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  ESC H9[53 days]

Overall Design734 single-cell transcriptomes from human fetal neocortex or human cerebral organoids from multiple time points were analyzed in this study. All single cell samples were processed on the microfluidic Fluidigm C1 platform and contain 92 external RNA spike-ins. Fetal neocortex data were generated at 12 weeks post conception (chip 1: 81 cells; chip 2: 83 cells) and 13 weeks post conception (62 cells). Cerebral organoid data were generated from dissociated whole organoids derived from induced pluripotent stem cell line 409B2 (iPSC 409B2) at 33 days (40 cells), 35 days (68 cells), 37 days (71 cells), 41 days (74 cells), and 65 days (80 cells) after the start of embryoid body culture. Cerebral organoid data were also generated from microdissected cortical-like regions from H9 embryonic stem cell derived organoids at 53 days (region 1, 48 cells; region 2, 48 cells) or from iPSC 409B2 organoids at 58 days (region 3, 43 cells; region 4, 36 cells).
SummaryCerebral organoids – three-dimensional cultures of human cerebral tissue derived from pluripotent stem cells – have emerged as models of human cortical development. However, the extent to which in vitro organoid systems recapitulate neural progenitor cell proliferation and neuronal differentiation programs observed in vivo remains unclear. Here we use single-cell RNA sequencing (scRNA-seq) to dissect and compare cell composition and progenitor-to-neuron lineage relationships in human cerebral organoids and fetal neocortex. Covariation network analysis using the fetal neocortex data reveals known and novel interactions among genes central to neural progenitor proliferation and neuronal differentiation. In the organoid, we detect diverse progenitors and differentiated cell types of neuronal and mesenchymal lineages, and identify cells that derived from regions resembling the fetal neocortex. We find that these organoid cortical cells use gene expression programs remarkably similar to those of the fetal tissue in order to organize into cerebral cortex-like regions. Our comparison of in vivo and in vitro cortical single cell transcriptomes illuminates the genetic features underlying human cortical development that can be studied in organoid cultures.
Dataset viewGSE75140
PMID26644564

Samples in ESC H9[53 days]

Displaying 51-60 of 96 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957431Illumina HiSeq 2500Homo sapiensmdOrg2_A2_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957432Illumina HiSeq 2500Homo sapiensmdOrg2_A5_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957433Illumina HiSeq 2500Homo sapiensmdOrg2_A7_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957434Illumina HiSeq 2500Homo sapiensmdOrg2_B10_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957435Illumina HiSeq 2500Homo sapiensmdOrg2_B2_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957436Illumina HiSeq 2500Homo sapiensmdOrg2_B3_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957437Illumina HiSeq 2500Homo sapiensmdOrg2_B4_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957438Illumina HiSeq 2500Homo sapiensmdOrg2_B6_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957439Illumina HiSeq 2500Homo sapiensmdOrg2_C10_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957440Illumina HiSeq 2500Homo sapiensmdOrg2_C11_hOrg_ESC_reg2_53dESC H9[53 days]

Gene rank in ESC H9[53 days]

Displaying 51-60 of 16781 results.
Rank orderGene SymbolEnsembl ID
51NREPENSG00000134986
52PPP1CBENSG00000213639
53MATR3ENSG00000015479
54HNRNPA2B1ENSG00000122566
55YWHAZENSG00000164924
56NACAENSG00000196531
57HMGCS1ENSG00000112972
58MARCH6ENSG00000145495
59TUBA1CENSG00000167553
60CFL1ENSG00000172757