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| Status |
Public on Aug 22, 2020 |
| Title |
Genome wide mRNA sequencing of induced pluripotent stem cell (iPSC) diffrentiated neural stem cells (NSCs). |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
The NSC differentiation of six validated iPSC lines were induced using commercially available PSC neural induction medium and following manufacturer method with minor modifications (Gibco). An extensive characterization of generated NSCs on day 14 (at passage P1) was performed using immunocytochemistry (ICC) analysis of the NSC specific markers and by genome wide mRNA sequencing. The iPSC differentiated NSCs expressed NSC specific markers Nestin, PAX6, SOX1 and SOX2 across all six samples. The average correlation coefficient at 95% CI between 6 NSC samples, calculated based on all expressed mRNAs, was 0.97 ± 0.008 suggesting a uniform differentiation of generated NSC lines. The generated NSC showed high expression of neuroepithelial genes/transcription factors (NES, SOX2, SOX1, PAX6, NOTCH1, MSI1,and CHD2) and genes/transcription factors of dorsal tube neuroepithelium (PAX3, GDF7, SOX9 and SNAI2) but lacked the expression of ventral tube neuroepithelial markers (NKX2-2, FOXA2 and SHH) suggesting a dorsal tube neuroepithelial transcriptomic and functional profile of the generated NSCs. A differential gene expression analysis of iPSC’s and NSC’s expressed transcription identified 4,033 mRNAs that were significantly differentially expressed (DE) between iPSCs and differentiated NSCs. The 2,006 DE mRNA were significantly upregulated in differentiated NSCs and were highly enriched in developmental functional categories such as embryonic development (572 mRNAs; FDR adjusted p-value range: 1.92x10-53 – 3.26x10-9), organism development (749 mRNAs; FDR adjusted p-value range: 1.92x10-53 – 4.30x10-9), nervous system development and function (629 mRNAs; FDR adjusted p-value range: 3.23x10-48 – 4.15x10-9), tissue development (655 mRNAs; FDR adjusted p-value range: 3.63x10-40 – 4.32x10-9) and organ development (406 mRNAs; FDR adjusted p-value range: 8.74x10-40 – 2.37x10-9).
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| Overall design |
To better understand the functional profile and disease modeling potential of iPSC generated NSCs. A genome wide mRNA sequencing analysis of iPSC generated NSCs was performed.
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| Contributor(s) |
Kumar S, Curran JE, Blangero J |
| Citation(s) |
32977388 |
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| Submission date |
Aug 21, 2020 |
| Last update date |
Nov 02, 2020 |
| Contact name |
Satish Kumar |
| E-mail(s) |
satish.kumar@utrgv.edu
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| Phone |
+1-956-665-6477
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| Organization name |
University of Texas Rio Grande Valley
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| Department |
Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine
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| Street address |
5300 North L Street (MBMRF-2.219)
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| City |
McAllen |
| State/province |
Texas |
| ZIP/Postal code |
78504 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA658523 |
| SRA |
SRP278375 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE156617_NSC-mRNA.txt.gz |
1.5 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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