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| Status |
Public on Oct 24, 2014 |
| Title |
RNA-Seq Analysis in purified iPS cell-derived neuronal samples |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We characterized the gene expression differences in mDA neurons from all PD (Parkinson's disease) cases (6 independent samples) and controls (8 independent samples), identifying 1,028 differentially expressed genes making up the PD expression signature. Strikingly, MAOB gene was identified as significantly differentially expressed (p = 0.046). The heat map clearly differentiates cases from controls, where interestingly most differentially expressed genes had lower expression in PD cases compared to controls. In the clustering, the RNA expression pattern of the control (C2) with a family history of PD located close to the PD expression signature suggested a susceptibility to PD.
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| Overall design |
RNA was isolated from FAC-sorted cells of 14 samples (biological duplicates for each cell line, 7 cell lines in total) using RNeasy Micro Kit (QIAGEN). Quality control of the RNA was carried out with the Agilent Bio-analyzer, Qubit 2.0 at the MPSR of Columbia University. 100 ng of RNA with RIN ≥ 9 were used for generating mRNA-focused libraries using TruSeq RNA Sample Preparation Kit v2 and sequencing on an Illumina 2000/2500 V3 Instrument offered by the Columbia Genome Center.
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| Contributor(s) |
Woodard CM, Campos BA, Li A, Noggle SA |
| Citation(s) |
25456120 |
| Submission date |
Oct 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Aiqun Li |
| E-mail(s) |
leeaiqun@hotmail.com
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| Phone |
2128515422
|
| Organization name |
The New York Stem Cell Foundation
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| Department |
Research Institute
|
| Street address |
3960 Broadway
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platforms (1) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA264625 |
| SRA |
SRP049203 |
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