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Sample GSM2392487 Query DataSets for GSM2392487
Status Public on Nov 16, 2016
Title SFC831-03-01
Sample type RNA
 
Source name induced pluripotent stem cell line derived from dermal fibroblasts, SNCA triplication donor 831, clone 1
Organism Homo sapiens
Characteristics cell type: induced pluripotent stem cell line derived from dermal fibroblasts
gender: female
disease state: Parkinson's disease
genotype/variation: SNCA triplication
Treatment protocol untreated cell samples, all grown in mTeSR-1 medium + ES-qualified matrigel prior to harvest
Extracted molecule total RNA
Extraction protocol RNA was extracted using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit and with on-column Dnase treatment. Quality control was performed with Agilent Bioanalyser and was RIN 10 for each sample.
Label biotin
Label protocol Biotinylated cRNA were prepared as standard for Illumina arrays, by Wellcome Trust Centre for Human Genomics, Oxford
 
Hybridization protocol Standard Illumina hybridization protocol
Scan protocol Standard Illumina scanning protocol
Description single replicate
Data processing Quality control results were within expected range. The data were normalised using cubic spline normalisation with background subtraction in GenomeStudio v2011.1 Gene Expression module 1.9.0. Missing values were imputed by the software. Manifest file used was HumanHT-12_V4_R2_15002873_B
 
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 GPL10558
Series (2)
GSE89883 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 [gene expression]
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 cubic spline normalized
Detection Pval

Data table
ID_REF VALUE Detection Pval
ILMN_1762337 16.33603 0.187013
ILMN_2055271 49.58371 0.02727273
ILMN_1736007 21.12302 0.1337662
ILMN_2383229 -12.26842 0.8428571
ILMN_1806310 1.782421 0.4025974
ILMN_1779670 4.280635 0.3649351
ILMN_1653355 22.67545 0.1181818
ILMN_1717783 -13.05963 0.8623376
ILMN_1705025 -2.328994 0.5298702
ILMN_1814316 21.54706 0.1298701
ILMN_2359168 -8.892809 0.7272727
ILMN_1731507 -18.19148 0.9428571
ILMN_1787689 21.26009 0.1337662
ILMN_3241953 102.1283 0.002597403
ILMN_1745607 -20.15236 0.9805195
ILMN_2136495 8.960524 0.2818182
ILMN_1668111 -5.604871 0.6168831
ILMN_2295559 -9.305088 0.7415584
ILMN_1735045 10.15259 0.2545455
ILMN_1680754 40.01865 0.04155844

Total number of rows: 47323

Table truncated, full table size 1403 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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