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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 31-40 of 62 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957783Illumina HiSeq 2500Homo sapiensfetal3_E1_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957784Illumina HiSeq 2500Homo sapiensfetal3_E2_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957785Illumina HiSeq 2500Homo sapiensfetal3_E3_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957786Illumina HiSeq 2500Homo sapiensfetal3_E4_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957787Illumina HiSeq 2500Homo sapiensfetal3_E5_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957788Illumina HiSeq 2500Homo sapiensfetal3_F10_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957789Illumina HiSeq 2500Homo sapiensfetal3_F11_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957790Illumina HiSeq 2500Homo sapiensfetal3_F1_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957791Illumina HiSeq 2500Homo sapiensfetal3_F2_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957792Illumina HiSeq 2500Homo sapiensfetal3_F3_fetal_13wpcfetal human cortex 2[13 weeks post-conception]

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

Displaying 31-40 of 16781 results.
Rank orderGene SymbolEnsembl ID
31YWHAZENSG00000164924
32UBCENSG00000150991
33C1orf61ENSG00000125462
34HSPA8ENSG00000109971
35EIF4A2ENSG00000156976
36CKBENSG00000166165
37MATR3ENSG00000015479
38NNATENSG00000053438
39CALM1ENSG00000198668
40COX7A2ENSG00000112695