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  iPSC 409B2[41 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[41 days]

Displaying 1-10 of 74 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957227Illumina HiSeq 2500Homo sapienswhOrg4_A10_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957228Illumina HiSeq 2500Homo sapienswhOrg4_A1_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957229Illumina HiSeq 2500Homo sapienswhOrg4_A2_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957230Illumina HiSeq 2500Homo sapienswhOrg4_A3_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957231Illumina HiSeq 2500Homo sapienswhOrg4_A4_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957232Illumina HiSeq 2500Homo sapienswhOrg4_A5_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957233Illumina HiSeq 2500Homo sapienswhOrg4_A6_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957234Illumina HiSeq 2500Homo sapienswhOrg4_A7_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957235Illumina HiSeq 2500Homo sapienswhOrg4_A8_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957236Illumina HiSeq 2500Homo sapienswhOrg4_B10_hOrg41diPSC 409B2[41 days]

Gene rank in iPSC 409B2[41 days]

Displaying 1-10 of 16781 results.
Rank orderGene SymbolEnsembl ID
1H3F3BENSG00000132475
2GPX4ENSG00000167468
3ACTBENSG00000075624
4GAPDHENSG00000111640
5ACTG1ENSG00000184009
6EEF1A1ENSG00000156508
7FTLENSG00000087086
8GNB2L1
9UBBENSG00000170315
10HNRNPH1ENSG00000169045