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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 31-40 of 80 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957331Illumina HiSeq 2500Homo sapienswhOrg5_C7_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957332Illumina HiSeq 2500Homo sapienswhOrg5_C8_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957333Illumina HiSeq 2500Homo sapienswhOrg5_C9_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957334Illumina HiSeq 2500Homo sapienswhOrg5_D10_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957335Illumina HiSeq 2500Homo sapienswhOrg5_D11_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957336Illumina HiSeq 2500Homo sapienswhOrg5_D12_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957337Illumina HiSeq 2500Homo sapienswhOrg5_D1_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957338Illumina HiSeq 2500Homo sapienswhOrg5_D2_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957339Illumina HiSeq 2500Homo sapienswhOrg5_D3_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957340Illumina HiSeq 2500Homo sapienswhOrg5_D4_hOrg65diPSC 409B2[65 days]

Gene rank in iPSC 409B2[65 days]

Displaying 16681-16690 of 16781 results.
Rank orderGene SymbolEnsembl ID
16681VHLLENSG00000189030
16682VIPR2ENSG00000106018
16683VITENSG00000205221
16684VMACENSG00000187650
16685VN1R2ENSG00000196131
16686VPREB3ENSG00000128218
16687VSIG1ENSG00000101842
16688VSIG2ENSG00000019102
16689VSIG4ENSG00000155659
16690VSIG8ENSG00000243284