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  iPSC 409B2[35 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[35 days]

Displaying 21-30 of 68 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957135Illumina HiSeq 2500Homo sapienswhOrg2_E12_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957134Illumina HiSeq 2500Homo sapienswhOrg2_E11_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957133Illumina HiSeq 2500Homo sapienswhOrg2_E10_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957132Illumina HiSeq 2500Homo sapienswhOrg2_D9_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957131Illumina HiSeq 2500Homo sapienswhOrg2_D8_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957130Illumina HiSeq 2500Homo sapienswhOrg2_D7_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957129Illumina HiSeq 2500Homo sapienswhOrg2_D6_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957128Illumina HiSeq 2500Homo sapienswhOrg2_D5_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957127Illumina HiSeq 2500Homo sapienswhOrg2_D4_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957126Illumina HiSeq 2500Homo sapienswhOrg2_D3_hOrg35diPSC 409B2[35 days]

Gene rank in iPSC 409B2[35 days]

Displaying 51-60 of 16781 results.
Rank orderGene SymbolEnsembl ID
51CALM1ENSG00000198668
52RANENSG00000132341
53MYL6ENSG00000092841
54SNRPD2ENSG00000125743
55XRCC5ENSG00000079246
56HSP90AB1ENSG00000096384
57SKP1ENSG00000113558
58HDAC2ENSG00000196591
59ATRXENSG00000085224
60MDKENSG00000110492