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  iPSC 409B2[35 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[35 days]

Displaying 51-60 of 68 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957138Illumina HiSeq 2500Homo sapienswhOrg2_E3_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957139Illumina HiSeq 2500Homo sapienswhOrg2_E4_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957140Illumina HiSeq 2500Homo sapienswhOrg2_E5_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957141Illumina HiSeq 2500Homo sapienswhOrg2_E6_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957142Illumina HiSeq 2500Homo sapienswhOrg2_E7_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957143Illumina HiSeq 2500Homo sapienswhOrg2_E8_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957144Illumina HiSeq 2500Homo sapienswhOrg2_E9_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957145Illumina HiSeq 2500Homo sapienswhOrg2_F10_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957146Illumina HiSeq 2500Homo sapienswhOrg2_F11_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957147Illumina HiSeq 2500Homo sapienswhOrg2_F12_hOrg35diPSC 409B2[35 days]

Gene rank in iPSC 409B2[35 days]

Displaying 16751-16760 of 16781 results.
Rank orderGene SymbolEnsembl ID
16751ZFYENSG00000067646
16752ZG16BENSG00000162078
16753ZIM2ENSG00000269699
16754ZMYND12ENSG00000066185
16755ZNF157ENSG00000147117
16756ZNF229ENSG00000278318
16757ZNF257ENSG00000197134
16758ZNF365ENSG00000138311
16759ZNF366ENSG00000178175
16760ZNF385CENSG00000187595