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Sample GSM1255293 Query DataSets for GSM1255293
Status Public on Dec 01, 2015
Title genomic DNA from IPSC-derived DAn SP-09-CON
Sample type genomic
Source name 30 days-neuron control
Organism Homo sapiens
Characteristics patient id: SP-09
patient id2: C-03
gender: male
disease state: Healthy
number of ipsc obtained to generate neurons: 4
family history of pd: no
age at onset (years): NA
age at tissue collection (years): 66
l-dopa response: NA
initial symptoms: NA
cell type: IPSC-derived DAn
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 7973219134_R03C02
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 0.954862708
cg00021786 0.959464506
cg00072839 0.047822581
cg00074638 0.539106637
cg00266918 0.055504671
cg00378717 0.021728635
cg00378950 0.817328244
cg00381376 0.013637275
cg00388637 0.614708316
cg00423014 0.653638666
cg00457389 0.045704899
cg00551957 0.870331171
cg00573298 0.0400896
cg00685229 0.44465151
cg00697812 0.733467337
cg00751785 0.041062639
cg00812634 0.952125869
cg00824273 0.65907088
cg00824714 0.866682187
cg00839572 0.025201899

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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