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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 11-20 of 86 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE86982GSM2318073Illumina HiSeq 2500Homo sapiens54Dn5_G04_smart-seqcultured embryonic stem cells[DCX-][RM165048]
GSE86982GSM2318074Illumina HiSeq 2500Homo sapiens54Dn5_G05_smart-seqcultured embryonic stem cells[DCX-][RM165048]
GSE86982GSM2318075Illumina HiSeq 2500Homo sapiens54Dn5_G06_smart-seqcultured embryonic stem cells[DCX-][RM165048]
GSE86982GSM2318076Illumina HiSeq 2500Homo sapiens54Dn5_G07_smart-seqcultured embryonic stem cells[DCX-][RM165048]
GSE86982GSM2318077Illumina HiSeq 2500Homo sapiens54Dn5_G08_smart-seqcultured embryonic stem cells[DCX-][RM165048]
GSE86982GSM2318078Illumina HiSeq 2500Homo sapiens54Dn5_G09_smart-seqcultured embryonic stem cells[DCX-][RM165048]
GSE86982GSM2318079Illumina HiSeq 2500Homo sapiens54Dn5_G10_smart-seqcultured embryonic stem cells[DCX-][RM165048]
GSE86982GSM2318080Illumina HiSeq 2500Homo sapiens54Dn5_G11_smart-seqcultured embryonic stem cells[DCX-][RM165048]
GSE86982GSM2318081Illumina HiSeq 2500Homo sapiens54Dn5_H01_smart-seqcultured embryonic stem cells[DCX-][RM165048]
GSE86982GSM2318082Illumina HiSeq 2500Homo sapiens54Dn5_H02_smart-seqcultured embryonic stem cells[DCX-][RM165048]

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

Displaying 22791-22800 of 23045 results.
Rank orderGene SymbolEnsembl ID
22791c2_tRNA-Val-GTA
22792c2_tRNA-Val-GTG
22793c2_tRNA-Val-GTY
22794c3_SSU-rRNA_Hsa
22795c3_tRNA-Ala-GCA
22796c3_tRNA-Arg-AGA
22797c3_tRNA-Arg-AGG
22798c3_tRNA-Arg-CGG
22799c3_tRNA-Arg-CGY_
22800c3_tRNA-Asp-GAY