Sample_geo_accession  GSM575149

Sample_status  Public on Aug 03 2011

Sample_submission_date  Aug 04 2010

Sample_last_update_date  Aug 03 2011

Sample_type  RNA

Sample_channel_count  1

Sample_organism_ch1  Homo sapiens

Sample_taxid_ch1  9606

Sample_treatment_protocol_ch1  MzChA1 cells were treated with felodipine (20uM) or diluent control for 24 hrs and then collected for RNA extraction

Sample_growth_protocol_ch1  MzChA1 cells were cultured in 100mm dishes with CMRL medium

Sample_molecule_ch1  total RNA

Sample_extract_protocol_ch1  RNA was extracted with RNeasy mini kit (Qiagen, Valencia, CA)

Sample_label_ch1  biotin

Sample_label_protocol_ch1  labelling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual

Sample_hyb_protocol  microarrays were hybridized overnight with 5 mg biotin labelled sscDNA, and washed in fluidics station wash protocol: MES_EukGEWS2v5_450

Sample_scan_protocol  Genechip scanner 3000 7G

Sample_data_processing  Normalization: The input files were normalized with full quantile normalization (Irizarry et al 2003). For each input array, for each probe expression value, the array ith percentile probe value was replaced with the average of all array ith percentile points.

Sample_data_processing  Background Correction: Arrays are corrected for background the method described in Robust Multiarray Average (RMA). (Irrizary, et al 2003). After normalization, the array probe values are adjusted for background by assuming that Perfect Match (PM) probe scores are distributed as the sum of independent Exponential (S=Signal) and Normal (B=Background) distributions. Or

Sample_data_processing = PM  S + B ~ Exp(Lambda) + N(Mu,Sigma^2)

Sample_data_processing  The signal Exponential distribution has parameter lambda and the normal distribution has parameters mu, and sigma^2. For each array (hybridization) These parameters are estimated from an estimated probability density function (PDF) as follows. For a single array (or hybridization) let M_PM be the overall mode (the highest point) of the estimated CDF:

Sample_data_processing = Mu  mode of PM values such that PM is less than M_PM (PM 
Sample_data_processing = Sigma^2  (2 * Sum{PM 
Sample_data_processing = Lambda  mode of PMMu (for PM values greater than Mu  Mu).

Sample_data_processing  For each PM probe, the background corrected value is the Expected value of S given the observed PM which is given by Irrizary et al as

Sample_data_processing = E(SPM)  PM  Mu  Lambda * Sigma^2 + (Sigma * StdNormPDF(a) / (StdNormCDF(a)  1) )

Sample_data_processing  Where StdNormPDF is the probability density function of the standard Normal distribution and StdNormCDF(a) is the integral from negative infinity to a of StdNormPDF. The variable a=(PMMuLambda*Sigma^2)/Sigma.

Sample_data_processing  The PDF estimate used for parameter estimation is a kernel density estimate using the Epanechnikov kernel and 2^14 data points.

Sample_data_processing  Transformation: Probe scores were then transformed by taking the Base2 Logarithm of 0 plus the probe score.

Sample_data_processing  Estimating Gene (probeset) Expression From Probe Scores (Summarization)

Sample_data_processing = After normalization, background correction, and transformation, the perfect match (PM) probe scores were combined to estimate a gene level for each chip by means of median polish developed by Tucky and applied to microarray analysis by Irrizary et al. Specifically, Let TO be a table where, for a particular gene, the rows are chips and the columns are probes so that TO(i,j) is the score of the jth probe on the ith chip. First let T  TO and then alternately sweep rows and columns of T until a stopping criteria is met.

Sample_data_processing  Sweep Rows: For each chip i subtract the median of row i, R(i), from T (i.e. T(i,j)=T(i,j)R(i))

Sample_data_processing  Sweep Columns: For each chip i subtract the median of column j, C(j), from T (i.e. T(i,j)=T(i,j)R(j))

Sample_data_processing = Until stop criteria: Max Number Iteration  5 or all medians less than 0.05

Sample_data_processing  The values remaining in T are residuals after probe and chip effects have been removed and the final estimate of the expression of chip i is the row i average of TOT. Mismatch (MM) probes are not used in this step.

Sample_platform_id  GPL570

Sample_contact_name  Tushar,,Patel

Sample_contact_email  patel.tushar@mayo.edu

Sample_contact_laboratory 

Sample_contact_department 

Sample_contact_institute  Mayo Clinic

Sample_contact_address  4500 San Pablo Road

Sample_contact_city  Jacksonville

Sample_contact_state  FL

Sample_contact_zip/postal_code  32224

Sample_contact_country  USA

Sample_supplementary_file  ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575149/suppl/GSM575149.CEL.gz

Sample_series_id  GSE23427

Sample_data_row_count  54675

