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  cultured embryonic stem cells[DCX-][BG121099]

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-][BG121099]

Displaying 1-10 of 174 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE86982GSM2317319Illumina HiSeq 2500Homo sapiens26Dn4_A01_smart-seqcultured embryonic stem cells[DCX-][BG121099]
GSE86982GSM2317320Illumina HiSeq 2500Homo sapiens26Dn4_A02_smart-seqcultured embryonic stem cells[DCX-][BG121099]
GSE86982GSM2317321Illumina HiSeq 2500Homo sapiens26Dn4_A03_smart-seqcultured embryonic stem cells[DCX-][BG121099]
GSE86982GSM2317322Illumina HiSeq 2500Homo sapiens26Dn4_A04_smart-seqcultured embryonic stem cells[DCX-][BG121099]
GSE86982GSM2317323Illumina HiSeq 2500Homo sapiens26Dn4_A05_smart-seqcultured embryonic stem cells[DCX-][BG121099]
GSE86982GSM2317324Illumina HiSeq 2500Homo sapiens26Dn4_A07_smart-seqcultured embryonic stem cells[DCX-][BG121099]
GSE86982GSM2317325Illumina HiSeq 2500Homo sapiens26Dn4_A08_smart-seqcultured embryonic stem cells[DCX-][BG121099]
GSE86982GSM2317326Illumina HiSeq 2500Homo sapiens26Dn4_A09_smart-seqcultured embryonic stem cells[DCX-][BG121099]
GSE86982GSM2317327Illumina HiSeq 2500Homo sapiens26Dn4_A10_smart-seqcultured embryonic stem cells[DCX-][BG121099]
GSE86982GSM2317328Illumina HiSeq 2500Homo sapiens26Dn4_A11_smart-seqcultured embryonic stem cells[DCX-][BG121099]

Gene rank in cultured embryonic stem cells[DCX-][BG121099]

Displaying 1-10 of 23045 results.
Rank orderGene SymbolEnsembl ID
1c21_SSU-rRNA_Hsa
2TVAS5
3TUBA1AENSG00000167552
4GAPDHENSG00000111640
5ACTBENSG00000075624
6ACTG1ENSG00000184009
7BC018860
8EEF1A1ENSG00000156508
9MALAT1ENSG00000251562
10ENO1ENSG00000074800