CIBEX accession CBX14
Release date 2007-07-25
Experiment:
Experiment title Responses of normal human coronary artery endothelial cells against multiple cytokine
Experimental design type reference_design, compound_treatment_design
Experimental factor normal human coronary artery endothelial cells, cytokine
Common reference YES
Quality control description Peer_review_quality_control
Number of hybridization 14
Experimental description To identify genes the expression levels of which altered in single and multiple cytokines-specific manners and to minutely dissect the cellular responses of HCAECs to the cytokines, we obtained the gene expression profiles with five cytokines and analyzed them in parallel.
Submitter:
First name Watanabe
Last name Shinya
Organization Tokyo Medical and Dental University
Department Clinical Informatics
Address 1-5-45 Yushima, Bunkyo-ku, Tokyo 113-8519, Japan
Reference:
Title Differential responses of normal human coronary artery endothelial cells against multiple cytokines comparatively assessed by gene expression profiles
Author Miura A, Honma R, Togashi T, Yanagisawa Y, Ito E, Imai J, Isogai T, Goshima N, Watanabe S, Nomura N.
Journal FEBS Lett.
Year 2006
Volume 580
Issue 30
Page 6871-6879
Pubmed ID 17157299
Protocol:
Name Hybridization Protocol
Description Hybridization and subsequent washes of the arrays were performed with a Labeling and Hybridization Kit (MicroDiagnostic).
Name Scanning Protocol
Description Hybridization signals were measured with a GenePix 4000A 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 human common reference RNA) by the GenePix Pro 3.0 software (Axon Instruments Inc.).
Name Growth Condition Protocol
Description HCAECs were cultured under 5% CO_{2} at 37°C with EGM-2-MV medium (Cambrex Corp.) containing 5% fetal bovine serum (FBS), hydrocortisone, human fibroblast growth factor (hFGF)-B, vascular endothelial growth factor (VEGF), human recombinant insulin-like growth factor (R3-IGF-1), ascorbic acid, human epidermal growth factor (hEGF), and gentamicin/amphotericin B according to the manufacturer’s instructions. HCAECs were split at 1:4 with 0.02% EDTA and 0.25% trypsin at a confluent density.
Name Normalization Protocol
Description Normalization was performed for each ratio by multiplying the normalization factors calculated by the GenePix Pro 3.0 software (Axon Instruments Inc.).
Name Treatment Protocol
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to IL-1β (R&D Systems, MN, USA) (1.1 nM) and subsequently incubated for another 24 h.
Name Transformation Protocol
Description The primary expression ratios (ratios of cyanine 5 intensity of each sample to cyanine 3 intensity of the human common reference RNA) were converted into log2 values (designated as log ratios). To compare the cytokine-treated samples against the mock-treated samples (negative controls) for each cytokine, log ratios obtained for the mock-treated samples were subtracted from the log ratios obtained for each cytokine-treated sample.
Name Treatment Protocol2
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to TNF-α (R&D Systems) (0.3 nM) and subsequently incubated for another 24 h.
Name Treatment Protocol3
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to TNF-α (R&D Systems) (10 nM) and subsequently incubated for another 24 h.
Name Treatment Protocol4
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to IFN-β (PeproTech Inc., NJ, USA) (0.03 nM) and subsequently incubated for another 24 h.
Name Treatment Protocol5
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to IFN-β (PeproTech Inc., NJ, USA) (1.3 nM) and subsequently incubated for another 24 h.
Name Treatment Protocol6
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to IFN-γ (R&D Systems) (0.04 nM) and subsequently incubated for another 24 h.
Name Treatment Protocol7
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to IFN-γ (R&D Systems) (0.5 nM) and subsequently incubated for another 24 h.
Name Treatment Protocol8
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to OSM (R&D Systems) (1.1 nM) and subsequently incubated for another 24 h.
Name Treatment Protocol9
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to OSM (R&D Systems) (2.7 nM) and subsequently incubated for another 24 h.
Name Treatment Protocol10
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to fresh medium containing no cytokines as a negative control for IL-1beta_1.
Name Treatment Protocol11
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to fresh medium containing no cytokines as a negative control for IL-1beta_2.
Name Treatment Protocol12
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to fresh medium containing no cytokines as a negative control for TNF-alpha_1, IFN-beta_1, IFN-gamma_1, and OSM_1.
Name Treatment Protocol13
Description HCAECs were maintained at the near confluent density 24 h before the exposure experiments and subsequently replaced with fresh media and incubated for another 24 h. At the fully confluent density, HCAECs were exposed to fresh medium containing no cytokines as a negative control for TNF-alpha_2, IFN-beta_2, IFN-gamma_2, and OSM_2.
Name Extraction Protocol
Description The cells were harvested 24 h after exposure to cytokines with TRIzol Reagent (Invitrogen Corp., CA, USA). The cell lysates obtained were subjected to total RNA extraction according to the manufacturer’s instructions. Subsequently, total RNA was subjected to polyA(+) RNA isolation with a MicroPoly(A) Purist Kit (Ambion Inc., TX, USA) in accordance with the manufacturer’s instructions. Eventually, polyA(+) RNA was divided into aliquots of 2 µg, precipitated with ethanol, and stored at -20°C.
Name Labeling Protocol
Description Two micrograms of poly(A)+ RNA were labeled with SuperScript II (Invitrogen Corp.) and cyanine 5-deoxyuridine triphosphate (dUTP) (PerkinElmer Inc., MA, USA).
Name Pooling Protocol
Description .
