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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of cultured human cells response to stress (heat shock)

ABSTRACT: TT3 and TN are cell cycle time courses and should be centered or transformed before clustering or computing fourier scores. The preferred method is SVD centering preceded by KNNImpute missing-value estimation, although mean-centering is a viable alternative. Hela Heat 42 degrees time course has 2 zeroes (the second is labeled "Cold 25 degrees 0h"). Normalization is by centering or zero transformation (average 2 zeroes) WI38 Crowding (1-3 days) was by plating cells at ~50%? confluence and allowing to age. The zeroes are the same as for WI38 Heat Shock (there are 2) Other time courses should be self-explanatory. They have 1-4 zeroes each and can be treated either by centering or zero-transforming. WI38

ORGANISM(S): Homo sapiens

SUBMITTER: Janos Demeter

PROVIDER: E-SMDB-1577 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Diverse and specific gene expression responses to stresses in cultured human cells.

Murray John Isaac JI Whitfield Michael L ML Trinklein Nathan D ND Myers Richard M RM Brown Patrick O PO Botstein David D

Molecular biology of the cell 20040305 5

We used cDNA microarrays in a systematic study of the gene expression responses of HeLa cells and primary human lung fibroblasts to heat shock, endoplasmic reticulum stress, oxidative stress, and crowding. Hierarchical clustering of the data revealed groups of genes with coherent biological themes, including genes that responded to specific stresses and others that responded to multiple types of stress. Fewer genes increased in expression after multiple stresses than in free-living yeasts, which ...[more]

PMID: 15004229

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Diverse and specific gene expression responses to stresses in cultured human cells.

Project description:TT3 and TN are cell cycle time courses and should be centered or transformed before clustering or computing fourier scores. The preferred method is SVD centering preceded by KNNImpute missing-value estimation, although mean-centering is a viable alternative. Hela Heat 42 degrees time course has 2 zeroes (the second is labeled "Cold 25 degrees 0h"). Normalization is by centering or zero transformation (average 2 zeroes) WI38 Crowding (1-3 days) was by plating cells at ~50%? confluence and allowing to age. The zeroes are the same as for WI38 Heat Shock (there are 2) Other time courses should be self-explanatory. They have 1-4 zeroes each and can be treated either by centering or zero-transforming. WI38 Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

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Diverse and specific gene expression responses to stresses in cultured human cells.

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Listeria infection of Caco-2 cells

Project description:This experiment set contains all of the arrays described in Baldwin et al., Genome Biology, 2002. All experiments are time courses, with the exception of multiple measurements for the zero time point in the parallel time course for the purpose of zero transformation. The parallel four hour time course was performed on a single day and three independent measurements were taken prior to infection. The eight hour time courses were each performed on different days, with single time zero measurements. Each array represents a measurement of human mRNA from cultured intestinal epithelial cells (red channel), relative to the control reference pool of mRNA (green channel), at different time points during the course of an infection by Listeria monocytogenes, or the mutants actA (defective in actin-based motility) and prfA (defective in virulence factor gene expression). Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set

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Project description:Mouse HSF1+/+ and HSF1-/- Fibroblasts Heat Shock Time Courses Scanned on Scanner 7 (Axon 4000B)

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