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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 31-40 of 71 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957186Illumina HiSeq 2500Homo sapienswhOrg3_D1_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957187Illumina HiSeq 2500Homo sapienswhOrg3_D3_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957188Illumina HiSeq 2500Homo sapienswhOrg3_D4_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957189Illumina HiSeq 2500Homo sapienswhOrg3_D5_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957190Illumina HiSeq 2500Homo sapienswhOrg3_D7_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957191Illumina HiSeq 2500Homo sapienswhOrg3_D8_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957192Illumina HiSeq 2500Homo sapienswhOrg3_D9_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957193Illumina HiSeq 2500Homo sapienswhOrg3_E10_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957194Illumina HiSeq 2500Homo sapienswhOrg3_E11_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957195Illumina HiSeq 2500Homo sapienswhOrg3_E12_hOrg37diPSC 409B2[37 days]

Gene rank in iPSC 409B2[37 days]

Displaying 16541-16550 of 16781 results.
Rank orderGene SymbolEnsembl ID
16541TMEM26ENSG00000196932
16542TMEM30BENSG00000182107
16543TMEM30CENSG00000235156
16544TMEM40ENSG00000088726
16545TMEM52ENSG00000178821
16546TMEM54ENSG00000121900
16547TMEM61ENSG00000143001
16548TMEM82ENSG00000162460
16549TMEM89ENSG00000183396
16550TMPPEENSG00000188167