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  cultured embryonic stem cells[DCX-][RM165049]

Overall DesignThe transcriptomes of 1846 single cells were profiled by SmartSeq2 at different timepoints throughout a 54-day differentiation protocol that converted H1 human embryonic stem cells to a variety of brain cell types. Some cells were positively labeled by a expression of a barcoded viral transgene to help establish clonality (marked by an SK).
SummaryDuring development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered SOX2Cit/+ and DCXCit/Y hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development. During development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered SOX2Cit/+ and DCXCit/Y hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development. During development of the human brain, multiple cell types with diverse regional identities are generated. Here we report a system to generate early human brain forebrain and mid/hindbrain cell types from human embryonic stem cells (hESCs), and infer and experimentally confirm a lineage tree for the generation of these types based on single-cell RNA-Seq analysis. We engineered SOX2Cit/+ and DCXCit/Y hESC lines to target progenitors and neurons throughout neural differentiation for single-cell transcriptomic profiling, then identified discrete cell types consisting of both rostral (cortical) and caudal (mid/hindbrain) identities. Direct comparison of the cell types were made to primary tissues using gene expression atlases and fetal human brain single-cell gene expression data, and this established that the cell types resembled early human brain cell types, including preplate cells. From the single-cell transcriptomic data a Bayesian algorithm generated a unified lineage tree, and predicted novel regulatory transcription factors. The lineage tree highlighted a prominent bifurcation between cortical and mid/hindbrain cell types, confirmed by clonal analysis experiments. We demonstrated that cell types from either branch could preferentially generated by manipulation of the canonical Wnt/beta-catenin pathway. In summary, we present an experimentally validated lineage tree that encompasses multiple brain regions, and our work sheds light on the molecular regulation of region-specific neural lineages during human brain development.
Dataset viewGSE86982
PMIDNA

Samples in cultured embryonic stem cells[DCX-][RM165049]

Displaying 21-30 of 174 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE86982GSM2316637Illumina HiSeq 2500Homo sapiens26Dn1_B10_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316638Illumina HiSeq 2500Homo sapiens26Dn1_B11_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316639Illumina HiSeq 2500Homo sapiens26Dn1_C01_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316640Illumina HiSeq 2500Homo sapiens26Dn1_C02_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316641Illumina HiSeq 2500Homo sapiens26Dn1_C03_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316642Illumina HiSeq 2500Homo sapiens26Dn1_C04_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316643Illumina HiSeq 2500Homo sapiens26Dn1_C05_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316644Illumina HiSeq 2500Homo sapiens26Dn1_C06_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316645Illumina HiSeq 2500Homo sapiens26Dn1_C07_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316646Illumina HiSeq 2500Homo sapiens26Dn1_C08_smart-seqcultured embryonic stem cells[DCX-][RM165049]

Gene rank in cultured embryonic stem cells[DCX-][RM165049]

Displaying 22931-22940 of 23045 results.
Rank orderGene SymbolEnsembl ID
22931c7_tRNA-Gln-CAA
22932c7_tRNA-Gln-CAA_
22933c7_tRNA-Gln-CAG
22934c7_tRNA-Glu-GAG_
22935c7_tRNA-Gly-GGA
22936c7_tRNA-Gly-GGG
22937c7_tRNA-Gly-GGY
22938c7_tRNA-His-CAY_
22939c7_tRNA-Ile-ATA
22940c7_tRNA-Ile-ATT