|
| Status |
Public on Dec 01, 2015 |
| Title |
genomic DNA from IPSC-derived DAn SP-16-IPD |
| Sample type |
genomic |
| |
|
| Source name |
30-days neuron-idiopathic PD
|
| Organism |
Homo sapiens |
| Characteristics |
patient id: SP-16
patient id2: PD-04
gender: female
disease state: Parkinson's disease
number of ipsc obtained to generate neurons: 4
family history of pd: no
age at onset (years): 51
age at tissue collection (years): 51
l-dopa response: NA
initial symptoms: Bradykinesia
cell type: IPSC-derived DAn
disease state: Parkinson's disease
|
| Treatment protocol |
No specific treatment of cells
|
| Growth protocol |
Keratinocytes or dermal fibroblasts were cultured using standard protocols from skin biopsy obtained from participating subjects [Sanchez-Danes et al., 2012]. Briefly, keratinocytes and/ or fibroblasts were transformed to induced pluripotent stem cells (iPSC) by retroviral transduction of three transcription factors (OTC4, SOX2 and KLF4). Subsequently, iPSC were differentiated into DAn specific growth factor medium supplementation (bFGF, FGF-8 and SHH) and lentiviral LMX1A delivery.Described in Sanchez-Danes et al., EMBO Mol Med. 2012 ;4(5):380-95. doi: 10.1002/emmm.201200215.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA extracted according to AllPrep DNA/RNA/Protein Mini Kit - Qiagen
|
| Label |
Cy5 and Cy3
|
| Label protocol |
Standard Illumina Protocol
|
| |
|
| Hybridization protocol |
Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using the standard Illumina protocol
|
| Scan protocol |
Arrays were imaged using the iScan reader using standard recommended Illumina scanner setting
|
| Description |
7990895162_R03C01
|
| Data processing |
Using the minfi R package available through Bioconductor
|
| |
|
| Submission date |
Oct 30, 2013 |
| Last update date |
Dec 01, 2015 |
| Contact name |
Mario Ezquerra |
| E-mail(s) |
ezquerra@clinic.cat
|
| Phone |
0034 932273122
|
| Organization name |
Fundacio Clinic/IDIBAPS
|
| Department |
Neurology
|
| Lab |
Neurodegenerative Diseases
|
| Street address |
Villarroel 170
|
| City |
Barcelona |
| State/province |
Catalonia |
| ZIP/Postal code |
08027 |
| Country |
Spain |
| |
|
| Platform ID |
GPL13534 |
| Series (2) |
| GSE51921 |
DNA methylation analysis in idiopathic and LRRK2-associated Parkinson's disease (PD) |
| GSE51923 |
Idiopathic and LRRK2-associated Parkinson's disease |
|
