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  fetal human cortex 1[12 weeks post-conception]

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 fetal human cortex 1[12 weeks post-conception]

Displaying 11-20 of 164 results.
SeriesSampleInstrumentOrganismTitleCell Source
GSE75140GSM1957590Illumina HiSeq 2500Homo sapiensfetal1_A8_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957592Illumina HiSeq 2500Homo sapiensfetal1_A9_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957594Illumina HiSeq 2500Homo sapiensfetal1_B10_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957596Illumina HiSeq 2500Homo sapiensfetal1_B11_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957599Illumina HiSeq 2500Homo sapiensfetal1_B12_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957601Illumina HiSeq 2500Homo sapiensfetal1_B1_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957603Illumina HiSeq 2500Homo sapiensfetal1_B2_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957605Illumina HiSeq 2500Homo sapiensfetal1_B3_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957607Illumina HiSeq 2500Homo sapiensfetal1_B4_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]
GSE75140GSM1957608Illumina HiSeq 2500Homo sapiensfetal1_B5_fetal_12wpc_c1fetal human cortex 1[12 weeks post-conception]

Gene rank in fetal human cortex 1[12 weeks post-conception]

Displaying 1-10 of 16781 results.
Rank orderGene SymbolEnsembl ID
1TUBA1AENSG00000167552
2ACTBENSG00000075624
3STMN1ENSG00000117632
4HNRNPH1ENSG00000169045
5CALM2ENSG00000143933
6ACTG1ENSG00000184009
7NFIBENSG00000147862
8DPYSL2ENSG00000092964
9H3F3BENSG00000132475
10GNB2L1