 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 17, 2017 |
| Title |
RNA-seq Analysis of 15q Duplication and AS Deletion DPSC derived neurons. |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
A major problem in studying neurogenetic syndromes is obtaining live neurons from people with these disorders. We have taken a novel approach to studying gene expression in neurons from Angelman or Dup15q syndrome subjects using dental pulp stem cells (DPSC). Shed teeth were collected to generate DPSC lines from 3 AS deletion, 3 15q Duplication and three neurotypical subjects. mRNAseq was performed on DPSC and DPSC derived neurons. We identified 20 genes in AS, 120 genes in 15q duplication and 3 genes in both groups (DPT, MED12L and AKRIC1) that were significantly different from control DPSC-neurons. Copy number correlated to gene expression for most genes across the 15q11.2-q13.1 critical region. Two thirds of the genes differentially regulated in 15q duplication were down-regulated compared to controls including the transcription factors FOXO1 and HAND2, while in AS the genes did not show a clear trend except in the 15q region. Pathway analysis revealed increased cytokine activity related genes including four genes that increased in 15q duplication samples: CCL7, CCL2, MMP2 and MMP3; while steroid hormone biosynthesis genes were slightly enriched in both 15q duplication and AS neurons. Overall there were more dramatic changes in gene expression in the 15q) duplication than AS deletion cell lines, perhaps because the mechanism of AS may be through protein targeting by UBE3A. Nonetheless, the finding of a significant increase in both HERC2 and UBE3A in 15q duplication neurons and significant decrease in these two genes in AS deletion neurons may impact the AS phenotype, at least in deletion cases.
|
| |
|
| Overall design |
RNA-seq Analysis of 3 15q Duplication, 3 Angelman syndrome deletion and 3 neurotypical control DPSC derived neurons (~3 weeks post maturation)
|
| |
|
| Contributor(s) |
Urraca N, Tran QT, Belgard GT, Memon R, Goorha S, Valdez C, Sanchez S, Ramirez J, Donaldson M, Bridges D, Reiter LT |
| Citation(s) |
29423132 |
| Submission date |
Mar 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Quynh Tran |
| E-mail(s) |
qtran@stjude.org
|
| Organization name |
St. Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place, C4029, Mail Stop 250
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL16558 |
AB 5500 Genetic Analyzer (Homo sapiens) |
|
| Samples (18)
|
|
| Relations |
| BioProject |
PRJNA279008 |
| SRA |
SRP056387 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE67122_counts_table.csv.gz |
542.8 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
Less...
More...