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| Status |
Public on Sep 18, 2018 |
| Title |
Next-generation sequencing facilitates quantitative analysis of the transcriptomes of FOXG1 100% dosage, FOXG1 60% dosage, FOXG1 30% dosage, and FOXG1 0% dosage GABA interneurons derived from human embryonic stem cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Next-generation sequencing facilitates quantitative analysis of the transcriptomes of FOXG1 100% dosage GABA interneurons, FOXG1 60% dosage GABA interneurons, FOXG1 30% dosage GABA interneurons, and FOXG1 0% dosage GABA interneurons derived from human embryonic stem cells.
We report a genetic manipulation system that enable precise dosage control of FOXG1 protein in human pluripotent stem cells (hPSCs). Using this system, we explored how the various reduced dosage affect human ventrol GABA interneuron development. We employed RNA seq on hPSC-derived GABA interneurons (day 60) to invest the expression pattern under different FOXG1 dosage conditions. RNA-Seq on GABA interneurons (Day 60) indicates that compared to the FOXG1 100% group, variable insufficiency of FOXG1 produces more than 1000 differently expressed genes (DEGs), and more DEGs in the group with less FOXG1 dosage. Heat map on Pearson Correlation indicates that groups with more discriminated FOXG1 exhibit much weaker correlation. Venn diagram reveals that each group has a set of distinct DEGs, suggesting that each FOXG1 protein dosage could results in different expression pattern during differentiation. The DEGs can be divided into two clusters, with one showing dosage-dependent regulation by FOXG1 and the other one typical binary. Key regulatory genes for GABA interneuron induction (NKX2-1, NKX6-2, GAD1, etc.) and for functional GABAergic-speciļ¬c synapse formation (GABBR1, GABRA1, GABRB1, GABRG1, GABRQ, SHANK1, etc.) are down regulated along with reduction of FOXG1 protein.
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| Overall design |
The genetic manipulation system we built, which we call it SPIDe, is controlled by a small molecule (ASV). During the differentiation procedure from hPSCs to cortical GABA interneuron, treat the cells with ASV to induce FOXG1 protein degradation and then collect the samples on day 60 for RNA-seq.
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| Contributor(s) |
Hu B, Zhu W |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Sep 17, 2018 |
| Last update date |
Jan 07, 2019 |
| Contact name |
Baoyang Hu |
| E-mail(s) |
byhu@ioz.ac.cn
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| Phone |
010-64806297
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| Organization name |
Institute of Zoology
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| Department |
State Key Laboratory of Stem Cell and Reproductive Biology
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| Street address |
Beichenxilu
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| City |
Beijing |
| State/province |
Select State/Province |
| ZIP/Postal code |
100000 |
| Country |
China |
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| Platforms (1) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA491512 |
| SRA |
SRP161946 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE120079_RAW.tar |
16.6 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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