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Sample GSM2644522 Query DataSets for GSM2644522
Status Public on Jun 01, 2017
Title SFC848-03-02
Sample type genomic
 
Source name induced pluripotent stem cell line derived from dermal fibroblasts, control donor 848, clone 2
Organism Homo sapiens
Characteristics gender: male
donor: control donor
culture conditions: mTeSR-1 + matrigel
cell type: induced pluripotent stem cells derived from dermal fibroblasts
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 hybridization protocol
Scan protocol Standard Illumina scanning protocol for BeadChip Arrays
Description single replicate
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_24v1-1_a for GPL22678. Raw data was also uploaded to KaryoStudio (Illumina) for generation of karyotype reports (see publication).
 
Submission date May 31, 2017
Last update date Jun 01, 2017
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 GPL22678
Series (2)
GSE99471 SNP genotype data from induced Pluripotent Stem cells from Parkinson's Disease patients harboring mutations in the GBA1 gene, and from healthy control donors
GSE99473 SNP Genotype and Gene Expression data from induced Pluripotent Stem cells from Parkinson's Disease patients harboring mutations in the GBA1 gene, and from healthy control donors

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

Data table
ID_REF VALUE GCScore Theta R B Allele Freq Log R Ratio
rs1000000 AB 0.7878883 0.39274 2.085935 -0.07528235 0.4603263
rs1000002 AA 0.879837 0.03082416 0.9529991 -0.115765 0.0173315
rs10000023 AB 0.7550569 0.4107465 2.19252 -0.01649307 0.4436004
rs1000003 AA 0.7900333 0.04020992 1.639437 0.003046721 0.007750829
rs10000030 AB 0.7818998 0.6583051 0.9945916 0.3599322 0.4825787
rs10000037 AB 0.8993763 0.4624286 1.405386 0.03305494 0.5387679
rs10000041 AA 0.9236166 0.04606439 1.137496 0.03411753 0.01875955
rs10000042 BB 0.7844193 0.9730771 1.022915 0.09203462 1
rs10000049 AA 0.4321642 0.04949958 1.275566 0.01005971 0.01402566
rs1000007 AA 0.908865 0.02527229 0.9775095 0.04983227 0.004006688
rs10000073 AA 0.9258915 0.04826476 1.092496 0.004987465 0.01909006
rs10000081 AA 0.9052351 0.0259502 0.9922419 0.2291797 0
rs10000092 AB 0.839045 0.4908023 1.091678 0.1192909 0.5327391
rs10000105 BB 0.8648784 0.9567782 1.116943 0.1073376 0.9777977
rs10000119 BB 0.9077633 0.9712467 1.244313 -0.03256079 0.9993447
rs10000124 BB 0.8103635 0.9710649 1.376433 -0.1297794 0.9977136
rs10000154 AB 0.9269766 0.5245588 1.213326 0.08917938 0.5014409
rs1000016 AA 0.8704742 0.02689309 1.354689 -0.04570321 0.01265937
rs10000160 BB 0.9014667 0.9556577 1.078498 0.02143921 0.9898367
rs10000169 AB 0.9196957 0.5502865 1.263777 0.05450578 0.4944546

Total number of rows: 713014

Table truncated, full table size 43242 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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