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  fetal human cortex 1[12 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 1[12 weeks post-conception]

Displaying 21-30 of 164 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957609Illumina HiSeq 2500Homo sapiensfetal1_B6_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957610Illumina HiSeq 2500Homo sapiensfetal1_B7_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957611Illumina HiSeq 2500Homo sapiensfetal1_C10_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957612Illumina HiSeq 2500Homo sapiensfetal1_C12_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957613Illumina HiSeq 2500Homo sapiensfetal1_C1_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957614Illumina HiSeq 2500Homo sapiensfetal1_C2_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957615Illumina HiSeq 2500Homo sapiensfetal1_C3_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957616Illumina HiSeq 2500Homo sapiensfetal1_C4_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957617Illumina HiSeq 2500Homo sapiensfetal1_C6_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957618Illumina HiSeq 2500Homo sapiensfetal1_C9_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]

Gene rank in fetal human cortex 1[12 weeks post-conception]

Displaying 41-50 of 16781 results.
Rank orderGene SymbolEnsembl ID
41TMSB4XENSG00000205542
42EIF4G2ENSG00000110321
43ATRXENSG00000085224
44H2AFZENSG00000164032
45YWHAZENSG00000164924
46SONENSG00000159140
47GABARAPENSG00000170296
48NFIAENSG00000162599
49TUBA1BENSG00000123416
50COX7CENSG00000127184