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  cultured embryonic stem cells[DCX-][BG121095]

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-][BG121095]

Displaying 21-30 of 176 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE86982GSM2317211Illumina HiSeq 2500Homo sapiens54Dn2_G02_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2317210Illumina HiSeq 2500Homo sapiens54Dn2_G01_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2317209Illumina HiSeq 2500Homo sapiens54Dn2_F11_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2317208Illumina HiSeq 2500Homo sapiens54Dn2_F10_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2317207Illumina HiSeq 2500Homo sapiens54Dn2_F09_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2317206Illumina HiSeq 2500Homo sapiens54Dn2_F08_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2317205Illumina HiSeq 2500Homo sapiens54Dn2_F07_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2317204Illumina HiSeq 2500Homo sapiens54Dn2_F06_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2317203Illumina HiSeq 2500Homo sapiens54Dn2_F05_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2317202Illumina HiSeq 2500Homo sapiens54Dn2_F04_smart-seqcultured embryonic stem cells[DCX-][BG121095]

Gene rank in cultured embryonic stem cells[DCX-][BG121095]

Displaying 11-20 of 23045 results.
Rank orderGene SymbolEnsembl ID
11RPL41ENSG00000229117
12RPS27ENSG00000177954
13MALAT1ENSG00000251562
14RPL23ENSG00000125691
15STRF6
16VIMENSG00000026025
17RPS25ENSG00000118181
18RPL7ENSG00000147604
19RPS3AENSG00000145425
20FTLENSG00000087086