Loading

Cell View

Cell Information

  cultured embryonic stem cells[SOX2-][26]

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
PMIDNA

Samples in cultured embryonic stem cells[SOX2-][26]

Displaying 1-10 of 48 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE86977GSM2312633Illumina HiSeq 2500Homo sapiens26Sn3a_C01cultured embryonic stem cells[SOX2-][26]
GSE86977GSM2312634Illumina HiSeq 2500Homo sapiens26Sn3a_G11cultured embryonic stem cells[SOX2-][26]
GSE86977GSM2312635Illumina HiSeq 2500Homo sapiens26Sn3a_D11cultured embryonic stem cells[SOX2-][26]
GSE86977GSM2312636Illumina HiSeq 2500Homo sapiens26Sn3a_C11cultured embryonic stem cells[SOX2-][26]
GSE86977GSM2312637Illumina HiSeq 2500Homo sapiens26Sn3a_G10cultured embryonic stem cells[SOX2-][26]
GSE86977GSM2312638Illumina HiSeq 2500Homo sapiens26Sn3a_C10cultured embryonic stem cells[SOX2-][26]
GSE86977GSM2312639Illumina HiSeq 2500Homo sapiens26Sn3a_D10cultured embryonic stem cells[SOX2-][26]
GSE86977GSM2312640Illumina HiSeq 2500Homo sapiens26Sn3a_D09cultured embryonic stem cells[SOX2-][26]
GSE86977GSM2312641Illumina HiSeq 2500Homo sapiens26Sn3a_D08cultured embryonic stem cells[SOX2-][26]
GSE86977GSM2312642Illumina HiSeq 2500Homo sapiens26Sn3a_C09cultured embryonic stem cells[SOX2-][26]

Gene rank in cultured embryonic stem cells[SOX2-][26]

Displaying 1-10 of 23636 results.
Rank orderGene SymbolEnsembl ID
1MALAT1ENSG00000251562
2TUBA1AENSG00000167552
3EEF1A1ENSG00000156508
4MAP1BENSG00000131711
5ACTG1ENSG00000184009
6GAPDHENSG00000111640
7GNB2L1
8GNASENSG00000087460
9DLK1ENSG00000185559
10RPL13ENSG00000167526