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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 51-60 of 74 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957277Illumina HiSeq 2500Homo sapienswhOrg4_F1_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957278Illumina HiSeq 2500Homo sapienswhOrg4_F2_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957279Illumina HiSeq 2500Homo sapienswhOrg4_F3_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957280Illumina HiSeq 2500Homo sapienswhOrg4_F4_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957281Illumina HiSeq 2500Homo sapienswhOrg4_F6_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957282Illumina HiSeq 2500Homo sapienswhOrg4_F7_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957283Illumina HiSeq 2500Homo sapienswhOrg4_F8_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957284Illumina HiSeq 2500Homo sapienswhOrg4_F9_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957285Illumina HiSeq 2500Homo sapienswhOrg4_G10_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957286Illumina HiSeq 2500Homo sapienswhOrg4_G11_hOrg41diPSC 409B2[41 days]

Gene rank in iPSC 409B2[41 days]

Displaying 16691-16700 of 16781 results.
Rank orderGene SymbolEnsembl ID
16691VMACENSG00000187650
16692VMO1ENSG00000182853
16693VN1R2ENSG00000196131
16694VPREB3ENSG00000128218
16695VSIG1ENSG00000101842
16696VSIG8ENSG00000243284
16697VSTM2AENSG00000170419
16698VSTM5ENSG00000214376
16699VSX1ENSG00000100987
16700VSX2ENSG00000119614