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Sample GSM2392479 Query DataSets for GSM2392479
Status Public on Nov 16, 2016
Title SFC840-03-06
Sample type RNA
 
Source name induced pluripotent stem cell line derived from dermal fibroblasts, control donor 840, clone 6
Organism Homo sapiens
Characteristics cell type: induced pluripotent stem cell line derived from dermal fibroblasts
gender: female
disease state: control
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 14.88901 0.1792208
ILMN_2055271 39.8765 0.03766234
ILMN_1736007 -6.480113 0.648052
ILMN_2383229 -8.487669 0.7103896
ILMN_1806310 22.89422 0.1194805
ILMN_1779670 6.957784 0.2974026
ILMN_1653355 21.25636 0.1337662
ILMN_1717783 -22.67924 0.9974026
ILMN_1705025 6.002859 0.3116883
ILMN_1814316 -9.086791 0.7350649
ILMN_2359168 -9.501353 0.7597402
ILMN_1731507 -20.79917 0.9831169
ILMN_1787689 25.14028 0.1012987
ILMN_3241953 146.31 0.001298701
ILMN_1745607 -7.910023 0.6961039
ILMN_2136495 -2.261067 0.5103896
ILMN_1668111 3.380888 0.3636364
ILMN_2295559 -4.677494 0.5844156
ILMN_1735045 35.49414 0.05454545
ILMN_1680754 49.21438 0.02207792

Total number of rows: 47323

Table truncated, full table size 1401 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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