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Sample GSM1255317 Query DataSets for GSM1255317
Status Public on Dec 01, 2015
Title genomic DNA from fibroblasts FIB-SP-04-sPD
Sample type genomic
Source name IPSC-idiopathic PD
Organism Homo sapiens
Characteristics patient id: SP-04
patient id2: PD-08
gender: male
disease state: Parkinson's disease
number of ipsc obtained to generate neurons: NA
family history of pd: no
age at onset (years): 40
age at tissue collection (years): 46
l-dopa response: good
initial symptoms: Bradykinesia
cell type: fibroblasts
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
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
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

Data table header descriptions
VALUE Average beta values

Data table
cg00014152 0.774503722
cg00021786 0.953610852
cg00072839 0.032098234
cg00074638 0.538493307
cg00266918 0.064354367
cg00378717 0.01813617
cg00378950 0.456116894
cg00381376 0.027645744
cg00388637 0.606821958
cg00423014 0.629029947
cg00457389 0.040183818
cg00551957 0.8162483
cg00573298 0.037161133
cg00685229 0.898234651
cg00697812 0.796900941
cg00751785 0.039331825
cg00812634 0.943611447
cg00824273 0.648074512
cg00824714 0.652850953
cg00839572 0.043569037

Total number of rows: 478178

Table truncated, full table size 10698 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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