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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 11-20 of 74 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957237Illumina HiSeq 2500Homo sapienswhOrg4_B11_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957238Illumina HiSeq 2500Homo sapienswhOrg4_B1_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957239Illumina HiSeq 2500Homo sapienswhOrg4_B3_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957240Illumina HiSeq 2500Homo sapienswhOrg4_B4_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957241Illumina HiSeq 2500Homo sapienswhOrg4_B5_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957242Illumina HiSeq 2500Homo sapienswhOrg4_B6_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957243Illumina HiSeq 2500Homo sapienswhOrg4_B8_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957244Illumina HiSeq 2500Homo sapienswhOrg4_B9_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957245Illumina HiSeq 2500Homo sapienswhOrg4_C10_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957246Illumina HiSeq 2500Homo sapienswhOrg4_C12_hOrg41diPSC 409B2[41 days]

Gene rank in iPSC 409B2[41 days]

Displaying 16701-16710 of 16781 results.
Rank orderGene SymbolEnsembl ID
16701VWA3AENSG00000175267
16702VWA3BENSG00000168658
16703VWA5B2ENSG00000145198
16704VWC2LENSG00000174453
16705VWDEENSG00000146530
16706WASENSG00000015285
16707WBSCR27ENSG00000165171
16708WDFY4ENSG00000128815
16709WDR31ENSG00000148225
16710WDR38ENSG00000136918