biostudies-arrayexpress00600Lucinda ThompsonHelicobacter pylorihttps://www.ebi.ac.uk/biostudies/studies/E-GEOD-3988This experiment set contains the raw data for 8 arrays that were used in the genomic typing of the pre- and post-mouse H. pylori strains SS1 and SS2000. 10700 is the pre-mouse clinical isolate of SS1 and PMSS2000 is the pre-mouse clinical isolate of SS2000. gDNA from these strains were labeled and hybridized to H. pylori microarrays as described in Salama et al. {Salama et al. 2000 PNAS 97:14668-73}. In each case the test gDNA sample was labeled with Cy5 (red) and this was hybridized with Cy3 (green) labeled reference DNA of equal amount. The reference DNA consisted of equal amounts of gDNA from the two H. pylori strains used to make the H. pylori microarray, 26695 and J99. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computedbiostudies-arrayexpressMIAME ScoreAssays and DataProcessed DataMAGE-TAB FilesArray DesignsFeature Extraction - VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)Assay Data Transformation - ID_REF = ID_REF<br>CH1I_MEAN = Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>CH2I_MEAN = Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale<br>CH1B_MEDIAN = The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background<br>CH2B_MEDIAN = The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background<br>CH1D_MEAN = The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel<br>CH2D_MEAN = .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>CH1I_MEDIAN = Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>CH2I_MEDIAN = Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale<br>CH1B_MEAN = The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background<br>CH2B_MEAN = The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background<br>CH1D_MEDIAN = The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale<br>CH2D_MEDIAN = The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale<br>CH1_PER_SAT = The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale<br>CH2_PER_SAT = The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale<br>CH1I_SD = The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel<br>CH2I_SD = The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>CH1B_SD = The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background<br>CH2B_SD = The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background<br>PERGTBCH1I_1SD = The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>PERGTBCH2I_1SD = The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale<br>PERGTBCH1I_2SD = The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>PERGTBCH2I_2SD = The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>SUM_MEAN = The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale<br>SUM_MEDIAN = The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale<br>RAT1_MEAN = Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale<br>RAT2_MEAN = The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale<br>RAT2_MEDIAN = The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale<br>PIX_RAT2_MEAN = The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale<br>PIX_RAT2_MEDIAN = The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale<br>RAT2_SD = The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale<br>TOT_SPIX = The total number of feature pixels.; Type: integer; Scale: linear_scale<br>TOT_BPIX = The total number of background pixels.; Type: integer; Scale: linear_scale<br>REGR = The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale<br>CORR = The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high LOG_RAT2N_MEDIANs imply better fit & good spot quality.; Type: float; Scale: linear_scale<br>DIAMETER = The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale<br>X_COORD = X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale<br>Y_COORD = Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale<br>TOP = Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>BOT = Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>LEFT = Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>RIGHT = Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale<br>FLAG = The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale<br>CH2IN_MEAN = Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>CH2BN_MEDIAN = Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background<br>CH2DN_MEAN = Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>RAT2N_MEAN = Type: float; Scale: linear_scale<br>CH2IN_MEDIAN = Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale<br>CH2DN_MEDIAN = Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale<br>RAT1N_MEAN = Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale<br>RAT2N_MEDIAN = Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale<br>VALUE = same as UNF_VALUE but with flagged values removed<br>LOG_RAT2N_MEDIAN = Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2<br>UNF_VALUE = Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2Assay Data Transformation - ID_REF = ID_REF<br>CH1I_MEAN = Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>CH2I_MEAN = Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale<br>CH1B_MEDIAN = The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background<br>CH2B_MEDIAN = The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background<br>CH1D_MEAN = The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel<br>CH2D_MEAN = .