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Title: Transcription profiling of two rat cell lines using different blocking reagents and doses to optimize cDNA microarray procedures without using an external standard      
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available
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instance of dataset
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not applicable
refinement:
curated
dateReleased:
05-02-2014
ID:
E-TABM-202
description:
We performed a dye-swap microarray experiment using a total of 24 Rat 15k cDNA duplicates microarrays. The study included RNA from samples with high expected differential gene expression termed ‘high contrasts’ compared to self-self hybridization (rat cell lines AR42J and NRK52E). We than optimized a pipeline to maximize the number of genes found differentially expressed between the two different RNA samples while at the same time making sure that the methodology finds no differentially expressed genes in self–self experiments with the same cell lines. In this high-contrast vs. self-self method (HCSSM) significantly expressed genes is determined by estimating the false discovery rate (FDR) using a null distribution obtained from self-self experiment. The optimization criterion requires only 4 microarrays per evaluation, and the effects of blocking reagent dose, filtering, and background corrections methodologies were investigated. In our experiments a dose of 250 ng LNA dT blocker gave the highest number of differentially expressed genes. When the criterion was used to evaluate steps in the computational analysis of microarray data we found that no background correction and weight based filtering gave the largest number of differentially expressed genes. Background correction method, however, has a greater influence on the number of differentially expressed genes found than filtering.
keywords:
transcription profiling by array
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HTML
storedIn:
Array Express
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not compressed
accessType:
landing page
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none
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accessURL: https://www.ebi.ac.uk/arrayexpress/experiments/E-TABM-202
format:
JSON
storedIn:
OmicsDI
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accessType:
download
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false
accessURL: www.omicsdi.org/ws/dataset/arrayexpress-repository/E-TABM-202.json
format:
XML
storedIn:
OmicsDI
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not compressed
accessType:
download
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none
authentication:
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primary:
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accessURL: http://www.omicsdi.org/ws/dataset/arrayexpress-repository/E-TABM-202.xml
ID:
SCR:014747
name:
Omics Discovery Index
abbreviation:
OmicsDI
homePage: http://www.omicsdi.org/