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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 1-10 of 80 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957301Illumina HiSeq 2500Homo sapienswhOrg5_A10_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957302Illumina HiSeq 2500Homo sapienswhOrg5_A11_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957303Illumina HiSeq 2500Homo sapienswhOrg5_A12_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957304Illumina HiSeq 2500Homo sapienswhOrg5_A1_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957305Illumina HiSeq 2500Homo sapienswhOrg5_A2_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957306Illumina HiSeq 2500Homo sapienswhOrg5_A4_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957307Illumina HiSeq 2500Homo sapienswhOrg5_A5_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957308Illumina HiSeq 2500Homo sapienswhOrg5_A6_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957309Illumina HiSeq 2500Homo sapienswhOrg5_A7_hOrg65diPSC 409B2[65 days]
GSE75140GSM1957310Illumina HiSeq 2500Homo sapienswhOrg5_A8_hOrg65diPSC 409B2[65 days]

Gene rank in iPSC 409B2[65 days]

Displaying 51-60 of 16781 results.
Rank orderGene SymbolEnsembl ID
51SOX4ENSG00000124766
52MAGED1ENSG00000179222
53HSP90B1ENSG00000166598
54ENO1ENSG00000074800
55SNRPD2ENSG00000125743
56ATRXENSG00000085224
57ARPC2ENSG00000163466
58MORF4L1ENSG00000185787
59TUBA1CENSG00000167553
60WSB1ENSG00000109046