Loading
scRNASeqDB
Home » Search by Cell » Cell View

Cell View

Cell Information

  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 61-70 of 96 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957441Illumina HiSeq 2500Homo sapiensmdOrg2_C3_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957442Illumina HiSeq 2500Homo sapiensmdOrg2_C4_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957443Illumina HiSeq 2500Homo sapiensmdOrg2_D10_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957444Illumina HiSeq 2500Homo sapiensmdOrg2_D11_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957445Illumina HiSeq 2500Homo sapiensmdOrg2_D12_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957446Illumina HiSeq 2500Homo sapiensmdOrg2_D1_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957447Illumina HiSeq 2500Homo sapiensmdOrg2_D2_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957448Illumina HiSeq 2500Homo sapiensmdOrg2_D4_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957449Illumina HiSeq 2500Homo sapiensmdOrg2_D5_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957450Illumina HiSeq 2500Homo sapiensmdOrg2_D6_hOrg_ESC_reg2_53dESC H9[53 days]

Gene rank in ESC H9[53 days]

Displaying 121-130 of 16781 results.
Rank orderGene SymbolEnsembl ID
121SEPT7ENSG00000122545
122SEPT11ENSG00000138758
123NONOENSG00000147140
124PPIAENSG00000196262
125COX6A1ENSG00000111775
126HNRNPRENSG00000125944
127PSMB4ENSG00000159377
128PSMA4ENSG00000041357
129SEPT2ENSG00000168385
130TTC3ENSG00000182670