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Sample GSM1255319 Query DataSets for GSM1255319
Status Public on Dec 01, 2015
Title genomic DNA from fibroblasts FIB-SP-06-L2PD
Sample type genomic
Source name IPSC-PD LRRK2 G2019S mutation carrier
Organism Homo sapiens
Characteristics patient id: SP-06
patient id2: PD-05
gender: male
disease state: Parkinson's disease
number of ipsc obtained to generate neurons: NA
family history of pd: yes
age at onset (years): 33
age at tissue collection (years): 44
l-dopa response: good
initial symptoms: tremor
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 0.837099494
cg00021786 0.954408039
cg00072839 0.057266667
cg00074638 0.540068292
cg00266918 0.085211347
cg00378717 0.015106395
cg00378950 0.461821502
cg00381376 0.026201053
cg00388637 0.60332981
cg00423014 0.63428849
cg00457389 0.034648394
cg00551957 0.828960211
cg00573298 0.036100875
cg00685229 0.770636825
cg00697812 0.73097166
cg00751785 0.030997424
cg00812634 0.914809415
cg00824273 0.709445621
cg00824714 0.626257786
cg00839572 0.053796023

Total number of rows: 478178

Table truncated, full table size 10697 Kbytes.

Supplementary data files not provided
Processed data included within Sample table

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