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  iPSC 409B2[37 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[37 days]

Displaying 21-30 of 71 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957176Illumina HiSeq 2500Homo sapienswhOrg3_C1_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957177Illumina HiSeq 2500Homo sapienswhOrg3_C2_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957178Illumina HiSeq 2500Homo sapienswhOrg3_C3_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957179Illumina HiSeq 2500Homo sapienswhOrg3_C4_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957180Illumina HiSeq 2500Homo sapienswhOrg3_C5_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957181Illumina HiSeq 2500Homo sapienswhOrg3_C6_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957182Illumina HiSeq 2500Homo sapienswhOrg3_C7_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957183Illumina HiSeq 2500Homo sapienswhOrg3_C9_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957184Illumina HiSeq 2500Homo sapienswhOrg3_D11_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957185Illumina HiSeq 2500Homo sapienswhOrg3_D12_hOrg37diPSC 409B2[37 days]

Gene rank in iPSC 409B2[37 days]

Displaying 16621-16630 of 16781 results.
Rank orderGene SymbolEnsembl ID
16621TRPM2ENSG00000142185
16622TRPM5ENSG00000070985
16623TRPM6ENSG00000119121
16624TRPV2ENSG00000187688
16625TRPV5ENSG00000127412
16626TSGA13ENSG00000213265
16627TSHBENSG00000134200
16628TSLPENSG00000145777
16629TSPAN1ENSG00000117472
16630TSPAN16ENSG00000130167