|
| Status |
Public on Dec 01, 2015 |
| Title |
RNA-30 days-neuron-idiopathic PD patient1 |
| Sample type |
RNA |
| |
|
| Source name |
30-days RNA from IPSC-derived DAn IPD
|
| Organism |
Homo sapiens |
| Characteristics |
patient id2: PD-09
number of ipsc obtained to generate neurons: 4
gender: female
family history of pd: no
age at onset (years): 58
age at tissue collection (years): 63
l-dopa response: NA
initial symptoms: Tremor-Badykinesia
cell type: iPSC-derived dopaminergic neuron
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 |
total RNA |
| Extraction protocol |
RNA isolation from cell pellets was performed using the Allprep DNA RNA Protein Minikit from Quiagen following manufacter instructions. The RNA concentration was measured by analysing the absorbance at 260 nanometers and RNA with the Nanodrop 1000 Spectrophotometer (Thermo Fisher Scientific). RNA quality was evaluated by using the 2100 Bioanalyzer (Agilent). Isolated samples were stored at -80ºC..
|
| Label |
biotin
|
| Label protocol |
Samples were enzymatically fragmented and biotinylated using the Affymetrix GeneChip WT sense target labelling and control reagents kit (Affymetrix)
|
| |
|
| Hybridization protocol |
Samples were hybridized using Affymetrix hybridization kit materials.
|
| Scan protocol |
Affymetrix Gene ChIP Scanner 3000 7G
|
| Data processing |
Chips were processed on an Affymetrix GeneChip Fluidics Station 450. Background adjustment by Robust Multi-Array (RMA) algorithm and quantile normalization was applied to probes intensities. Gene level expression were summarized from the corrected intensities using the 'core' exon annotations.
HuEx-1_0-st-v2.r2.pgf
HuEx-1_0-st-v2.r2.dt1.hg18.core.mps
|
| |
|
| Submission date |
Oct 30, 2013 |
| Last update date |
Dec 01, 2015 |
| Contact name |
Mario Ezquerra |
| E-mail(s) |
[email protected]
|
| 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 |
GPL5175 |
| Series (2) |
| GSE51922 |
Microarray expression analysis in idiopathic and LRRK2-associated Parkinson's disease (PD) |
| GSE51923 |
Idiopathic and LRRK2-associated Parkinson's disease |
|
