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Sample GSM1255304 Query DataSets for GSM1255304
Status Public on Dec 01, 2015
Title genomic DNA from IPSC-derived DAn SP-06-L2PD
Sample type genomic
 
Source name 30-days neuron-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: 6
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: 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_R01C02
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
E-mail(s) ezquerra@clinic.cat
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
ID_REF
VALUE Average beta values

Data table
ID_REF VALUE
cg00014152 0.881020788
cg00021786 0.966025516
cg00072839 0.030047968
cg00074638 0.544144228
cg00266918 0.079298246
cg00378717 0.025433526
cg00378950 0.864763009
cg00381376 0.031747154
cg00388637 0.6159662
cg00423014 0.680652174
cg00457389 0.040861759
cg00551957 0.918005214
cg00573298 0.033095272
cg00685229 0.237550395
cg00697812 0.795899348
cg00751785 0.035074195
cg00812634 0.945252507
cg00824273 0.776876499
cg00824714 0.934495786
cg00839572 0.021612265

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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