In contrast, recently developed genomics enables to employ thousands of genes as parameters to assess diverse biological phenomena on a single platform such as gene expression profiling.

Thus, the integration of genomics into toxicology should exploit novel fields for the biological assessment of substances, describing alterations after exposure of substances to animals or cultured cells with multiple parameters in a single platform across diverse specimens.

In this study, we administered five chemical substances - methacrylamide, sulfolane, 2-iso-propoxyethanol, hydrazine monohydrate, and 4-ethylmorpholine - independently to male for 28 days repeatedly, prepared multiple tissue samples of each animal, and comprehensively investigated gene expression levels in the prostate with DNA microarrays containing probes representing approximately 11,000 species of rat transcripts.

We expect the data obtained in this study may contribute to establish novel accurate approaches for the assessment of chemical substances existing and generated in the future by comparing with the previously accumulated findings obtained by repeated dose 28-day oral administration to rats. Submitter: First name Watanabe Last name Shinya Organization Fukushima Medical University Department Clinical Genomics Address 3-8-22 Sendagaya, Shibuya-ku, Tokyo 151-0051, Japan Reference: Title Gene expression profile analysis of rat prostate exposed by chemical compouds Author Shinya Watanabe, et al. Protocol: Name Array Design Protocol (Rat) Description A set of synthetic polynucleotides (80-mers) representing 11,468 species of rat transcript sequences that are mostly originated from the Reference Sequence (RefSeq) project clones deposited in the National Center for Biotechnology Information (NCBI) database was purchased (MicroDiagnostic, Tokyo, Japan) and printed on a glass slide (coated glass slide for the microarray, type I; Matsunami Glass Ind., Ltd., Kishiwada, Japan) with a custom-made arrayer. Name Growth Condition Protocol (rat) Description Six-week-old male Sprague Dawley rats (Charles River Laboratory) were purchased and housed in a room maintained at 23°C±2°C with 55%±10% relative humidity, and lighting was maintained for 12 hr daily. All animals were allowed free access to commercial rodent chow, MF (Oriental Yeast Co.) and to tap water Name Treatment Protocol 1 (WFI) Description Water for injection was orally administered daily for 28 days to male Sprague Dawley rats. Name Treatment Protocol 2 (mca) Description Methacrylamide was orally administered daily to male Sprague-Dawley rats at 150 mg/kg for 28 days. Name Treatment Protocol 3 (suf) Description Sulfolane was orally administered daily to male Sprague Dawley rats at 700 mg/kg for 28 days. Name Treatment Protocol 4 (2ip) Description 2-iso-propoxyethanol was orally administered daily to maleSprague Dawley rats at 500 mg/kg for 28 days. Name Treatment Protocol 5 (hmh) Description Hydrazine monohydrate was orally administered daily to male Sprague Dawley rats at 30 mg/kg for 28 days Name Treatment Protocol 6 (4em) Description 4-Ethylmorpholine was orally administered daily to male Sprague Dawley rats at 500 mg/kg for 28 days Name Extraction Protocol Description The obtained solid organs were immediately frozen in liquid nitrogen and lysed with an ISOGEN reagent (NIPPON GENE). Total RNA was prepared from the lysate according to the manufacturer’s instructions. Poly(A)+ RNA was prepared from total RNA with a Poly(A)Purist Kit (Ambion, TX, USA), according to the manufacturers instructions. Name Labelling Protocol (rat) Description Labeling, hybridization and subsequent washes of microarrays were performed with a Labeling & Hybridization Kit (MicroDiagnostic), according to the manufacturer’s instructions. Name Hybridization Protocol Description Hybridization and subsequent washes of arrays were performed with a Labeling and Hybridization Kit (MicroDiagnostic, Tokyo, Japan). Name Scanning Protocol Description Hybridization signals were measured with a GenePix 4000B scanner (Axon Instruments Inc., Union City, CA). Name Image Analysis Protocol Description Measured hybridization signals were processed into primary expression ratios (ratios of cyanine 5 intensity of each sample to cyanine 3 intensity of the rat common reference RNA) by the GenePix Pro 6.0 software (Axon Instruments Inc.). Name Normalization Protocol Description Normalization was performed for each ratio by multiplying the normalization factors calculated by the GenePix Pro 6.0 software (Axon Instruments Inc.). Array design: Array sesign accession CAR292 Model name Rat_11K Technology type spotted_ss_oligo_features Surface type aminosilane Number of features 11468 Design provider Original Reporter type synthetic oligo-nucleotides Strand type single_stranded Substrate type glass Attachment covalent Array design protocol Array Design Protocol (Rat) File ArrayDesignFile_Rat_060509.txt Array design text field: Field Description Block The block number of the feature Column The column number of the feature. Row The row number of the feature. Name The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks). ID Accession number Sample: Name #1896_Control_Prostate_1 Organism rat Sex male Age 10 weeks Organism part