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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 10, 2017 |
| Title |
Single cell RNAseq characterization of cell types produced over time in an in vitro model of human inhibitory interneuron differentiation. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Diverse cell types are produced from dorsal and ventral regions of the developing neural tube. In this study we describe a system for generating human inhibitory interneurons by ventralizing human embryonic stem cells in vitro and characterizing the gene expression of the cell types produced over time. We engineered a DCX-Citrine/Y hESC line to sort and characterize progenitor and neuron transcriptomics separately at both the subpopulation and single cell level. The cells generated in vitro were compared to similar populations present in human fetal brain samples by mapping gene expression data from human fetal cells onto the principal component analysis (PCA) space of in vitro-derived populations. Weighted gene co-expression network analysis (WGCNA) was used to determine the discreet cell types present at D24, D54, D100 and D125 of culture, and describe the gene expression changes that occur in progenitor and neuron populations over time. Immature lateral ganglionic eminence and medial ganglionic eminence cells are present at early timepoints, along with MGE-like and dorsal pallium-like neuronal progenitors. At later timepoints we observe the emergence of SST-expressing interneurons, as well as oligodendrocyte and astrocyte progenitors. We also identified genes that were upregulated in somatostatin-expressing interneurons as they mature.
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| Overall design |
The transcriptomes of 1732 ventralized single cells were profiled by SmartSeq2 at different timepoints throughout a 125-day differentiation protocol that converted H1 human embryonic stem cells to a variety of ventrally-derived cell types.
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| Contributor(s) |
Close J, Yao Z, Levi BP, Milller JA, Bakken TE, Menon V, Ting J, Wall A, Krostag A, Thomsen ER, Nelson AM, Mich JK, Hodge RD, Shehata SI, Glass I, Bort S, Shapovalova NV, Fong O, Ngo K, Grimley JS, Phillips JW, Thompson CL, Ramanathan S, Lein E |
| Citation(s) |
28279351 |
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| Submission date |
Jan 13, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Allen Institute |
| Organization name |
The Allen Institute for Brain Science
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| Street address |
615 Westlake Ave N
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (1733)
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| This SubSeries is part of SuperSeries: |
| GSE93802 |
Characterization of cell types produced over time in an in vitro model of human inhibitory interneuron differentiation. |
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| Relations |
| BioProject |
PRJNA361254 |
| SRA |
SRP096727 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE93593_counts.csv.gz |
23.5 Mb |
(ftp)(http) |
CSV |
| GSE93593_tpm.csv.gz |
29.9 Mb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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