .fastQ files by the CASAVA1.8.2 software. FastQ files were aligned to the human genome (hg19) using STAR.and annotated with gencode.v19. DESeq2 was used to determine differential expression. Criteria to determine significantly dysregulated genes were as follows: adjusted p-value below 0.05 and log2FC (fold change) of greater than one. Only genes with a mean expression value of greater than one RPKM (reads per kilobase per million mapped reads) throughout the dataset were considered. Control and PD samples were analyzed as two independent datasets.</p> <p>Upon IL-17 treatment only 17 genes were found to be dysregulated in controls but 125 genes were dysregulated in iPSC-derived midbrain neurons from PD patients. The 125 IL-17-dependent genes in PD iPSC-derived neurons separated the treated from untreated PD samples using an unsupervised, hierarchical clustering applying an Euclidean distance metric.</p> <p>More detailed study information can be found in Sommer A, Maxreiter F, Krach F, Fadler T, Grosch J, Maroni M, Graef D, Eberhardt E, Riemenschneider MJ, Yeo GW, Kohl Z, Xiang W, Gage FH, Winkler J, Prots I, Winner B. Th17 Lymphocytes Induce Neuronal Cell Death in a Human iPSC-Based Model of Parkinson's Disease. Cell Stem Cell. 2018 Jul 5;23(1):123-131.e6. doi: 10.1016/j.stem.2018.06.015. PMID: 29979986</p>
Project description:sample 666823 and 666824 control IgG pulldown in human iPSC derived APPDp neurons
sample 666825 and 666826 TERT pulldown in human iPSC derived APPDp neurons
Project description:Bardet-Biedl Syndrome (BBS) is a rare autosomal recessive disorder caused by mutations in genes encoding components of the primary cilium and characterized by hyperphagic obesity. We developed a cellular model of BBS using induced pluripotent stem cell (iPSCs)-derived hypothalamic arcuate-like neurons. Single-cell RNA sequencing of iPSC-derived hypothalamic neurons from BBS1M390R and isogenic control identified affected cell subpopulations and several down-regulated pathways in BBS1 hypomorphic neurons, including axon guidance, insulin signaling and cAMP pathway.
Project description:The contribution of the different CNS cell types to Aicardi-Goutiéres Syndrome pathogenesis is still unclear. With the aim to elucidate how oligodendrocytes, neurons and astrocytes impact AGS human phenotype we interrogate transcriptomes of the different cell populations performing single-cell RNA-Seq (scRNASeq). We compared cells deriving from AGS patient-derived iPSC harboring mutations in TREX1 (AGS1) or RNASEH2B (AGS2) to healthy donor control (WT) cells differentiated into mixed neuronal/glial cell populations.
Project description:We have assessed the importance of SQSTM1 in human induced pluripotent stem cell (iPSC)-derived cortical neurons with and without SQSTM1. By combining high-content imaging, RNA-Seq, and functional mitochondrial readouts, we showed that SQSTM1 depletion causes aberrations in mitochondrial gene expression and functionality in iPSC-derived neurons.
