biostudies-arrayexpressUnknownTranscriptomicsGenomicsProteomicsRachel ScholeyIllumina HiSeq 4000RNA-seq of coding RNAHomo sapiensHomo sapienshttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-16303NOTCH3 variants cause CADASIL (cerebral autosomal dominant arteriopathy and subcortical infarcts and leukoencephalopathy), the most common monogenetic form of small vessel disease (SVD) and vascular dementia (VaD). Although CADASIL is well recognized clinically, the molecular mechanisms underlying its pathogenesis remain poorly understood, and no targeted therapies are currently available. NOTCH3 is predominantly expressed in vascular smooth muscle cells (VSMCs), which originate from distinct embryonic lineages. Using human induced pluripotent stem cell (iPSC) models, we generated origin-specific VSMCs and found that cerebral, but not peripheral, VSMC-mimics are selectively vulnerable to NOTCH3 variants. In this study, we focused on the neural crest-derived VSMCs and performed RNA-seq to compare gene expression profiles between wild-type and CADASIL patient iPSC-derived neural crest VSMCs.biostudies-arrayexpressLibrary Construction - Illumina TruSeq Stranded mRNA kit, according to the manufacturer’s protocol.Sequencing - Sequenced paired end 76bp on HISEQ4000 at the Genomic Technologies Core Facility University of Manchester.Sample Collection - CADASIL patient and control iPSCs were differentiated into neural crest-specific VSMCs. Neural crest progenitors were generated by culturing iPSCs on vitronectin-coated plates under defined Essential 6 medium (Gibco; A1516401) with 10 ng/mL FGF2 (PeproTech; 100-18B) and 10 μM SB431542 (Tocris; 1614) that promote neural crest specification. Cells were first passaged at day 5 and subsequently upon reaching confluence, with continued supplementation of FGF2 and SB431542, up to passage 12. After this intermediate stage, cells were dissociated and transferred into SMC differentiation medium composed of Essential 6 supplemented with 10 ng/mL PDGF-BB (PeproTech; 100-14B) and 2 ng/mL TGF-β1 (PeproTech; 100-21) for a minimum of 12 days. Neural crest-derived VSMCs reached maturity by day18, at which point total RNA was isolated from the fully differentiated iPSC-derived VSMCs for RNA-seq analysis. The induced pluripotent stem cells were cultured in Essential 8 Medium (Thermo Fisher Scientific)Nucleic Acid Extraction - Total RNA from CADASIL patient and control iPSCs derived neural crest-specific VSMCs was extracted using the RNeasy Mini Kit (Qiagen).OrganizationMINSEQE ScoreAssays and DataMAGE-TAB FilesTao WangRachel ScholeyfalseRNA sequencing analysis of neural crest-derived vascular smooth muscle cells differentiated from CADASIL patient and control iPSCs.NOTCH3 variants cause CADASIL (cerebral autosomal dominant arteriopathy and subcortical infarcts and leukoencephalopathy), the most common monogenetic form of small vessel disease (SVD) and vascular dementia (VaD). Although CADASIL is well recognized clinically, the molecular mechanisms underlying its pathogenesis remain poorly understood, and no targeted therapies are currently available. NOTCH3 is predominantly expressed in vascular smooth muscle cells (VSMCs), which originate from distinct embryonic lineages. Using human induced pluripotent stem cell (iPSC) models, we generated origin-specific VSMCs and found that cerebral, but not peripheral, VSMC-mimics are selectively vulnerable to NOTCH3 variants. In this study, we focused on the neural crest-derived VSMCs and performed RNA-seq to compare gene expression profiles between wild-type and CADASIL patient iPSC-derived neural crest VSMCs.2025-12-11T00:00:00Z2025-12-11T13:08:41.12Z2025-11-27T09:50:36.392ZE-MTAB-16303ERP185733EFO_0002944EFO_0004170EFO_0005518EFO_0003738EFO_0004184