NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2392420 Query DataSets for GSM2392420
Status Public on Nov 16, 2016
Title SFC828-03-04
Sample type genomic
 
Source name induced pluripotent stem cell line derived from dermal fibroblasts, SNCA A53T donor 828, clone 4
Organism Homo sapiens
Characteristics cell type: induced pluripotent stem cell line derived from dermal fibroblasts
genotype/variation: SNCA A53T
gender: female
Treatment protocol untreated cell samples; Fibroblasts grown in ADMEM + 10% FCS; iPSc lines all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest
Extracted molecule genomic DNA
Extraction protocol genomic DNA was extracted using QIAGEN DNeasy blood and tissue kit
Label Biotin (C, G), Dinitrophenyl (A, T)
Label protocol Standard Illumina labelling protocol
 
Hybridization protocol Standard Illumina hybridisation protocol
Scan protocol Standard Illumina scanning protocol for BeadChip Arrays
Description mTeSR-1 + matrigel
single replicate
humanomniexpress_24v1-0_a
Data processing The scanned data files were processed by GenomeStudio Genotyping module v1.9, using the cluster file and manifest HumanCytoSNP-12v2-1_H provided by Illumina for GPL13829, and humanomniexpress_24v1-0_a or humanomniexpress-24-v1-1-a for GPL19699 as indicated (sheets GPL19699 1-0 and GPL19699 1-1 respectively). Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).
 
Submission date Nov 15, 2016
Last update date Nov 16, 2016
Contact name Sally A Cowley
E-mail(s) sally.cowley@path.ox.ac.uk
Phone +44 (0) 1865 275600
Organization name University of Oxford
Department Sir William Dunn School of Pathology
Lab James Martin Stem Cell Facility
Street address South Parks Road
City Oxford
ZIP/Postal code OX1 3RE
Country United Kingdom
 
Platform ID GPL21168
Series (2)
GSE89878 Gene expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring amplification of, or mutations in the SNCA gene, and from healthy control donors [genotype]
GSE89886 Gene expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harbouring amplification of, or mutations in the SNCA gene, and from healthy control donors

Data table header descriptions
ID_REF
VALUE Genotype (AA, AB, BB, NC[--])
SFC828-03-04.Score
SFC828-03-04.Theta
SFC828-03-04.R
SFC828-03-04.B Allele Freq
SFC828-03-04.Log R Ratio

Data table
ID_REF VALUE SFC828-03-04.Score SFC828-03-04.Theta SFC828-03-04.R SFC828-03-04.B Allele Freq SFC828-03-04.Log R Ratio
rs1000000 AB 0.7713807 0.4429884 1.986262 0.5270392 -0.04998989
rs1000002 AB 0.8739321 0.5039868 1.419453 0.5601078 0.3129652
rs10000023 AB 0.8232387 0.4582367 2.14886 0.4943827 -0.0272589
rs1000003 AA 0.8941414 0.03631173 1.133566 0.008390915 -0.1108717
rs10000030 BB 0.7495437 0.9314815 0.7473224 1 0.4783439
rs10000037 AB 0.866731 0.4401415 1.283191 0.5194244 -0.04062228
rs10000041 AA 0.9013059 0.06353381 1.25337 0.03918864 0.09898832
rs10000042 BB 0.7429622 0.9491844 1.037924 0.9945877 0.1220009
rs10000049 AA 0.3681846 0.04074695 1.149563 0 -0.146567
rs1000007 AA 0.9101931 0.03435154 1.024925 0.01467032 -0.1213274
rs10000073 AA 0.8821601 0.04027771 0.8797365 0.0194183 -0.1095967
rs10000081 AA 0.8843419 0.05317772 0.9531617 0.01134296 0.2849146
rs10000092 AA 0.8239049 0.06072126 0.6441708 0.035783 -0.2992567
rs10000105 BB 0.8521731 0.9739789 1.189468 1 0.2314887
rs10000119 BB 0.8816444 0.9758756 1.303402 1 0.05642389
rs10000124 BB 0.7992214 0.9733486 1.40627 1 -0.06171197
rs10000154 AA 0.8964227 0.04600644 1.003847 0.02099724 0.04241335
rs1000016 AA 0.8463081 0.004968455 1.457068 0 -0.03090407
rs10000160 BB 0.8386789 0.967336 1.211941 1 0.197387
rs10000169 AB 0.9009966 0.5252383 1.2278 0.4772418 0.09315043

Total number of rows: 716503

Table truncated, full table size 42344 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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