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  fetal human cortex 2[13 weeks post-conception]

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 fetal human cortex 2[13 weeks post-conception]

Displaying 1-10 of 62 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957753Illumina HiSeq 2500Homo sapiensfetal3_A12_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957754Illumina HiSeq 2500Homo sapiensfetal3_A4_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957755Illumina HiSeq 2500Homo sapiensfetal3_A6_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957756Illumina HiSeq 2500Homo sapiensfetal3_A7_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957757Illumina HiSeq 2500Homo sapiensfetal3_A8_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957758Illumina HiSeq 2500Homo sapiensfetal3_A9_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957759Illumina HiSeq 2500Homo sapiensfetal3_B10_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957760Illumina HiSeq 2500Homo sapiensfetal3_B11_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957761Illumina HiSeq 2500Homo sapiensfetal3_B12_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957762Illumina HiSeq 2500Homo sapiensfetal3_B2_fetal_13wpcfetal human cortex 2[13 weeks post-conception]

Gene rank in fetal human cortex 2[13 weeks post-conception]

Displaying 16641-16650 of 16781 results.
Rank orderGene SymbolEnsembl ID
16641WBSCR27ENSG00000165171
16642WDFY4ENSG00000128815
16643WDR24ENSG00000127580
16644WDR31ENSG00000148225
16645WDR38ENSG00000136918
16646WDR4ENSG00000160193
16647WDR63ENSG00000162643
16648WDR64ENSG00000162843
16649WDR72ENSG00000166415
16650WDR78ENSG00000152763