Loading

Cell View

Cell Information

  cultured embryonic stem cells[DCX-][RM165049]

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-][RM165049]

Displaying 121-130 of 174 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE86982GSM2316670Illumina HiSeq 2500Homo sapiens26Dn1_E10_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316669Illumina HiSeq 2500Homo sapiens26Dn1_E09_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316668Illumina HiSeq 2500Homo sapiens26Dn1_E08_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316667Illumina HiSeq 2500Homo sapiens26Dn1_E07_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316666Illumina HiSeq 2500Homo sapiens26Dn1_E06_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316665Illumina HiSeq 2500Homo sapiens26Dn1_E05_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316664Illumina HiSeq 2500Homo sapiens26Dn1_E04_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316663Illumina HiSeq 2500Homo sapiens26Dn1_E03_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316662Illumina HiSeq 2500Homo sapiens26Dn1_E02_smart-seqcultured embryonic stem cells[DCX-][RM165049]
GSE86982GSM2316661Illumina HiSeq 2500Homo sapiens26Dn1_E01_smart-seqcultured embryonic stem cells[DCX-][RM165049]

Gene rank in cultured embryonic stem cells[DCX-][RM165049]

Displaying 22921-22930 of 23045 results.
Rank orderGene SymbolEnsembl ID
22921c6_tRNA-Thr-ACG_
22922c6_tRNA-Thr-ACY_
22923c6_tRNA-Trp-TGG
22924c6_tRNA-Tyr-TAC
22925c6_tRNA-Val-GTA
22926c6_tRNA-Val-GTG
22927c7_tRNA-Ala-GCY
22928c7_tRNA-Arg-AGG
22929c7_tRNA-Arg-CGY_
22930c7_tRNA-Asp-GAY