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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 1-10 of 96 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957381Illumina HiSeq 2500Homo sapiensmdOrg1_A10_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957382Illumina HiSeq 2500Homo sapiensmdOrg1_A12_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957383Illumina HiSeq 2500Homo sapiensmdOrg1_A3_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957384Illumina HiSeq 2500Homo sapiensmdOrg1_A4_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957385Illumina HiSeq 2500Homo sapiensmdOrg1_A6_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957386Illumina HiSeq 2500Homo sapiensmdOrg1_A8_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957387Illumina HiSeq 2500Homo sapiensmdOrg1_A9_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957388Illumina HiSeq 2500Homo sapiensmdOrg1_B11_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957389Illumina HiSeq 2500Homo sapiensmdOrg1_B12_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957390Illumina HiSeq 2500Homo sapiensmdOrg1_B1_hOrg_ESC_reg1_53dESC H9[53 days]

Gene rank in ESC H9[53 days]

Displaying 1-10 of 16781 results.
Rank orderGene SymbolEnsembl ID
1ACTBENSG00000075624
2TUBA1AENSG00000167552
3ACTG1ENSG00000184009
4HNRNPH1ENSG00000169045
5TMSB4XENSG00000205542
6UBBENSG00000170315
7CALM2ENSG00000143933
8GAPDHENSG00000111640
9STMN1ENSG00000117632
10GNB2L1