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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 11-20 of 96 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957391Illumina HiSeq 2500Homo sapiensmdOrg1_B5_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957392Illumina HiSeq 2500Homo sapiensmdOrg1_B7_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957393Illumina HiSeq 2500Homo sapiensmdOrg1_B8_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957394Illumina HiSeq 2500Homo sapiensmdOrg1_B9_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957395Illumina HiSeq 2500Homo sapiensmdOrg1_C12_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957396Illumina HiSeq 2500Homo sapiensmdOrg1_C1_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957397Illumina HiSeq 2500Homo sapiensmdOrg1_C2_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957398Illumina HiSeq 2500Homo sapiensmdOrg1_C5_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957399Illumina HiSeq 2500Homo sapiensmdOrg1_C6_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957400Illumina HiSeq 2500Homo sapiensmdOrg1_C7_hOrg_ESC_reg1_53dESC H9[53 days]

Gene rank in ESC H9[53 days]

Displaying 11-20 of 16781 results.
Rank orderGene SymbolEnsembl ID
11MAP1BENSG00000131711
12CKBENSG00000166165
13ALDOAENSG00000149925
14DDX5ENSG00000108654
15TPI1ENSG00000111669
16LDHBENSG00000111716
17EEF1A1ENSG00000156508
18NGFRAP1
19H3F3BENSG00000132475
20C1orf61ENSG00000125462