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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 1-10 of 176 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE86982GSM2316968Illumina HiSeq 2500Homo sapiens26Dn2_A01_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2316969Illumina HiSeq 2500Homo sapiens26Dn2_A02_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2316970Illumina HiSeq 2500Homo sapiens26Dn2_A03_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2316971Illumina HiSeq 2500Homo sapiens26Dn2_A04_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2316972Illumina HiSeq 2500Homo sapiens26Dn2_A05_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2316973Illumina HiSeq 2500Homo sapiens26Dn2_A06_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2316974Illumina HiSeq 2500Homo sapiens26Dn2_A07_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2316975Illumina HiSeq 2500Homo sapiens26Dn2_A08_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2316976Illumina HiSeq 2500Homo sapiens26Dn2_A09_smart-seqcultured embryonic stem cells[DCX-][BG121095]
GSE86982GSM2316977Illumina HiSeq 2500Homo sapiens26Dn2_A10_smart-seqcultured embryonic stem cells[DCX-][BG121095]

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

Displaying 1-10 of 23045 results.
Rank orderGene SymbolEnsembl ID
1c21_SSU-rRNA_Hsa
2TVAS5
3GAPDHENSG00000111640
4TUBA1AENSG00000167552
5BC018860
6EEF1A1ENSG00000156508
7ACTBENSG00000075624
8ACTG1ENSG00000184009
9TMSL3
10ENO1ENSG00000074800