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  ESC H9[53 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 ESC H9[53 days]

Displaying 21-30 of 96 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957401Illumina HiSeq 2500Homo sapiensmdOrg1_C8_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957402Illumina HiSeq 2500Homo sapiensmdOrg1_C9_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957403Illumina HiSeq 2500Homo sapiensmdOrg1_D3_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957404Illumina HiSeq 2500Homo sapiensmdOrg1_D9_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957405Illumina HiSeq 2500Homo sapiensmdOrg1_E10_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957406Illumina HiSeq 2500Homo sapiensmdOrg1_E11_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957407Illumina HiSeq 2500Homo sapiensmdOrg1_E12_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957408Illumina HiSeq 2500Homo sapiensmdOrg1_E1_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957409Illumina HiSeq 2500Homo sapiensmdOrg1_E3_hOrg_ESC_reg1_53dESC H9[53 days]
GSE75140GSM1957410Illumina HiSeq 2500Homo sapiensmdOrg1_E4_hOrg_ESC_reg1_53dESC H9[53 days]

Gene rank in ESC H9[53 days]

Displaying 16771-16780 of 16781 results.
Rank orderGene SymbolEnsembl ID
16771ZNF804BENSG00000182348
16772ZNF812
16773ZNF835ENSG00000127903
16774ZNF837ENSG00000152475
16775ZNF860ENSG00000197385
16776ZNF865ENSG00000261221
16777ZNF98ENSG00000197360
16778ZP1ENSG00000149506
16779ZPBP2ENSG00000186075
16780ZSWIM2ENSG00000163012