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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 81-90 of 96 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957461Illumina HiSeq 2500Homo sapiensmdOrg2_F6_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957462Illumina HiSeq 2500Homo sapiensmdOrg2_F7_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957463Illumina HiSeq 2500Homo sapiensmdOrg2_G10_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957464Illumina HiSeq 2500Homo sapiensmdOrg2_G1_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957465Illumina HiSeq 2500Homo sapiensmdOrg2_G2_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957466Illumina HiSeq 2500Homo sapiensmdOrg2_G3_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957467Illumina HiSeq 2500Homo sapiensmdOrg2_G8_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957468Illumina HiSeq 2500Homo sapiensmdOrg2_G9_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957469Illumina HiSeq 2500Homo sapiensmdOrg2_H10_hOrg_ESC_reg2_53dESC H9[53 days]
GSE75140GSM1957470Illumina HiSeq 2500Homo sapiensmdOrg2_H11_hOrg_ESC_reg2_53dESC H9[53 days]

Gene rank in ESC H9[53 days]

Displaying 31-40 of 16781 results.
Rank orderGene SymbolEnsembl ID
31SONENSG00000159140
32H2AFZENSG00000164032
33ENO1ENSG00000074800
34HSPA8ENSG00000109971
35CALM1ENSG00000198668
36MYL6ENSG00000092841
37FTLENSG00000087086
38ANKRD10ENSG00000088448
39FDFT1ENSG00000079459
40SRSF3ENSG00000112081