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Cell Information

  cultured embryonic stem cells[DCX+][40]

Overall DesignThe transcriptomes of 2684 single cells were profiled by CelSeq at different timepoints throughout a 54-day differentiation protocol that converted H1 human embryonic stem cells to a variety of brain cell types.
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.
Dataset viewGSE86977

Samples in cultured embryonic stem cells[DCX+][40]

Displaying 1-10 of 346 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE86977GSM2313551Illumina HiSeq 2500Homo sapiens40Dp2b_E06cultured embryonic stem cells[DCX+][40]
GSE86977GSM2313550Illumina HiSeq 2500Homo sapiens40Dp1a_A04cultured embryonic stem cells[DCX+][40]
GSE86977GSM2313549Illumina HiSeq 2500Homo sapiens40Dp2a_B08cultured embryonic stem cells[DCX+][40]
GSE86977GSM2313544Illumina HiSeq 2500Homo sapiens40Dp2b_F10cultured embryonic stem cells[DCX+][40]
GSE86977GSM2313543Illumina HiSeq 2500Homo sapiens40Dp2a_C10cultured embryonic stem cells[DCX+][40]
GSE86977GSM2313542Illumina HiSeq 2500Homo sapiens40Dp2c_F07cultured embryonic stem cells[DCX+][40]
GSE86977GSM2313541Illumina HiSeq 2500Homo sapiens40Dp2b_F11cultured embryonic stem cells[DCX+][40]
GSE86977GSM2313540Illumina HiSeq 2500Homo sapiens40Dp1a_G09cultured embryonic stem cells[DCX+][40]
GSE86977GSM2313539Illumina HiSeq 2500Homo sapiens40Dp1a_H02cultured embryonic stem cells[DCX+][40]
GSE86977GSM2313538Illumina HiSeq 2500Homo sapiens40Dp2c_D01cultured embryonic stem cells[DCX+][40]

Gene rank in cultured embryonic stem cells[DCX+][40]

Displaying 1-10 of 23636 results.
Rank orderGene SymbolEnsembl ID