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  iPSC 409B2[65 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[65 days]

Displaying 21-30 of 80 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957321Illumina HiSeq 2500Homo sapienswhOrg5_B9_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957322Illumina HiSeq 2500Homo sapienswhOrg5_C10_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957323Illumina HiSeq 2500Homo sapienswhOrg5_C11_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957324Illumina HiSeq 2500Homo sapienswhOrg5_C12_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957325Illumina HiSeq 2500Homo sapienswhOrg5_C1_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957326Illumina HiSeq 2500Homo sapienswhOrg5_C2_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957327Illumina HiSeq 2500Homo sapienswhOrg5_C3_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957328Illumina HiSeq 2500Homo sapienswhOrg5_C4_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957329Illumina HiSeq 2500Homo sapienswhOrg5_C5_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957330Illumina HiSeq 2500Homo sapienswhOrg5_C6_hOrg65diPSC 409B2[65 days]

Gene rank in iPSC 409B2[65 days]

Displaying 21-30 of 16781 results.
Rank orderGene SymbolEnsembl ID
21DDX5ENSG00000108654
22PPP1CBENSG00000213639
23UBCENSG00000150991
24EIF1ENSG00000173812
25FTLENSG00000087086
26SRSF3ENSG00000112081
27HIST1H4CENSG00000197061
28NACAENSG00000196531
29EIF4G2ENSG00000110321
30MORF4L2ENSG00000123562