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  iPSC 409B2[37 days]

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 iPSC 409B2[37 days]

Displaying 1-10 of 71 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957226Illumina HiSeq 2500Homo sapienswhOrg3_H8_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957225Illumina HiSeq 2500Homo sapienswhOrg3_H7_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957224Illumina HiSeq 2500Homo sapienswhOrg3_H4_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957223Illumina HiSeq 2500Homo sapienswhOrg3_H3_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957222Illumina HiSeq 2500Homo sapienswhOrg3_H12_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957221Illumina HiSeq 2500Homo sapienswhOrg3_H11_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957220Illumina HiSeq 2500Homo sapienswhOrg3_H10_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957219Illumina HiSeq 2500Homo sapienswhOrg3_G9_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957218Illumina HiSeq 2500Homo sapienswhOrg3_G5_hOrg37diPSC 409B2[37 days]
GSE75140GSM1957217Illumina HiSeq 2500Homo sapienswhOrg3_G3_hOrg37diPSC 409B2[37 days]

Gene rank in iPSC 409B2[37 days]

Displaying 31-40 of 16781 results.
Rank orderGene SymbolEnsembl ID
31SNRPD2ENSG00000125743
32RANENSG00000132341
33TMBIM6ENSG00000139644
34ENO1ENSG00000074800
35FTLENSG00000087086
36SRSF3ENSG00000112081
37DPYSL2ENSG00000092964
38NAP1L1ENSG00000187109
39HNRNPA1ENSG00000135486
40COX7CENSG00000127184