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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 41-50 of 74 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957267Illumina HiSeq 2500Homo sapienswhOrg4_E1_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957268Illumina HiSeq 2500Homo sapienswhOrg4_E2_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957269Illumina HiSeq 2500Homo sapienswhOrg4_E3_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957270Illumina HiSeq 2500Homo sapienswhOrg4_E4_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957271Illumina HiSeq 2500Homo sapienswhOrg4_E6_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957272Illumina HiSeq 2500Homo sapienswhOrg4_E7_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957273Illumina HiSeq 2500Homo sapienswhOrg4_E9_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957274Illumina HiSeq 2500Homo sapienswhOrg4_F10_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957275Illumina HiSeq 2500Homo sapienswhOrg4_F11_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957276Illumina HiSeq 2500Homo sapienswhOrg4_F12_hOrg41diPSC 409B2[41 days]

Gene rank in iPSC 409B2[41 days]

Displaying 16661-16670 of 16781 results.
Rank orderGene SymbolEnsembl ID
16661UMODL1ENSG00000177398
16662UNC5AENSG00000113763
16663UNC93B1ENSG00000110057
16664UNCXENSG00000164853
16665UPK1AENSG00000105668
16666UPK3BENSG00000243566
16667UPP2ENSG00000007001
16668USH2AENSG00000042781
16669USP17L11ENSG00000233136
16670USP17L2ENSG00000223443