Name Extraction protocol2
Description The human common reference RNA was prepared by mixing equal amounts of poly(A)+ RNA extracted from 22 cell lines (A431, A549, AKI, HBL-100, HeLa, HepG2, HL60, IMR-32, Jurkat, K562, KP4, MKN7, NK-92, Raji, RD, Saos-2, SK-N-MC, SW-13, T24, U251, U937, and Y79). Each cell was cultured according to the manufacturer’s instructions. The cells were harvested with TRIzol Reagent (Invitrogen Corp., CA, USA). The cell lysates obtained were subjected to total RNA extraction according to the manufacturer’s instructions. Subsequently, total RNA was subjected to polyA(+) RNA isolation with a MicroPoly(A) Purist Kit (Ambion Inc., TX, USA) in accordance with the manufacturer’s instructions. Eventually, polyA(+) RNA was divided into aliquots of 2 µg, precipitated with ethanol, and stored at -20°C.
Name Labeling Protocol2
Description Two micrograms of poly(A)+ RNA were labeled with SuperScript II (Invitrogen Corp.) and cyanine 3-deoxyuridine triphosphate (dUTP) (PerkinElmer Inc. MA, USA).
Name ArrayDesign Protocol
Description A set of synthetic polynucleotides (80-mers) representing 22,512 species of human 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.
Array design:
Array sesign accession CAR15
Model name Custom made
Technology type spotted_ss_oligo_features
Surface type aminosilane
Number of features 22512
Design provider Original
Reporter type synthetic oligo-nucleotide
Strand type single_stranded
Substrate type glass
Attachment other
File ArrayDesignFile.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
Sequence 80 base sequence
Sample:
Name IL-1beta_2
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name OSM_2
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name TNF-alpha_1
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name Negative_control_1
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name TNF-alpha_2
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name Negative_control_2
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name IFN-beta_1
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name Negative_control_3
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name IFN-beta_2
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name IFN-gamma_1
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name Negative_control_4
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name IFN-gamma_2
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name common_reference_RNA
Growth condition protocol Growth Condition Protocol
Name OSM_1
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Name IL-1beta_1
Organism Homo sapience
Cell type Normal human coronary artery endothelial cells
Sex Female
Age 32 Y
Organism part Coronary artery
Growth condition protocol Growth Condition Protocol
Labeled Extract:
Label IL-1beta_2, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label TNF-alpha_1, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label OSM_2, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label TNF-alpha_2, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label Negative_control_1, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label IFN-beta_1, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label Negative_control_2, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label IFN-beta_2, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label Negative_control_3, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label IFN-gamma_1, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label Negative_control_4, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label IFN-gamma_2, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label common_reference_RNA, Cy3
Labeling protocol Labeling Protocol2
Extraction protocol Extraction protocol2
Pooling protocol Pooling Protocol
Label compound Cy3
Label OSM_1, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Label IL-1beta_1, Cy5
Labeling protocol Labeling Protocol
Extraction protocol Extraction Protocol
Pooling protocol Pooling Protocol
Label compound Cy5
Hybridization:
Name 042604-136
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 042604-136.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 042604-148
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 042604-148.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 042604-151
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 042604-151.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 042604-152
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 042604-152.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 042604-153
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 042604-153.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 042604-178
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 042604-178.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 042604-181
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 042604-181.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 042604-182
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 042604-182.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 042604-183
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 042604-183.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 042604-191
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 042604-191.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 102402-116
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 102402-116.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 102402-125
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 102402-125.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 102402-126
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 102402-126.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Name 102402-155
Array design accession CAR15
Hybridization protocol Hybridization Protocol
Scanning protocol Scanning Protocol
File 102402-155.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 µm 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 µm 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 µm 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 standard deviation of the feature background 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 R2 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.
Flags the type of flag associated with a feature.
Summary:
Name HCAEC_5cytokines
Normalization protocol Normalization Protocol
Transformation protocol Transformation Protocol
Description Overview of alteration of gene expression in HCAECs after cytokine stimulation
File Summary data_HCAEC_5cytokines.txt
Summary data text field:
Field Description
No. The row number of the feature.
Acc. No. GenBank accession number
Name The name of the feature derived from the Array list (up to 40 characters long, contained in quotation marks).
IL-1beta_1 The log ratio obtained for the IL-1β (1.1 nM)-treated sample, with the log ratio obtain for mock-treated sample (Negative_control_1) subtracted.
IL-1beta_2 The log ratio obtained for the IL-1β (1.1 nM)-treated sample, with the log ratio obtain for mock-treated sample (Negative_control_2) subtracted.
TNF-alpha_1 The log ratio obtained for the TNF-α (0.3 nM)-treated sample, with the log ratio obtain for mock-treated sample (Negative_control_3) subtracted.
IFN-beta_1 The log ratio obtained for the IFN-β (0.03 nM)-treated sample, with the log ratio obtain for mock-treated sample (Negative_control_3) subtracted.
IFN-gamma_1 The log ratio obtained for the IFN-γ (0.04 nM)-treated sample, with the log ratio obtain for mock-treated sample (Negative_control_3) subtracted.
OSM_1 The log ratio obtained for the OSM (1.1 nM)-treated sample, with the log ratio obtain for mock-treated sample (Negative_control_3) subtracted.
TNF-alpha_2 The log ratio obtained for the TNF-α (10 nM)-treated sample, with the log ratio obtain for mock-treated sample (Negative_control_4) subtracted.
IFN-beta_2 The log ratio obtained for the IFN-β (1.3 nM)-treated sample, with the log ratio obtain for mock-treated sample (Negative_control_4) subtracted.
IFN-gamma_2 The log ratio obtained for the IFN-ν (0.5 nM)-treated sample, with the log ratio obtain for mock-treated sample (Negative_control_4) subtracted.
OSM_2 The log ratio obtained for the OSM (2.7 nM)-treated sample, with the log ratio obtain for mock-treated sample (Negative_control_4) subtracted.