| Sample_geo_accession | GSM575149
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| Sample_status | Public on Aug 03 2011
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| Sample_submission_date | Aug 04 2010
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| Sample_last_update_date | Aug 03 2011
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| Sample_type | RNA
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| Sample_channel_count | 1
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| Sample_organism_ch1 | Homo sapiens
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| Sample_taxid_ch1 | 9606
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| Sample_treatment_protocol_ch1 | MzChA1 cells were treated with felodipine (20uM) or diluent control for 24 hrs and then collected for RNA extraction
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| Sample_growth_protocol_ch1 | MzChA1 cells were cultured in 100mm dishes with CMRL medium
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| Sample_molecule_ch1 | total RNA
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| Sample_extract_protocol_ch1 | RNA was extracted with RNeasy mini kit (Qiagen, Valencia, CA)
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| Sample_label_ch1 | biotin
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| Sample_label_protocol_ch1 | labelling was performed according to the Affymetrix (Santa Clara, CA) GeneChip Whole Transcript (WT) Sense Target Labelling Assay manual
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| Sample_hyb_protocol | microarrays were hybridized overnight with 5 mg biotin labelled ss-cDNA, and washed in fluidics station wash protocol: MES_EukGE-WS2v5_450
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| Sample_scan_protocol | Genechip scanner 3000 7G
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| 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.
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| Sample_data_processing | Background Correction: Arrays are corrected for background the method described in Robust Multi-array 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
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| Sample_data_processing = PM | S + B ~ Exp(Lambda) + N(Mu,Sigma^2)
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| 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:
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| 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 PM-Mu (for PM values greater than Mu - Mu).
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| 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
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| Sample_data_processing = E(S|PM) | PM - Mu - Lambda * Sigma^2 + (Sigma * StdNormPDF(a) / (StdNormCDF(a) - 1) )
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| 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=(PM-Mu-Lambda*Sigma^2)/Sigma.
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| Sample_data_processing | The PDF estimate used for parameter estimation is a kernel density estimate using the Epanechnikov kernel and 2^14 data points.
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| Sample_data_processing | Transformation: Probe scores were then transformed by taking the Base-2 Logarithm of 0 plus the probe score.
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| Sample_data_processing | Estimating Gene (probe-set) Expression From Probe Scores (Summarization)
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| 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.
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| 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))
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| 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))
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| Sample_data_processing = Until stop criteria: Max Number Iteration | 5 or all medians less than 0.05
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| 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 TO-T. Mismatch (MM) probes are not used in this step.
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| Sample_platform_id | GPL570
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| Sample_contact_name | Tushar,,Patel
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| Sample_contact_email | patel.tushar@mayo.edu
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| Sample_contact_laboratory |
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| Sample_contact_department |
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| Sample_contact_institute | Mayo Clinic
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| Sample_contact_address | 4500 San Pablo Road
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| Sample_contact_city | Jacksonville
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| Sample_contact_state | FL
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| Sample_contact_zip/postal_code | 32224
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| Sample_contact_country | USA
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| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM575nnn/GSM575149/suppl/GSM575149.CEL.gz
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| Sample_series_id | GSE23427
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| Sample_data_row_count | 54675
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