prostate Strain or line Sprague-Dawley Name #1922_Control_Prostate_2 Organism rat Sex male Age 10 weeks Organism part prostate Strain or line Sprague-Dawley Name #1948_Control_Prostate_3 Organism rat Sex male Age 10 weeks Organism part prostate Strain or line Sprague-Dawley Name #2026_Methacrylamide_Prostate_6 Organism rat Sex male Age 10 weeks Organism part prostate Strain or line Sprague-Dawley Name #2102_Sulfolane_Prostate_11 Organism rat Sex male Age 10 weeks Organism part prostate Strain or line Sprague-Dawley Name #2177_2-iso-Propoxyethanol_Prostate_16 Organism rat Sex male Age 10 weeks Organism part prostate Strain or line Sprague-Dawley Name #2252_Hydrazine monohydrate_Prostate_21 Organism rat Sex male Age 10 weeks Organism part prostate Strain or line Sprague-Dawley Name #2277_4-Ethylmorpholine_Prostate_24 Organism rat Sex male Age 10 weeks Organism part prostate Strain or line Sprague-Dawley Name #2303_4-Ethylmorpholine_Prostate_25 Organism rat Sex male Age 10 weeks Organism part prostate Strain or line Sprague-Dawley Name #2329_4-Ethylmorpholine_Prostate_26 Organism rat Sex male Age 10 weeks Organism part prostate Strain or line Sprague-Dawley Name common_reference Organism rat Sex mixed_sex Organism part mixed Strain or line Wistar Labeled Extract: Label #1896_Control_Prostate_1, Cy5 Labeling protocol Labelling Protocol (rat) Extraction protocol Extraction Protocol Label compound Cy5 Label #1922_Control_Prostate_2, Cy5 Labeling protocol Labelling Protocol (rat) Extraction protocol Extraction Protocol Label compound Cy5 Label #1948_Control_Prostate_3, Cy5 Labeling protocol Labelling Protocol (rat) Extraction protocol Extraction Protocol Label compound Cy5 Label #2026_Methacrylamide_Prostate_6, Cy5 Labeling protocol Labelling Protocol (rat) Extraction protocol Extraction Protocol Label compound Cy5 Label #2102_Sulfolane_Prostate_11, Cy5 Labeling protocol Labelling Protocol (rat) Extraction protocol Extraction Protocol Label compound Cy5 Label #2177_2-iso-Propoxyethanol_Prostate_16, Cy5 Labeling protocol Labelling Protocol (rat) Extraction protocol Extraction Protocol Label compound Cy5 Label #2252_Hydrazine monohydrate_Prostate_21, Cy5 Labeling protocol Labelling Protocol (rat) Extraction protocol Extraction Protocol Label compound Cy5 Label #2277_4-Ethylmorpholine_Prostate_24, Cy5 Labeling protocol Labelling Protocol (rat) Extraction protocol Extraction Protocol Label compound Cy5 Label #2303_4-Ethylmorpholine_Prostate_25, Cy5 Labeling protocol Labelling Protocol (rat) Extraction protocol Extraction Protocol Label compound Cy5 Label #2329_4-Ethylmorpholine_Prostate_26, Cy5 Labeling protocol Labelling Protocol (rat) Extraction protocol Extraction Protocol Label compound Cy5 Label common_reference, Cy3 Labeling protocol Labelling Protocol (rat) Extraction protocol Extraction Protocol Label compound Cy3 Hybridization: Name #1896_Control_Prostate_1 Array design accession CAR292 Hybridization protocol Hybridization Protocol Scanning protocol Scanning Protocol File 1896_Control_Prostate_1_Rat2000.txt Hybridization data text field: Field Description "Block" The block number of the feature. "Column" The column number of the feature. "Row" The row number of the feature. "Name" The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks). "ID" The unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks). "X" The X-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Y" The Y-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Dia." The diameter in ??m of the feature-indicator. "F635 Median" Median feature pixel intensity at wavelength #1 (635 nm). "F635 Mean" Mean feature pixel intensity at wavelength #1 (635 nm). "F635 SD" The standard deviation of the feature pixel intensity at wavelength #1 (635 nm). "B635 Median" The median feature background intensity at wavelength #1 (635 nm). "B635 Mean" The mean feature background intensity at wavelength #1 (635 nm). "B635 SD" The standard deviation of the feature background intensity at wavelength #1 (635 nm). "% > B635+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm). "% > B635+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm). "F635 % Sat." The percentage of feature pixels at wavelength #1 that are saturated. "F532 Median" Median feature pixel intensity at wavelength #2 (532 nm). "F532 Mean" Mean feature pixel intensity at wavelength #2 (532 nm). "F532 SD" The standard deviation of the feature intensity at wavelength #2 (532 nm). "B532 Median" The median feature background intensity at wavelength #2 (532 nm). "B532 Mean" The mean feature background intensity at wavelength #2 (532 nm). "B532 SD" The standard deviation of the feature background intensity at wavelength #2 (532 nm). "% > B532+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm). "% > B532+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm). "F532 % Sat." The percentage of feature pixels at wavelength #2 that are saturated. "Ratio of Medians" The ratio of the median intensities of each feature for each wavelength, with the median background subtracted. "Ratio of Means" The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted. "Median of Ratios" The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Mean of Ratios" The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Ratios