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>CH1I_MEDIAN = Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>CH2I_MEDIAN = Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale<br>CH1B_MEAN = The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background<br>CH2B_MEAN = The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background<br>CH1D_MEDIAN = The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale<br>CH2D_MEDIAN = The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale<br>CH1_PER_SAT = The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale<br>CH2_PER_SAT = The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale<br>CH1I_SD = The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel<br>CH2I_SD = The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>CH1B_SD = The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background<br>CH2B_SD = The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background<br>PERGTBCH1I_1SD = The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>PERGTBCH2I_1SD = The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale<br>PERGTBCH1I_2SD = The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>PERGTBCH2I_2SD = The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale<br>SUM_MEAN = The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale<br>SUM_MEDIAN = The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale<br>RAT1_MEAN = Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale<br>RAT2_MEAN = The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale<br>RAT2_MEDIAN = The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale<br>PIX_RAT2_MEAN = The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale<br>PIX_RAT2_MEDIAN = The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale<br>RAT2_SD = The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale<br>TOT_SPIX = The total number of feature pixels.; Type: integer; Scale: linear_scale<br>TOT_BPIX = The total number of background pixels.; Type: integer; Scale: linear_scale<br>REGR = The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale<br>CORR = The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high LOG_RAT2N_MEDIANs imply better fit & good spot quality.; Type: float; Scale: linear_scale<br>DIAMETER = The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale<br>X_COORD = X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale<br>Y_COORD = Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale<br>TOP = Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>BOT = Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>LEFT = Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale<br>RIGHT = Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale<br>FLAG = The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale<br>CH2IN_MEAN = Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>CH2BN_MEDIAN = Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background<br>CH2DN_MEAN = Normalized LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel<br>RAT2N_MEAN = Type: float; Scale: linear_scale<br>CH2IN_MEDIAN = Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale<br>CH2DN_MEDIAN = Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale<br>RAT1N_MEAN = Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale<br>RAT2N_MEDIAN = Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale<br>VALUE = Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2<br>LOG_RAT2N_MEDIAN = Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2UnknownTranscriptomicsGenomicsProteomicsThe mouse model of Helicobacter pylori-induced disease using Sydney strain 1 (SS1) has been used extensively in Helicobacter research. Herein we describe the isolation and characterization of a new mouse-colonizing strain for use in comparative studies. One strain capable of persistent mouse colonization was isolated from a total of 110 clinical isolates and is named here SS2000 (Sydney strain 2000). Genome typing revealed a number of differences between SS1 and SS2000 as well as between them and the respective original clinical isolates. In particular, SS2000 lacked the entire cag pathogenicity island, while SS1 contained all 27 genes of the island. C57BL/6 and BALB/c mice were infected with SS1 or SS2000 or were treated with broth medium (controls). After 6 months host-specific effects were evident, including lower colonization levels in the BALB/c animals. Few pathological differences were observed between SS1- and SS2000-infected animals. However, by 15 months postinfection, SS1-infected C57BL/6 mice had developed more severe gastritis than the SS2000-infected animals. In contrast SS2000-infected BALB/c mice showed increased accumulation of mucosa-associated lymphoid tissue compared to those infected with SS1. This improved comparative model of H. pylori-induced disease allowed dissection of both host and strain effects and thus will prove useful in further studies.unknown experiment typeHelicobacter pyloriChronic Helicobacter pylori infection with Sydney strain 1 and a newly identified mouse-adapted strain (Sydney strain 2000) in C57BL/6 and BALB/c mice.Nina SalamaLucinda ThompsonThompson LJ, Danon SJ, Wilson JE, O'Rourke JL, Salama NR, Falkow S, Mitchell H, Lee A60falseChronic Helicobacter pylori Infection with Sydney Strain 1 and Mouse-Adapted Sydney Strain 2000This experiment set contains the raw data for 8 arrays that were used in the genomic typing of the pre- and post-mouse H. pylori strains SS1 and SS2000. 10700 is the pre-mouse clinical isolate of SS1 and PMSS2000 is the pre-mouse clinical isolate of SS2000. gDNA from these strains were labeled and hybridized to H. pylori microarrays as described in Salama et al. {Salama et al. 2000 PNAS 97:14668-73}. In each case the test gDNA sample was labeled with Cy5 (red) and this was hybridized with Cy3 (green) labeled reference DNA of equal amount. The reference DNA consisted of equal amounts of gDNA from the two H. pylori strains used to make the H. pylori microarray, 26695 and J99. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. ComputedE-GEOD-3988GSE398815271928