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Sample GSM1255309 Query DataSets for GSM1255309
Status Public on Dec 01, 2015
Title genomic DNA from IPSC IPSC.SP-17-CON
Sample type genomic
Source name IPSC-control
Organism Homo sapiens
Characteristics patient id: SP-17
patient id2: C-04
gender: male
disease state: Healthy
number of ipsc obtained to generate neurons: NA
family history of pd: no
age at onset (years): NA
age at tissue collection (years): 52
l-dopa response: NA
initial symptoms: NA
cell type: IPSC
disease state: control
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 8918692127_R05C02
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 0.913852268
cg00021786 0.960832485
cg00072839 0.015153512
cg00074638 0.595052563
cg00266918 0.161665416
cg00378717 0.030871377
cg00378950 0.917926357
cg00381376 0.025181569
cg00388637 0.699218332
cg00423014 0.695946696
cg00457389 0.034803088
cg00551957 0.823130974
cg00573298 0.051690404
cg00685229 0.114553956
cg00697812 0.751940133
cg00751785 0.035240723
cg00812634 0.954909618
cg00824273 0.820296487
cg00824714 0.862360987
cg00839572 0.056231563

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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