Cell View

Cell Information

  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

Samples in iPSC 409B2[58 days]

Displaying 41-50 of 79 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957534Illumina HiSeq 2500Homo sapiensmdOrg3_H11_hOrg_iPSC_reg3_58diPSC 409B2[58 days]
GSE75140GSM1957535Illumina HiSeq 2500Homo sapiensmdOrg3_H12_hOrg_iPSC_reg3_58diPSC 409B2[58 days]
GSE75140GSM1957536Illumina HiSeq 2500Homo sapiensmdOrg3_H9_hOrg_iPSC_reg3_58diPSC 409B2[58 days]
GSE75140GSM1957538Illumina HiSeq 2500Homo sapiensmdOrg4_A1_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957537Illumina HiSeq 2500Homo sapiensmdOrg4_A11_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957539Illumina HiSeq 2500Homo sapiensmdOrg4_A4_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957540Illumina HiSeq 2500Homo sapiensmdOrg4_A6_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957541Illumina HiSeq 2500Homo sapiensmdOrg4_B10_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957542Illumina HiSeq 2500Homo sapiensmdOrg4_B12_hOrg_iPSC_reg4_58diPSC 409B2[58 days]
GSE75140GSM1957543Illumina HiSeq 2500Homo sapiensmdOrg4_B2_hOrg_iPSC_reg4_58diPSC 409B2[58 days]

Gene rank in iPSC 409B2[58 days]

Displaying 31-40 of 16781 results.
Rank orderGene SymbolEnsembl ID