SD" The geometric standard deviation of the pixel intensity ratios. "Rgn Ratio" The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature. "Rgn R?" The coefficient of determination for the current regression value. "F Pixels" The total number of feature pixels. "B Pixels" The total number of background pixels. "Sum of Medians" The sum of the median intensities for each wavelength, with the median background subtracted. "Sum of Means" The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted. "Log Ratio" log (base 2) transform of the ratio of the medians. "F635 Median - B635" The median feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Median - B532" The median feature pixel intensity at wavelength #2 with the median background subtracted. "F635 Mean - B635" The mean feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Mean - B532" The mean feature pixel intensity at wavelength #2 with the median background subtracted. Name #1922_Control_Prostate_2 Array design accession CAR292 Hybridization protocol Hybridization Protocol Scanning protocol Scanning Protocol File 1922_Control_Prostate_2_Rat2000.txt Hybridization data text field: Field Description "Block" The block number of the feature. "Column" The column number of the feature. "Row" The row number of the feature. "Name" The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks). "ID" The unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks). "X" The X-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Y" The Y-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Dia." The diameter in ??m of the feature-indicator. "F635 Median" Median feature pixel intensity at wavelength #1 (635 nm). "F635 Mean" Mean feature pixel intensity at wavelength #1 (635 nm). "F635 SD" The standard deviation of the feature pixel intensity at wavelength #1 (635 nm). "B635 Median" The median feature background intensity at wavelength #1 (635 nm). "B635 Mean" The mean feature background intensity at wavelength #1 (635 nm). "B635 SD" The standard deviation of the feature background intensity at wavelength #1 (635 nm). "% > B635+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm). "% > B635+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm). "F635 % Sat." The percentage of feature pixels at wavelength #1 that are saturated. "F532 Median" Median feature pixel intensity at wavelength #2 (532 nm). "F532 Mean" Mean feature pixel intensity at wavelength #2 (532 nm). "F532 SD" The standard deviation of the feature intensity at wavelength #2 (532 nm). "B532 Median" The median feature background intensity at wavelength #2 (532 nm). "B532 Mean" The mean feature background intensity at wavelength #2 (532 nm). "B532 SD" The standard deviation of the feature background intensity at wavelength #2 (532 nm). "% > B532+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm). "% > B532+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm). "F532 % Sat." The percentage of feature pixels at wavelength #2 that are saturated. "Ratio of Medians" The ratio of the median intensities of each feature for each wavelength, with the median background subtracted. "Ratio of Means" The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted. "Median of Ratios" The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Mean of Ratios" The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Ratios SD" The geometric standard deviation of the pixel intensity ratios. "Rgn Ratio" The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature. "Rgn R?" The coefficient of determination for the current regression value. "F Pixels" The total number of feature pixels. "B Pixels" The total number of background pixels. "Sum of Medians" The sum of the median intensities for each wavelength, with the median background subtracted. "Sum of Means" The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted. "Log Ratio" log (base 2) transform of the ratio of the medians. "F635 Median - B635" The median feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Median - B532" The median feature pixel intensity at wavelength #2 with the median background subtracted. "F635 Mean - B635" The mean feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Mean - B532" The mean feature pixel intensity at wavelength #2 with the median background subtracted. Name #1948_Control_Prostate_3 Array design accession CAR292 Hybridization protocol Hybridization Protocol Scanning protocol Scanning Protocol File 1948_Control_Prostate_3_Rat2000.txt Hybridization data text field: Field Description "Block" The block number of the feature. "Column" The column number of the feature. "Row" The row number of the feature. "Name" The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks). "ID" The unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks). "X" The X-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Y" The Y-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Dia." The diameter in ??m of the feature-indicator. "F635 Median" Median feature pixel intensity at wavelength #1 (635 nm). "F635 Mean" Mean feature pixel intensity at wavelength #1 (635 nm). "F635 SD" The standard deviation of the feature pixel intensity at wavelength #1 (635 nm). "B635 Median" The median feature background intensity