title: CORTECON: a temporal transcriptome analysis of in vitro human cerebral cortex development from human embryonic stem cells.
abstract: Many neurological and psychiatric disorders affect the cerebral cortex, and a clearer understanding of the molecular processes underlying human corticogenesis will provide greater insight into such pathologies. To date, knowledge of gene expression changes accompanying corticogenesis is largely based on murine data. Here we present a searchable, comprehensive, temporal gene expression data set encompassing cerebral cortical development from human embryonic stem cells (hESCs). Using a modified differentiation protocol that yields neurons suggestive of prefrontal cortex, we identified sets of genes and long noncoding RNAs that significantly change during corticogenesis and those enriched for disease-associations. Numerous alternatively spliced genes with varying temporal patterns of expression are revealed, including TGIF1, involved in holoprosencephaly, and MARK1, involved in autism. We have created a database (http://cortecon.neuralsci.org/) that provides online, query-based access to changes in RNA expression and alternatively spliced transcripts during human cortical development.
authors.affiliation: Neural Stem Cell Institute, Rensselaer, NY 12144, USA.
authors.forename: Joyce
authors.initials: J
authors.lastname: van de Leemput
authors.affiliation: Neural Stem Cell Institute, Rensselaer, NY 12144, USA.
authors.forename: Nathan C
authors.initials: NC
authors.lastname: Boles
authors.affiliation: Neural Stem Cell Institute, Rensselaer, NY 12144, USA; Department of Computer Science, College of Computing and Information, State University of New York, Albany, NY 12144, USA.
authors.forename: Thomas R
authors.initials: TR
authors.lastname: Kiehl
authors.affiliation: Neural Stem Cell Institute, Rensselaer, NY 12144, USA.
authors.forename: Barbara
authors.initials: B
authors.lastname: Corneo
authors.affiliation: Neural Stem Cell Institute, Rensselaer, NY 12144, USA.
authors.forename: Patty
authors.initials: P
authors.lastname: Lederman
authors.affiliation: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors.forename: Vilas
authors.initials: V
authors.lastname: Menon
authors.affiliation: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors.forename: Changkyu
authors.initials: C
authors.lastname: Lee
authors.affiliation: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors.forename: Refugio A
authors.initials: RA
authors.lastname: Martinez
authors.affiliation: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors.forename: Boaz P
authors.initials: BP
authors.lastname: Levi
authors.affiliation: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors.forename: Carol L
authors.initials: CL
authors.lastname: Thompson
authors.affiliation: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors.forename: Shuyuan
authors.initials: S
authors.lastname: Yao
authors.affiliation: Allen Institute for Brain Science, Seattle, WA 98103, USA.
authors.forename: Ajamete
authors.initials: A
authors.lastname: Kaykas
authors.affiliation: Neural Stem Cell Institute, Rensselaer, NY 12144, USA. Electronic address: sallytemple@neuralsci.org.
authors.forename: Sally
authors.initials: S
authors.lastname: Temple
authors.affiliation: Neural Stem Cell Institute, Rensselaer, NY 12144, USA. Electronic address: chrisfasano@neuralsci.org.
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Fasano
mesh_terms: D000818:Animals; D002454:Cell Differentiation / Q000235:genetics; D002478:Cells, Cultured; D002540:Cerebral Cortex / Q000166:cytology* / Q000196:embryology*; D030541:Databases, Genetic / Q000639:trends; D053595:Embryonic Stem Cells / Q000502:physiology*; D020869:Gene Expression Profiling / Q000379:methods* / Q000639:trends; D053263:Gene Regulatory Networks / Q000235:genetics*; D006801:Humans; D051379:Mice; D038081:Organogenesis / Q000502:physiology; D013997:Time Factors