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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 61-62 of 62 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957813Illumina HiSeq 2500Homo sapiensfetal3_H8_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957814Illumina HiSeq 2500Homo sapiensfetal3_H9_fetal_13wpcfetal human cortex 2[13 weeks post-conception]

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

Displaying 151-160 of 16781 results.
Rank orderGene SymbolEnsembl ID
151TUBB2AENSG00000137267
152PSMA3ENSG00000100567
153HNRNPRENSG00000125944
154FXYD6ENSG00000137726
155SRSF7ENSG00000115875
156EIF3EENSG00000104408
157CSRP2ENSG00000175183
158PPIAENSG00000196262
159MYT1LENSG00000186487
160NKTRENSG00000114857