treatment: GY118F iPS cells derived and maintained in N2B27 plus GCSF from which GCSF was withdrawn for 12 hours strain: 129xMF1 origin: adult neural stem cells gender: female cell type: iPSC transgene: GY118F
Extracted molecule
total RNA
Extraction protocol
Qiagen RNeasy kit
Label
biotin
Label protocol
Ambion's Illumina TotalPrep-96 RNA Amplification protocol for the amplification and labelling
Hybridization protocol
Illumina Hybridisation protocol
Scan protocol
Bead array Reader from Illumina
Data processing
The data were loaded into the R package lumi (Du, P., Kibbe, W. A. & Lin, S. M. lumi: a pipeline for processing Illumina microarray. Bioinformatics 24, 1547-1548 (2008)). A given probe needed to abide to the Illumina detection p-value of 0.01 in at least one of the samples. If failing this probe was excluded from analysis to prevent noise. Subsequently the data was transformed using variance stabilisation (Lin, S. M., Du, P., Huber, W. & Kibbe, W. A. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res 36, e11 (2008)) and then normalised using quantile normalisation.
Submission date
Mar 26, 2012
Last update date
May 01, 2012
Contact name
Jose Silva
Organization name
University of Cambridge, centre for stem cell research
A given probe needed to abide to the Illumina detection p-value of 0.01 in at least one of the samples. If failing this probe was excluded from analysis to prevent noise. Subsequently the data was transformed using variance stabilisation (Lin, S. M., Du, P., Huber, W. & Kibbe, W. A. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res 36, e11 (2008)) and then normalised using quantile normalisation.
