Project description:To gain molecular insight into the prenatal neurobiology of DS, we performed single-nucleus sequencing, spatial transcriptomics, and proteomics on mid-gestational prenatal human brain tissue. We captured altered expression dynamics of lineage commitment genes in DS neural progenitor cells, which suggest changes to the fate and functionality of neuronal and glial cells.
Project description:Given the importance of linking human and model system pathobiology, we also performed highly multiplexed RNA in situ spatial transcriptomics on a well-established trisomic mouse model (Ts65Dn) to study the cellular landscape of the trisomic brain during early life and aging. We profiled the spatial transcriptome of > 240,000 cells in the mouse brain and identified trisomy-associated gene expression patterns in the molecular control of neurogenesis, gliogenesis, and myelination. Multiplexed error-robust fluorescence in situ hybridization (MERFISH) was performed on postnatal day 0 (P0) and 6 month (6mo) euploid and trisomic (Ts65Dn) mice (n=3 per condition). Coronal sections of the entire brain were used for analysis.
Project description:This project used snRNA-seq and Molecular Cartography (single cell spatial transcriptomics) to investigate the relation between morphology and molecular identity in human brain organoids.
Project description:To gain molecular insight into the prenatal neurobiology of DS, we performed single-nucleus sequencing, spatial transcriptomics, and proteomics on mid-gestational prenatal human brain tissue. We captured altered expression dynamics of lineage commitment genes in DS neural progenitor cells, which suggest changes to the fate and functionality of neuronal and glial cells.
Project description:U1 small nuclear (sn)RNA, required for splicing of pre-mRNA, is encoded by genes on chromosome 1p36. Imperfect copies of these ‘true’ (t)U1 snRNA genes, located on chromosome 1q12-21, were thought to be pseudogenes. However, many of these ‘variant’ (v)U1 snRNA genes produce fully-processed transcripts that are packaged into potentially functional particles. Using antisense oligonucleotides, we have achieved functional knockdown of a specific vU1 snRNA in HeLa cells and identified over 400 transcriptome changes following interrogation of the Affymetrix Human Exon ST 1.0 array. Total RNA from 4 biological repeats of vU1.8 snRNA and control knock-down were analysed using Affymetrix Human Exon ST 1.0 Array.