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Sample GSM2392414 Query DataSets for GSM2392414
Status Public on Nov 16, 2016
Title SF829
Sample type genomic
 
Source name dermal fibroblasts, SNCA A53T donor 829
Organism Homo sapiens
Characteristics cell type: dermal fibroblasts
genotype/variation: SNCA A53T
gender: male
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 ADMEM + 10% FCS
single replicate
HumanCytoSNP-12v2-1_H
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 GPL13829
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[--])
SF829.Score
SF829.Theta
SF829.R
SF829.B Allele Freq
SF829.Log R Ratio

Data table
ID_REF VALUE SF829.Score SF829.Theta SF829.R SF829.B Allele Freq SF829.Log R Ratio
cnvi0111185 NC 0 0.9633911 1.335218 0.9859269 0.06025575
cnvi0111186 NC 0 0.03909028 0.6456076 0.01241254 0.3216212
cnvi0111187 NC 0 0.9853882 1.367704 1 -0.1320846
cnvi0111188 NC 0 0.01120468 1.349046 0 0.02968085
cnvi0111189 NC 0 0.03571844 1.50792 0.01371048 0.03191839
cnvi0111190 NC 0 0.02029381 0.6833352 0 0.635511
cnvi0111191 NC 0 0.0663661 0.4427009 0.03186312 -1.040357
cnvi0111192 NC 0 0.02471723 1.039552 0.003473785 -0.1400086
cnvi0111193 NC 0 0.01789937 1.192141 0.007082988 0.04443798
cnvi0111194 NC 0 0.983791 1.125262 0.9967669 -0.1577427
cnvi0111195 NC 0 0.03844458 2.00167 0.009306427 -0.09794982
cnvi0111196 NC 0 0.9848337 1.096489 0.9987612 -0.1729055
cnvi0111197 NC 0 0.01966433 1.026414 0.001581262 0.2656638
cnvi0111198 NC 0 0.9722565 1.26848 1 -0.0839983
cnvi0111199 NC 0 0.0323743 1.322582 0.02185819 -0.05866228
cnvi0111200 NC 0 0.9868347 0.9141188 0.9998927 0.1269181
cnvi0111201 NC 0 0.05307844 0.9509993 0.02551649 0.1192092
cnvi0111202 NC 0 0.9276477 1.262525 0.9818406 -0.08849207
cnvi0111203 NC 0 0.01903987 1.714139 0 -0.1082514
cnvi0111204 NC 0 0.9858585 1.209073 0.997135 0.0734527

Total number of rows: 298563

Table truncated, full table size 17886 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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