at wavelength #1 (635 nm). "B635 Mean" The mean feature background intensity at wavelength #1 (635 nm). "B635 SD" The standard deviation of the feature background intensity at wavelength #1 (635 nm). "% > B635+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm). "% > B635+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm). "F635 % Sat." The percentage of feature pixels at wavelength #1 that are saturated. "F532 Median" Median feature pixel intensity at wavelength #2 (532 nm). "F532 Mean" Mean feature pixel intensity at wavelength #2 (532 nm). "F532 SD" The standard deviation of the feature intensity at wavelength #2 (532 nm). "B532 Median" The median feature background intensity at wavelength #2 (532 nm). "B532 Mean" The mean feature background intensity at wavelength #2 (532 nm). "B532 SD" The standard deviation of the feature background intensity at wavelength #2 (532 nm). "% > B532+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm). "% > B532+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm). "F532 % Sat." The percentage of feature pixels at wavelength #2 that are saturated. "Ratio of Medians" The ratio of the median intensities of each feature for each wavelength, with the median background subtracted. "Ratio of Means" The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted. "Median of Ratios" The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Mean of Ratios" The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Ratios SD" The geometric standard deviation of the pixel intensity ratios. "Rgn Ratio" The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature. "Rgn R?" The coefficient of determination for the current regression value. "F Pixels" The total number of feature pixels. "B Pixels" The total number of background pixels. "Sum of Medians" The sum of the median intensities for each wavelength, with the median background subtracted. "Sum of Means" The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted. "Log Ratio" log (base 2) transform of the ratio of the medians. "F635 Median - B635" The median feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Median - B532" The median feature pixel intensity at wavelength #2 with the median background subtracted. "F635 Mean - B635" The mean feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Mean - B532" The mean feature pixel intensity at wavelength #2 with the median background subtracted. Name #2026_Methacrylamide_Prostate_6 Array design accession CAR292 Hybridization protocol Hybridization Protocol Scanning protocol Scanning Protocol File 2026_Methacrylamide_Prostate_6_Rat2000.txt Hybridization data text field: Field Description "Block" The block number of the feature. "Column" The column number of the feature. "Row" The row number of the feature. "Name" The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks). "ID" The unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks). "X" The X-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Y" The Y-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Dia." The diameter in ??m of the feature-indicator. "F635 Median" Median feature pixel intensity at wavelength #1 (635 nm). "F635 Mean" Mean feature pixel intensity at wavelength #1 (635 nm). "F635 SD" The standard deviation of the feature pixel intensity at wavelength #1 (635 nm). "B635 Median" The median feature background intensity at wavelength #1 (635 nm). "B635 Mean" The mean feature background intensity at wavelength #1 (635 nm). "B635 SD" The standard deviation of the feature background intensity at wavelength #1 (635 nm). "% > B635+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm). "% > B635+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm). "F635 % Sat." The percentage of feature pixels at wavelength #1 that are saturated. "F532 Median" Median feature pixel intensity at wavelength #2 (532 nm). "F532 Mean" Mean feature pixel intensity at wavelength #2 (532 nm). "F532 SD" The standard deviation of the feature intensity at wavelength #2 (532 nm). "B532 Median" The median feature background intensity at wavelength #2 (532 nm). "B532 Mean" The mean feature background intensity at wavelength #2 (532 nm). "B532 SD" The standard deviation of the feature background intensity at wavelength #2 (532 nm). "% > B532+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm). "% > B532+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm). "F532 % Sat." The percentage of feature pixels at wavelength #2 that are saturated. "Ratio of Medians" The ratio of the median intensities of each feature for each wavelength, with the median background subtracted. "Ratio of Means" The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted. "Median of Ratios" The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Mean of Ratios" The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Ratios SD" The geometric standard deviation of the pixel intensity ratios. "Rgn Ratio" The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature. "Rgn R?" The coefficient of determination for the current regression value. "F Pixels" The total number of feature pixels. "B Pixels" The total number of background pixels. "Sum of Medians" The sum of the median intensities for each wavelength, with the median background