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Series GSE62642 Query DataSets for GSE62642
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.
 
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.
 
Contributor(s) Woodard CM, Campos BA, Li A, Noggle SA
Citation(s) 25456120
Submission date Oct 23, 2014
Last update date Mar 20, 2019
Contact name Aiqun Li
E-mail leeaiqun@hotmail.com
Phone 2128515422
Organization name The New York Stem Cell Foundation
Department Research Institute
Street address 3960 Broadway
City New York
State/province NY
ZIP/Postal code 10032
Country USA
 
Platforms (1)
GPL16791 Illumina HiSeq 2500 (Homo sapiens)
Samples (14)
GSM1530722 C1_1
GSM1530723 C1_2
GSM1530724 C2_1
Relations
BioProject PRJNA264625
SRA SRP049203

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Supplementary file Size Download File type/resource
GSE62642_RAW.tar 12.9 Mb (http)(custom) TAR (of CSV)
Raw data are available in SRA
Processed data provided as supplementary file

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