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Sample GSM1255303 Query DataSets for GSM1255303
Status Public on Dec 01, 2015
Title genomic DNA from IPSC-derived DAn SP-05-L2PD
Sample type genomic
Source name 30-days neuron-PD LRRK2 G2019S mutation carrier
Organism Homo sapiens
Characteristics patient id: SP-05
patient id2: PD-03
gender: male
disease state: Parkinson's disease
number of ipsc obtained to generate neurons: 2
family history of pd: yes
age at onset (years): 52
age at tissue collection (years): 66
l-dopa response: good
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 7973219134_R06C01
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 0.913750398
cg00021786 0.970092146
cg00072839 0.024422269
cg00074638 0.586862951
cg00266918 0.064121794
cg00378717 0.042156162
cg00378950 0.856281803
cg00381376 0.030039249
cg00388637 0.654001817
cg00423014 0.679770469
cg00457389 0.056259729
cg00551957 0.885766316
cg00573298 0.045258743
cg00685229 0.457501402
cg00697812 0.718770965
cg00751785 0.048345373
cg00812634 0.96676232
cg00824273 0.77195836
cg00824714 0.91511929
cg00839572 0.041076375

Total number of rows: 478178

Table truncated, full table size 10699 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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