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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 21-30 of 68 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957108Illumina HiSeq 2500Homo sapienswhOrg2_B7_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957109Illumina HiSeq 2500Homo sapienswhOrg2_B8_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957110Illumina HiSeq 2500Homo sapienswhOrg2_B9_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957111Illumina HiSeq 2500Homo sapienswhOrg2_C10_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957112Illumina HiSeq 2500Homo sapienswhOrg2_C11_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957113Illumina HiSeq 2500Homo sapienswhOrg2_C12_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957114Illumina HiSeq 2500Homo sapienswhOrg2_C1_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957115Illumina HiSeq 2500Homo sapienswhOrg2_C2_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957116Illumina HiSeq 2500Homo sapienswhOrg2_C3_hOrg35diPSC 409B2[35 days]
GSE75140GSM1957117Illumina HiSeq 2500Homo sapienswhOrg2_C5_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