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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 21-30 of 74 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957247Illumina HiSeq 2500Homo sapienswhOrg4_C1_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957248Illumina HiSeq 2500Homo sapienswhOrg4_C2_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957249Illumina HiSeq 2500Homo sapienswhOrg4_C3_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957250Illumina HiSeq 2500Homo sapienswhOrg4_C5_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957251Illumina HiSeq 2500Homo sapienswhOrg4_C6_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957252Illumina HiSeq 2500Homo sapienswhOrg4_C7_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957253Illumina HiSeq 2500Homo sapienswhOrg4_C8_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957254Illumina HiSeq 2500Homo sapienswhOrg4_C9_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957255Illumina HiSeq 2500Homo sapienswhOrg4_D10_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957256Illumina HiSeq 2500Homo sapienswhOrg4_D11_hOrg41diPSC 409B2[41 days]

Gene rank in iPSC 409B2[41 days]

Displaying 16681-16690 of 16781 results.
Rank orderGene SymbolEnsembl ID
16681VCX2ENSG00000177504
16682VCX3AENSG00000169059
16683VCX3BENSG00000205642
16684VCYENSG00000129864
16685VCY1BENSG00000129862
16686VENTXENSG00000151650
16687VGFENSG00000128564
16688VHLLENSG00000189030
16689VIPR1ENSG00000114812
16690VIPR2ENSG00000106018