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  iPSC 409B2[33 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[33 days]

Displaying 1-10 of 40 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957048Illumina HiSeq 2500Homo sapienswhOrg1_B12_hOrg33d_c2iPSC 409B2[33 days]
GSE75140GSM1957049Illumina HiSeq 2500Homo sapienswhOrg1_B1_hOrg33d_c2iPSC 409B2[33 days]
GSE75140GSM1957050Illumina HiSeq 2500Homo sapienswhOrg1_B6_hOrg33d_c2iPSC 409B2[33 days]
GSE75140GSM1957051Illumina HiSeq 2500Homo sapienswhOrg1_B7_hOrg33d_c2iPSC 409B2[33 days]
GSE75140GSM1957052Illumina HiSeq 2500Homo sapienswhOrg1_C10_hOrg33d_c2iPSC 409B2[33 days]
GSE75140GSM1957053Illumina HiSeq 2500Homo sapienswhOrg1_C11_hOrg33d_c2iPSC 409B2[33 days]
GSE75140GSM1957054Illumina HiSeq 2500Homo sapienswhOrg1_C8_hOrg33d_c2iPSC 409B2[33 days]
GSE75140GSM1957055Illumina HiSeq 2500Homo sapienswhOrg1_D2_hOrg33d_c2iPSC 409B2[33 days]
GSE75140GSM1957056Illumina HiSeq 2500Homo sapienswhOrg1_F1_hOrg33d_c2iPSC 409B2[33 days]
GSE75140GSM1957057Illumina HiSeq 2500Homo sapienswhOrg1_F6_hOrg33d_c2iPSC 409B2[33 days]

Gene rank in iPSC 409B2[33 days]

Displaying 1-10 of 16781 results.
Rank orderGene SymbolEnsembl ID
1ACTBENSG00000075624
2C11orf31ENSG00000211450
3TUBA1AENSG00000167552
4GPX4ENSG00000167468
5GAPDHENSG00000111640
6CALM2ENSG00000143933
7LDHBENSG00000111716
8GNB2L1
9HNRNPH1ENSG00000169045
10EEF1A1ENSG00000156508