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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 211-220 of 16781 results.
Rank orderGene SymbolEnsembl ID
211HMGCS1ENSG00000112972
212PRRC2CENSG00000117523
213TBCAENSG00000171530
214PTPRSENSG00000105426
215KIDINS220ENSG00000134313
216UQCRC1ENSG00000010256
217PAPOLAENSG00000090060
218CRMP1ENSG00000072832
219DHX36ENSG00000174953
220FOXG1ENSG00000176165