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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
GSE75140GSM1957291Illumina HiSeq 2500Homo sapienswhOrg4_G5_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957292Illumina HiSeq 2500Homo sapienswhOrg4_G7_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957293Illumina HiSeq 2500Homo sapienswhOrg4_G8_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957294Illumina HiSeq 2500Homo sapienswhOrg4_G9_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957295Illumina HiSeq 2500Homo sapienswhOrg4_H10_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957296Illumina HiSeq 2500Homo sapienswhOrg4_H2_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957297Illumina HiSeq 2500Homo sapienswhOrg4_H3_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957298Illumina HiSeq 2500Homo sapienswhOrg4_H4_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957299Illumina HiSeq 2500Homo sapienswhOrg4_H7_hOrg41diPSC 409B2[41 days]
GSE75140GSM1957300Illumina HiSeq 2500Homo sapienswhOrg4_H8_hOrg41diPSC 409B2[41 days]

Gene rank in iPSC 409B2[41 days]

Displaying 161-170 of 16781 results.
Rank orderGene SymbolEnsembl ID
161TCEB2ENSG00000103363
162STRAPENSG00000023734
163HSPD1ENSG00000144381
164ATRXENSG00000085224
165C14orf2ENSG00000156411
166SEPT2ENSG00000168385
167HERPUD1ENSG00000051108
168ANKRD10ENSG00000088448
169TTC3ENSG00000182670
170RND3ENSG00000115963