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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 21-30 of 62 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957773Illumina HiSeq 2500Homo sapiensfetal3_C7_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957774Illumina HiSeq 2500Homo sapiensfetal3_C9_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957775Illumina HiSeq 2500Homo sapiensfetal3_D10_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957776Illumina HiSeq 2500Homo sapiensfetal3_D2_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957777Illumina HiSeq 2500Homo sapiensfetal3_D3_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957778Illumina HiSeq 2500Homo sapiensfetal3_D4_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957779Illumina HiSeq 2500Homo sapiensfetal3_D8_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957780Illumina HiSeq 2500Homo sapiensfetal3_D9_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957781Illumina HiSeq 2500Homo sapiensfetal3_E10_fetal_13wpcfetal human cortex 2[13 weeks post-conception]
GSE75140GSM1957782Illumina HiSeq 2500Homo sapiensfetal3_E11_fetal_13wpcfetal human cortex 2[13 weeks post-conception]

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

Displaying 21-30 of 16781 results.
Rank orderGene SymbolEnsembl ID
21STMN2ENSG00000104435
22C6orf62ENSG00000112308
23TMSB10ENSG00000034510
24UBBENSG00000170315
25GAPDHENSG00000111640
26NREPENSG00000134986
27TUBA1BENSG00000123416
28ATP5BENSG00000110955
29TUBA1CENSG00000167553
30LUC7L3ENSG00000108848