subtracted. "Sum of Means" The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted. "Log Ratio" log (base 2) transform of the ratio of the medians. "F635 Median - B635" The median feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Median - B532" The median feature pixel intensity at wavelength #2 with the median background subtracted. "F635 Mean - B635" The mean feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Mean - B532" The mean feature pixel intensity at wavelength #2 with the median background subtracted. Name #2102_Sulfolane_Prostate_11 Array design accession CAR292 Hybridization protocol Hybridization Protocol Scanning protocol Scanning Protocol File 2102_Sulfolane_Prostate_11_Rat2000.txt Hybridization data text field: Field Description "Block" The block number of the feature. "Column" The column number of the feature. "Row" The row number of the feature. "Name" The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks). "ID" The unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks). "X" The X-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Y" The Y-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Dia." The diameter in ??m of the feature-indicator. "F635 Median" Median feature pixel intensity at wavelength #1 (635 nm). "F635 Mean" Mean feature pixel intensity at wavelength #1 (635 nm). "F635 SD" The standard deviation of the feature pixel intensity at wavelength #1 (635 nm). "B635 Median" The median feature background intensity at wavelength #1 (635 nm). "B635 Mean" The mean feature background intensity at wavelength #1 (635 nm). "B635 SD" The standard deviation of the feature background intensity at wavelength #1 (635 nm). "% > B635+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm). "% > B635+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm). "F635 % Sat." The percentage of feature pixels at wavelength #1 that are saturated. "F532 Median" Median feature pixel intensity at wavelength #2 (532 nm). "F532 Mean" Mean feature pixel intensity at wavelength #2 (532 nm). "F532 SD" The standard deviation of the feature intensity at wavelength #2 (532 nm). "B532 Median" The median feature background intensity at wavelength #2 (532 nm). "B532 Mean" The mean feature background intensity at wavelength #2 (532 nm). "B532 SD" The standard deviation of the feature background intensity at wavelength #2 (532 nm). "% > B532+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm). "% > B532+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm). "F532 % Sat." The percentage of feature pixels at wavelength #2 that are saturated. "Ratio of Medians" The ratio of the median intensities of each feature for each wavelength, with the median background subtracted. "Ratio of Means" The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted. "Median of Ratios" The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Mean of Ratios" The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Ratios SD" The geometric standard deviation of the pixel intensity ratios. "Rgn Ratio" The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature. "Rgn R?" The coefficient of determination for the current regression value. "F Pixels" The total number of feature pixels. "B Pixels" The total number of background pixels. "Sum of Medians" The sum of the median intensities for each wavelength, with the median background subtracted. "Sum of Means" The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted. "Log Ratio" log (base 2) transform of the ratio of the medians. "F635 Median - B635" The median feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Median - B532" The median feature pixel intensity at wavelength #2 with the median background subtracted. "F635 Mean - B635" The mean feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Mean - B532" The mean feature pixel intensity at wavelength #2 with the median background subtracted. Name #2177_2-iso-Propoxyethanol_Prostate_16 Array design accession CAR292 Hybridization protocol Hybridization Protocol Scanning protocol Scanning Protocol File 2177_2-iso-Propoxyethanol_Prostate_16_Rat2000.txt Hybridization data text field: Field Description "Block" The block number of the feature. "Column" The column number of the feature. "Row" The row number of the feature. "Name" The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks). "ID" The unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks). "X" The X-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Y" The Y-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Dia." The diameter in ??m of the feature-indicator. "F635 Median" Median feature pixel intensity at wavelength #1 (635 nm). "F635 Mean" Mean feature pixel intensity at wavelength #1 (635 nm). "F635 SD" The standard deviation of the feature pixel intensity at wavelength #1 (635 nm). "B635 Median" The median feature background intensity at wavelength #1 (635 nm). "B635 Mean" The mean feature background intensity at wavelength #1 (635 nm). "B635 SD" The standard deviation of the feature background intensity at wavelength #1 (635 nm). "% > B635+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm). "% > B635+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm). "F635 % Sat." The percentage of feature pixels at wavelength #1 that are saturated. "F532 Median" Median feature pixel intensity at wavelength #2 (532 nm). "F532 Mean" Mean feature pixel intensity at wavelength #2 (532 nm). "F532 SD" The standard deviation of the feature intensity at wavelength #2 (532 nm). "B532 Median" The median feature background intensity at wavelength #2 (532 nm). "B532 Mean" The mean feature background intensity at wavelength #2 (532 nm). "B532 SD" The standard deviation of the feature background intensity at wavelength #2 (532 nm). "% > B532+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm). "% > B532+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm). "F532 % Sat." The percentage of feature pixels at wavelength #2 that are saturated. "Ratio of Medians" The ratio of the median intensities of each feature for each wavelength, with the median background subtracted. "Ratio of Means" The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted. "Median of Ratios" The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Mean of Ratios" The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Ratios SD" The geometric standard deviation of the pixel intensity ratios. "Rgn Ratio" The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature. "Rgn R?" The coefficient of determination for the current regression value. "F Pixels" The total number of feature pixels. "B Pixels" The total number of background pixels. "Sum of Medians" The sum of the median intensities for each wavelength, with the median background subtracted. "Sum of Means" The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted. "Log Ratio" log (base 2) transform of the ratio of the medians. "F635 Median - B635" The median feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Median - B532" The median feature pixel intensity at wavelength #2 with the median background subtracted. "F635 Mean - B635" The mean feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Mean - B532" The mean feature pixel intensity at wavelength #2 with the median background subtracted. Name #2252_Hydrazine monohydrate_Prostate_21 Array design accession CAR292 Hybridization protocol Hybridization Protocol Scanning protocol Scanning Protocol File 2252_Hydrazine_monohydrate_Prostate_21_Rat2000.txt Hybridization data text field: Field Description "Block" The block number of the feature. "Column" The column number of the feature. "Row" The row number of the feature. "Name" The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks). "ID" The unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks). "X" The X-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Y" The Y-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Dia." The diameter in ??m of the feature-indicator. "F635 Median" Median feature pixel intensity at wavelength #1 (635 nm). "F635 Mean" Mean feature pixel intensity at wavelength #1 (635 nm). "F635 SD" The standard deviation of the feature pixel intensity at wavelength #1 (635 nm). "B635 Median" The median feature background intensity at wavelength #1 (635 nm). "B635 Mean" The mean feature background intensity at wavelength #1 (635 nm). "B635 SD" The standard deviation of the feature background intensity at wavelength #1 (635 nm). "% > B635+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm). "% > B635+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm). "F635 % Sat." The percentage of feature pixels at wavelength #1 that are saturated. "F532 Median" Median feature pixel intensity at wavelength #2 (532 nm). "F532 Mean" Mean feature pixel intensity at wavelength #2 (532 nm). "F532 SD" The standard deviation of the feature intensity at wavelength #2 (532 nm). "B532 Median" The median feature background intensity at wavelength #2 (532 nm). "B532 Mean" The mean feature background intensity at wavelength #2 (532 nm). "B532 SD" The standard deviation of the feature background intensity at wavelength #2 (532 nm). "% > B532+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm). "% > B532+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm). "F532 % Sat." The percentage of feature pixels at wavelength #2 that are saturated. "Ratio of Medians" The ratio of the median intensities of each feature for each wavelength, with the median background subtracted. "Ratio of Means" The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted. "Median of Ratios" The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Mean of Ratios" The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Ratios SD" The geometric standard deviation of the pixel intensity ratios. "Rgn Ratio" The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature. "Rgn R?" The coefficient of determination for the current regression value. "F Pixels" The total number of feature pixels. "B Pixels" The total number of background pixels. "Sum of Medians" The sum of the median intensities for each wavelength, with the median background subtracted. "Sum of Means" The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted. "Log Ratio" log (base 2) transform of the ratio of the medians. "F635 Median - B635" The median feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Median - B532" The median feature pixel intensity at wavelength #2 with the median background subtracted. "F635 Mean - B635" The mean feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Mean - B532" The mean feature pixel intensity at wavelength #2 with the median background subtracted. Name #2277_4-Ethylmorpholine_Prostate_24 Array design accession CAR292 Hybridization protocol Hybridization Protocol Scanning protocol Scanning Protocol File 2277_4-Ethylmorpholine_Prostate_24_Rat2000.txt Hybridization data text field: Field Description "Block" The block number of the feature. "Column" The column number of the feature. "Row" The row number of the feature. "Name" The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks). "ID" The unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks). "X" The X-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Y" The Y-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Dia." The diameter in ??m of the feature-indicator. "F635 Median" Median feature pixel intensity at wavelength #1 (635 nm). "F635 Mean" Mean feature pixel intensity at wavelength #1 (635 nm). "F635 SD" The standard deviation of the feature pixel intensity at wavelength #1 (635 nm). "B635 Median" The median feature background intensity at wavelength #1 (635 nm). "B635 Mean" The mean feature background intensity at wavelength #1 (635 nm). "B635 SD" The standard deviation of the feature background intensity at wavelength #1 (635 nm). "% > B635+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm). "% > B635+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm). "F635 % Sat." The percentage of feature pixels at wavelength #1 that are saturated. "F532 Median" Median feature pixel intensity at wavelength #2 (532 nm). "F532 Mean" Mean feature pixel intensity at wavelength #2 (532 nm). "F532 SD" The standard deviation of the feature intensity at wavelength #2 (532 nm). "B532 Median" The median feature background intensity at wavelength #2 (532 nm). "B532 Mean" The mean feature background intensity at wavelength #2 (532 nm). "B532 SD" The standard deviation of the feature background intensity at wavelength #2 (532 nm). "% > B532+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm). "% > B532+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm). "F532 % Sat." The percentage of feature pixels at wavelength #2 that are saturated. "Ratio of Medians" The ratio of the median intensities of each feature for each wavelength, with the median background subtracted. "Ratio of Means" The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted. "Median of Ratios" The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Mean of Ratios" The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Ratios SD" The geometric standard deviation of the pixel intensity ratios. "Rgn Ratio" The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature. "Rgn R?" The coefficient of determination for the current regression value. "F Pixels" The total number of feature pixels. "B Pixels" The total number of background pixels. "Sum of Medians" The sum of the median intensities for each wavelength, with the median background subtracted. "Sum of Means" The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted. "Log Ratio" log (base 2) transform of the ratio of the medians. "F635 Median - B635" The median feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Median - B532" The median feature pixel intensity at wavelength #2 with the median background subtracted. "F635 Mean - B635" The mean feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Mean - B532" The mean feature pixel intensity at wavelength #2 with the median background subtracted. Name #2303_4-Ethylmorpholine_Prostate_25 Array design accession CAR292 Hybridization protocol Hybridization Protocol Scanning protocol Scanning Protocol File 2303_4-Ethylmorpholine_Prostate_25_Rat2000.txt Hybridization data text field: Field Description "Block" The block number of the feature. "Column" The column number of the feature. "Row" The row number of the feature. "Name" The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks). "ID" The unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks). "X" The X-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Y" The Y-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Dia." The diameter in ??m of the feature-indicator. "F635 Median" Median feature pixel intensity at wavelength #1 (635 nm). "F635 Mean" Mean feature pixel intensity at wavelength #1 (635 nm). "F635 SD" The standard deviation of the feature pixel intensity at wavelength #1 (635 nm). "B635 Median" The median feature background intensity at wavelength #1 (635 nm). "B635 Mean" The mean feature background intensity at wavelength #1 (635 nm). "B635 SD" The standard deviation of the feature background intensity at wavelength #1 (635 nm). "% > B635+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm). "% > B635+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm). "F635 % Sat." The percentage of feature pixels at wavelength #1 that are saturated. "F532 Median" Median feature pixel intensity at wavelength #2 (532 nm). "F532 Mean" Mean feature pixel intensity at wavelength #2 (532 nm). "F532 SD" The standard deviation of the feature intensity at wavelength #2 (532 nm). "B532 Median" The median feature background intensity at wavelength #2 (532 nm). "B532 Mean" The mean feature background