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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 1-10 of 174 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE86982GSM2317834Illumina HiSeq 2500Homo sapiens26Dn3_A03_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2317835Illumina HiSeq 2500Homo sapiens26Dn3_A04_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2317836Illumina HiSeq 2500Homo sapiens26Dn3_A05_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2317837Illumina HiSeq 2500Homo sapiens26Dn3_A06_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2317838Illumina HiSeq 2500Homo sapiens26Dn3_A07_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2317839Illumina HiSeq 2500Homo sapiens26Dn3_A08_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2317840Illumina HiSeq 2500Homo sapiens26Dn3_A09_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2317841Illumina HiSeq 2500Homo sapiens26Dn3_A10_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2317842Illumina HiSeq 2500Homo sapiens26Dn3_A11_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2317843Illumina HiSeq 2500Homo sapiens26Dn3_B01_smart-seqcultured embryonic stem cells[DCX-][RM165049]

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

Displaying 11-20 of 23045 results.
Rank orderGene SymbolEnsembl ID
11RPS27ENSG00000177954
12RPL5ENSG00000122406
13ACTG1ENSG00000184009
14RPS14ENSG00000164587
15RPL9ENSG00000163682
16MALAT1ENSG00000251562
17HNRNPA1ENSG00000135486
18RPS25ENSG00000118181
19RPL3ENSG00000100316
20RPS3AENSG00000145425