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  iPSC 409B2[41 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[41 days]

Displaying 61-70 of 74 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957287Illumina HiSeq 2500Homo sapienswhOrg4_G12_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957288Illumina HiSeq 2500Homo sapienswhOrg4_G1_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957289Illumina HiSeq 2500Homo sapienswhOrg4_G3_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957290Illumina HiSeq 2500Homo sapienswhOrg4_G4_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957291Illumina HiSeq 2500Homo sapienswhOrg4_G5_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957292Illumina HiSeq 2500Homo sapienswhOrg4_G7_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957293Illumina HiSeq 2500Homo sapienswhOrg4_G8_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957294Illumina HiSeq 2500Homo sapienswhOrg4_G9_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957295Illumina HiSeq 2500Homo sapienswhOrg4_H10_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957296Illumina HiSeq 2500Homo sapienswhOrg4_H2_hOrg41diPSC 409B2[41 days]

Gene rank in iPSC 409B2[41 days]

Displaying 91-100 of 16781 results.
Rank orderGene SymbolEnsembl ID
91HINT1ENSG00000169567
92PTMAENSG00000187514
93HDLBPENSG00000115677
94OST4ENSG00000228474
95COX4I1ENSG00000131143
96ATP5LENSG00000167283
97NDUFS5ENSG00000168653
98CCT6AENSG00000146731
99CKBENSG00000166165
100FAUENSG00000149806