intensity at wavelength #2 (532 nm). "B532 SD" The standard deviation of the feature background intensity at wavelength #2 (532 nm). "% > B532+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm). "% > B532+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm). "F532 % Sat." The percentage of feature pixels at wavelength #2 that are saturated. "Ratio of Medians" The ratio of the median intensities of each feature for each wavelength, with the median background subtracted. "Ratio of Means" The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted. "Median of Ratios" The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Mean of Ratios" The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Ratios SD" The geometric standard deviation of the pixel intensity ratios. "Rgn Ratio" The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature. "Rgn R?" The coefficient of determination for the current regression value. "F Pixels" The total number of feature pixels. "B Pixels" The total number of background pixels. "Sum of Medians" The sum of the median intensities for each wavelength, with the median background subtracted. "Sum of Means" The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted. "Log Ratio" log (base 2) transform of the ratio of the medians. "F635 Median - B635" The median feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Median - B532" The median feature pixel intensity at wavelength #2 with the median background subtracted. "F635 Mean - B635" The mean feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Mean - B532" The mean feature pixel intensity at wavelength #2 with the median background subtracted. Name #2329_4-Ethylmorpholine_Prostate_26 Array design accession CAR292 Hybridization protocol Hybridization Protocol Scanning protocol Scanning Protocol File 2329_4-Ethylmorpholine_Prostate_26_Rat2000.txt Hybridization data text field: Field Description "Block" The block number of the feature. "Column" The column number of the feature. "Row" The row number of the feature. "Name" The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks). "ID" The unique identifier of the feature derived from the Array List (up to 40 characters long, contained in quotation marks). "X" The X-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Y" The Y-coordinate in ??m of the center of the feature-indicator associated with the feature, where (0,0) is the top left of the image. "Dia." The diameter in ??m of the feature-indicator. "F635 Median" Median feature pixel intensity at wavelength #1 (635 nm). "F635 Mean" Mean feature pixel intensity at wavelength #1 (635 nm). "F635 SD" The standard deviation of the feature pixel intensity at wavelength #1 (635 nm). "B635 Median" The median feature background intensity at wavelength #1 (635 nm). "B635 Mean" The mean feature background intensity at wavelength #1 (635 nm). "B635 SD" The standard deviation of the feature background intensity at wavelength #1 (635 nm). "% > B635+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #1 (635 nm). "% > B635+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #1 (635 nm). "F635 % Sat." The percentage of feature pixels at wavelength #1 that are saturated. "F532 Median" Median feature pixel intensity at wavelength #2 (532 nm). "F532 Mean" Mean feature pixel intensity at wavelength #2 (532 nm). "F532 SD" The standard deviation of the feature intensity at wavelength #2 (532 nm). "B532 Median" The median feature background intensity at wavelength #2 (532 nm). "B532 Mean" The mean feature background intensity at wavelength #2 (532 nm). "B532 SD" The standard deviation of the feature background intensity at wavelength #2 (532 nm). "% > B532+1SD" The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength #2 (532 nm). "% > B532+2SD" The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength #2 (532 nm). "F532 % Sat." The percentage of feature pixels at wavelength #2 that are saturated. "Ratio of Medians" The ratio of the median intensities of each feature for each wavelength, with the median background subtracted. "Ratio of Means" The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted. "Median of Ratios" The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Mean of Ratios" The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted. "Ratios SD" The geometric standard deviation of the pixel intensity ratios. "Rgn Ratio" The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature. "Rgn R?" The coefficient of determination for the current regression value. "F Pixels" The total number of feature pixels. "B Pixels" The total number of background pixels. "Sum of Medians" The sum of the median intensities for each wavelength, with the median background subtracted. "Sum of Means" The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted. "Log Ratio" log (base 2) transform of the ratio of the medians. "F635 Median - B635" The median feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Median - B532" The median feature pixel intensity at wavelength #2 with the median background subtracted. "F635 Mean - B635" The mean feature pixel intensity at wavelength #1 with the median background subtracted. "F532 Mean - B532" The mean feature pixel intensity at wavelength #2 with the median background subtracted.