Unknown,Transcriptomics,Genomics,Proteomics

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On the relevance of technical variation due to building pools in microarray experiments

ABSTRACT: The objective of the study was to assess the technical error due to blending of individual samples into pools in experimental data. The blending error variance component corresponds to random effects for inaccuracies, which were modeled on the logarithmic scale of normalized gene expression. It's estimation based on a linear mixed model, fitted for each transcript. Ovaries from 30 animals of line FL1 and of the control line DUKsi were collected at the metestrous stage. They were combined to 6 pools of 5 individuals each and processed for microarray analysis. Additionally, the 10 individuals used for the first two pools of each line were processed.

ORGANISM(S): Mus musculus

SUBMITTER: Henrik Rudolf

PROVIDER: E-GEOD-72861 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Liver and BAT expression differences between the fat F-line, and congenic Fob3b-line. Normalised data appended as follows: TABLE 1: LIVER - 1st set (7.5K) of the 2 slide NIA NIH 15K set -source1 = F-line liver male - 2 pools each made from 5 different individuals -source2 = Fob3b-line (aka Fchr15D-line) liver male - 2 pools each made from 5 different individuals -values are normalised using mixed model across 6 slides: 1 F-line vs Fline 2 Fob3b-line vs Fob3b-line 3 F-line pool1 vs Fob3b-line pool1 4 F-line pool1 vs Fob3b-line pool1 -dye swap 5 F-line pool2 vs Fob3b-line pool2 6 F-line pool2 vs Fob3b-line pool2 -dye swap TABLE 2: LIVER - 2nd set (7.5K) of the 2 slide NIA NIH 15K set -source1 = F-line liver male - 2 pools each made from 5 differnt individuals -source2 = Fob3b-line (aka Fchr15D-line) liver male - 2 pools each made from 5 differnt individuals -values are normalised using mixed model across 6 slides: 1 F-line Vs F-line 2 Fob3b-line vs Fob3b-line 3 F-line pool1 vs Fob3b-line pool2 4 F-line pool1 vs Fob3b-line pool2 dye swap 5 F-line pool2 vs Fob3b-line pool1 6 F-line pool2 vs Fob3b-line pool1 dye swap TABLE 3: Brown Adipose Tissue (BAT) 1st (7.5K) array set of 15K NIA NIH set -source1 = F-line male BAT from 2 pools each made from 5 different individuals -source2 = Fob3b-line (aka Fchr15D-line) male BAT from 2 pools each made from 5 different individuals -values are normalised using mixed model across 4 slides: 1 F-line pool1 vs Fob3b-line pool1 2 F-line pool1 vs Fob3b-line pool1 dye swap 3 F-line pool2 vs Fob3b-line pool2 4 F-line pool2 vs Fob3b-line pool2 dye swap TABLE 4: Brown Adipose Tissue (BAT) 2nd (7.5K) array of the 15K NIA NIH set -source1 = F-line male BAT (2 pools each from 5 individual mice) -source2 = Fob3b-line (aka Fchr15D-line) male BAT (2 pools each from 5 individual mice) -values are normalised using mixed model across 4 slides: 1 F-line pool1 vs Fob3b-line pool1 2 F-line pool1 vs Fob3b-line pool1 dye swap 3 F-line pool2 vs Fob3b-line pool2 4 F-line pool2 vs Fob3b-line pool2 dye swap Keywords = Obesity Keywords = Fob3b Keywords = QTL Keywords = congenic Keywords: other

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On the relevance of technical variation due to building pools in microarray experiments

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