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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 71-80 of 96 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957451Illumina HiSeq 2500Homo sapiensmdOrg2_D7_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957452Illumina HiSeq 2500Homo sapiensmdOrg2_D8_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957453Illumina HiSeq 2500Homo sapiensmdOrg2_E2_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957454Illumina HiSeq 2500Homo sapiensmdOrg2_E6_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957455Illumina HiSeq 2500Homo sapiensmdOrg2_E8_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957456Illumina HiSeq 2500Homo sapiensmdOrg2_E9_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957457Illumina HiSeq 2500Homo sapiensmdOrg2_F12_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957458Illumina HiSeq 2500Homo sapiensmdOrg2_F2_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957459Illumina HiSeq 2500Homo sapiensmdOrg2_F3_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957460Illumina HiSeq 2500Homo sapiensmdOrg2_F5_hOrg_ESC_reg2_53dESC H9[53 days]

Gene rank in ESC H9[53 days]

Displaying 41-50 of 16781 results.
Rank orderGene SymbolEnsembl ID
41SKP1ENSG00000113558
42TMBIM6ENSG00000139644
43HSP90AA1ENSG00000080824
44UBCENSG00000150991
45EIF4G2ENSG00000110321
46SOX4ENSG00000124766
47TMSB10ENSG00000034510
48WSB1ENSG00000109046
49NPM1ENSG00000181163
50EIF1ENSG00000173812