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| Status |
Public on Jul 23, 2022 |
| Title |
Burlk and single cell RNA sequencing of neural stem cells derived from human trisomic iPSCs |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Down syndrome (DS) is the most common genetic condition that causes intellectual disability in humans. The molecular mechanisms behind the DS phenotype remain unclear. Therefore, in the present study, induced pluripotent stem cells (iPSCs) from a patient with DS and a normal control (NC) patient were differentiated into iPSCs‐derived neural stem cells (NSCs). Single-cell RNA sequencing was performed to achieve a comprehensive single-cell level differentiation roadmap for DS-iPSCs. The results demonstrated that iPSCs can differentiate into NSCs in both DS and NC samples. Furthermore, 19,422 cells were obtained from iPSC samples (8,500 cells for DS and 10,922 cells for the NC) and 16,506 cells from NSC samples (7,182 cells for DS and 9,324 cells for the NC), which had differentiated from the iPSCs. A cluster of DS-iPSCs, named DS-iPSCs-not differentiated (DSi-PSCs-ND), which had abnormal expression patterns compared with NC-iPSCs, were demonstrated to be unable to differentiate into DS-NSCs. Further analysis of the differentially expressed genes revealed that inhibitor of differentiation family members, which exhibited abnormal expression patterns throughout the differentiation process from DS-iPSCs to DS-NSCs, may potentially have contributed to the neural differentiation of DS-iPSCs. Moreover, abnormal differentiation fate was observed in DS-NSCs, which resulted in the increased differentiation of glial cells, such as astrocytes, but decreased differentiation into neuronal cells. Furthermore, functional analysis demonstrated that DS-NSCs and DS-NPCs had disorders in axon and visual system development. Biological experiments were also performed to validate these results and the present study provided a new insight into the pathogenesis of DS.
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| Overall design |
Burlk and single cell RNA sequencing of neural stem cells derived from human trisomic iPSCs
This submission contains scRNA-Seq data.
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| Contributor(s) |
Qiu J, Liu Y, Wei H, Zeng F, Yan J |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Jul 20, 2022 |
| Last update date |
Jul 23, 2022 |
| Contact name |
Jiajun Qiu |
| E-mail(s) |
jiajunqiu@hotmail.com
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| Organization name |
Shanghai Children’s Hospital, Shanghai Institute of Medical Genetics, Shanghai Jiao Tong University School of Medicine
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| Street address |
West BeiJing Road
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| City |
Shanghai |
| ZIP/Postal code |
200040 |
| Country |
China |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA860359 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE208625_D_I_filtered_barcodes.tsv.gz |
42.6 Kb |
(ftp)(http) |
TSV |
| GSE208625_D_I_filtered_features.tsv.gz |
311.3 Kb |
(ftp)(http) |
TSV |
| GSE208625_D_I_filtered_matrix.mtx.gz |
116.5 Mb |
(ftp)(http) |
MTX |
| GSE208625_D_N_filtered_barcodes.tsv.gz |
36.4 Kb |
(ftp)(http) |
TSV |
| GSE208625_D_N_filtered_features.tsv.gz |
311.3 Kb |
(ftp)(http) |
TSV |
| GSE208625_D_N_filtered_matrix.mtx.gz |
127.8 Mb |
(ftp)(http) |
MTX |
| GSE208625_N_I_filtered_barcodes.tsv.gz |
53.9 Kb |
(ftp)(http) |
TSV |
| GSE208625_N_I_filtered_features.tsv.gz |
311.3 Kb |
(ftp)(http) |
TSV |
| GSE208625_N_I_filtered_matrix.mtx.gz |
138.7 Mb |
(ftp)(http) |
MTX |
| GSE208625_N_N_filtered_barcodes.tsv.gz |
46.4 Kb |
(ftp)(http) |
TSV |
| GSE208625_N_N_filtered_features.tsv.gz |
311.3 Kb |
(ftp)(http) |
TSV |
| GSE208625_N_N_filtered_matrix.mtx.gz |
108.4 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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