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  iPSC 409B2[37 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[37 days]

Displaying 41-50 of 71 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957196Illumina HiSeq 2500Homo sapienswhOrg3_E1_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957197Illumina HiSeq 2500Homo sapienswhOrg3_E2_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957198Illumina HiSeq 2500Homo sapienswhOrg3_E3_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957199Illumina HiSeq 2500Homo sapienswhOrg3_E5_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957200Illumina HiSeq 2500Homo sapienswhOrg3_E6_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957201Illumina HiSeq 2500Homo sapienswhOrg3_E7_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957202Illumina HiSeq 2500Homo sapienswhOrg3_E8_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957203Illumina HiSeq 2500Homo sapienswhOrg3_E9_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957204Illumina HiSeq 2500Homo sapienswhOrg3_F10_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957205Illumina HiSeq 2500Homo sapienswhOrg3_F11_hOrg37diPSC 409B2[37 days]

Gene rank in iPSC 409B2[37 days]

Displaying 16561-16570 of 16781 results.
Rank orderGene SymbolEnsembl ID
16561TNFRSF13CENSG00000159958
16562TNFRSF14ENSG00000157873
16563TNFRSF17ENSG00000048462
16564TNFRSF6BENSG00000243509
16565TNFRSF9ENSG00000049249
16566TNFSF12ENSG00000239697
16567TNFSF12-TNFSF13ENSG00000248871
16568TNFSF13BENSG00000102524
16569TNFSF14ENSG00000125735
16570TNFSF4ENSG00000117586