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  cultured embryonic stem cells[DCX+][RM165048]

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+][RM165048]

Displaying 1-10 of 86 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE86982GSM2318005Illumina HiSeq 2500Homo sapiens54Dp5_H11_smart-seqcultured embryonic stem cells[DCX+][RM165048]
GSE86982GSM2318004Illumina HiSeq 2500Homo sapiens54Dp5_H10_smart-seqcultured embryonic stem cells[DCX+][RM165048]
GSE86982GSM2318003Illumina HiSeq 2500Homo sapiens54Dp5_H09_smart-seqcultured embryonic stem cells[DCX+][RM165048]
GSE86982GSM2318002Illumina HiSeq 2500Homo sapiens54Dp5_H08_smart-seqcultured embryonic stem cells[DCX+][RM165048]
GSE86982GSM2318001Illumina HiSeq 2500Homo sapiens54Dp5_H07_smart-seqcultured embryonic stem cells[DCX+][RM165048]
GSE86982GSM2318000Illumina HiSeq 2500Homo sapiens54Dp5_H06_smart-seqcultured embryonic stem cells[DCX+][RM165048]
GSE86982GSM2317999Illumina HiSeq 2500Homo sapiens54Dp5_H05_smart-seqcultured embryonic stem cells[DCX+][RM165048]
GSE86982GSM2317998Illumina HiSeq 2500Homo sapiens54Dp5_H04_smart-seqcultured embryonic stem cells[DCX+][RM165048]
GSE86982GSM2317997Illumina HiSeq 2500Homo sapiens54Dp5_H03_smart-seqcultured embryonic stem cells[DCX+][RM165048]
GSE86982GSM2317996Illumina HiSeq 2500Homo sapiens54Dp5_H02_smart-seqcultured embryonic stem cells[DCX+][RM165048]

Gene rank in cultured embryonic stem cells[DCX+][RM165048]

Displaying 11-20 of 23045 results.
Rank orderGene SymbolEnsembl ID
11OK/SW-cl.16
12TMSB10ENSG00000034510
13ACTG1ENSG00000184009
14AD1
15TMSL3
16COX7CENSG00000127184
17MLLT11ENSG00000213190
18c16_SSU-rRNA_Hsa
19ACTBENSG00000075624
20RPS13ENSG00000110700