Affymetrix GeneChip Rat Genome U34A [RG_U34A]

Hormone-Induced Protection against Mammary Tumorigenesis Is Conserved in Multiple Rat Strains and Identifies a Core Gene Expression Signature Induced by Pregnancy

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Microarray analysis of parity induced gene expression changes in the mammary glands of four strains of rats to identify a common gene signature associated with protection against methylnitrosourea induced mammary tumorigenesis.

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strain

Transcription profiling of mammary glands from virgin or parous rats of four strains

Microarray analysis of parity induced gene expression changes in the mammary glands of four strains of rats to identify a common gene signature associated with protection against methylnitrosourea induced mammary tumorigenesis.


Affymetrix:Protocol:Hybridization-Unknown

P-AFFY-2

Labeling of samples was carried out according to the manufacturer’s standard protocol

P-AFFY-6

Title: Affymetrix CEL analysis. Description:

P-MEXP-34720

Snap-frozen tissue was homogenized in guanidine thiocyanate supplemented with 7 µl/ml 2-mercaptoethanol, and RNA isolated by centrifugation through cesium chloride as previously described (Chirgwin et al., Biochemistry 18, p5294-5299 1979).

P-TABM-1087

Expression values for individual hybridized samples were generated as log2 values using the standard "justRMA" function in the Bioconductor "affy" library. CEL files for all rat strains were normalized together. Fold change values for parous over virgin gene expression were calculated for each strain separately by taking the antilog of the difference between the mean log2 expression in the virgin and parous glands. For hierachical clustering the median log2 expression in the virgin and parous samples for each strain was used.

P-TABM-1088

Lewis, Wistar-Furth, Fischer 344, and Copenhagen rats (Harlan, Indianapolis, IN) were housed under 12-hour light/12-hour dark cycles with access to food and water ad libitum. Animal care was performed according to institutional guidelines. To generate parous (G1P1) rats, 9-week-old females were mated and allowed to lactate for 21 days after parturition. After 28 days of postlactational involution, rats were sacrificed by carbon dioxide asphyxiation and the abdominal mammary glands were harvested and snap-frozen. Tissues were harvested from age-matched nulliparous (G0P0) animals in an identical manner. After extraction with the indicated protocol ten micrograms of RNA was used for labelling for each sample. For the Lewis strain material from 3 animals was pooled for each sample hybridized. For the other three strains all arrays were derived from individual animals.

Hormone-induced protection against mammary tumorigenesis is conserved in multiple rat strains and identifies a core gene expression signature induced by pregnancy.

Transcription profiling of mammary glands from virgin or parous rats of four strains

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