NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM1255295 Query DataSets for GSM1255295
Status Public on Dec 01, 2015
Title genomic DNA from IPSC-derived DAn SP-15-CON
Sample type genomic
 
Source name 30 days-neuron control
Organism Homo sapiens
Characteristics patient id: SP-15
patient id2: C-01
gender: female
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): 47
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 7990895162_R02C01
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 0.84809061
cg00021786 0.882725379
cg00072839 0.079945001
cg00074638 0.535822952
cg00266918 0.089680326
cg00378717 0.017083217
cg00378950 0.807011988
cg00381376 0.038005824
cg00388637 0.67344147
cg00423014 0.64600539
cg00457389 0.030548333
cg00551957 0.825848457
cg00573298 0.025275678
cg00685229 0.346088145
cg00697812 0.698509846
cg00751785 0.028074169
cg00812634 0.91298377
cg00824273 0.692792095
cg00824714 0.698643574
cg00839572 0.033512532

Total number of rows: 478178

Table truncated, full table size 10697 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap