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  iPSC 409B2[58 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 iPSC 409B2[58 days]

Displaying 1-10 of 79 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957564Illumina HiSeq 2500Homo sapiensmdOrg4_G10_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957565Illumina HiSeq 2500Homo sapiensmdOrg4_G12_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957566Illumina HiSeq 2500Homo sapiensmdOrg4_G4_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957567Illumina HiSeq 2500Homo sapiensmdOrg4_G7_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957568Illumina HiSeq 2500Homo sapiensmdOrg4_G8_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957569Illumina HiSeq 2500Homo sapiensmdOrg4_G9_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957570Illumina HiSeq 2500Homo sapiensmdOrg4_H11_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957571Illumina HiSeq 2500Homo sapiensmdOrg4_H3_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957572Illumina HiSeq 2500Homo sapiensmdOrg4_H9_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957477Illumina HiSeq 2500Homo sapiensmdOrg3_A10_hOrg_iPSC_reg3_58diPSC 409B2[58 days]

Gene rank in iPSC 409B2[58 days]

Displaying 21-30 of 16781 results.
Rank orderGene SymbolEnsembl ID
21MAP1BENSG00000131711
22MARCKSENSG00000277443
23DPYSL2ENSG00000092964
24EIF4G2ENSG00000110321
25TMBIM6ENSG00000139644
26TUBA1BENSG00000123416
27NACAENSG00000196531
28H2AFZENSG00000164032
29MYL6ENSG00000092841
30NPM1ENSG00000181163