|
Status |
Public on Jan 12, 2012 |
Title |
P39_06_19_07 |
Sample type |
RNA |
|
|
Channel 1 |
Source name |
Stratagene Universal Human Reference
|
Organism |
Homo sapiens |
Characteristics |
reference: Stratagene Universal Human Reference
|
Extracted molecule |
total RNA |
Extraction protocol |
not provided
|
Label |
Cy3
|
Label protocol |
not provided
|
|
|
Channel 2 |
Source name |
Primary Human Tissue Skin
|
Organism |
Homo sapiens |
Characteristics |
tissue: skin age: 76 years organism part: posterior neck disease state: active individual: 39 Sex: M
|
Extracted molecule |
total RNA |
Extraction protocol |
Poly-adenylated RNA was extracted from snap-frozen skin biopsy specimens (DM and lupus) using a two step method. First, total RNA was extracted with phenol-guanidine thiocyaniate extraction (RNAbee ,Tel-Test, Friendswood TX). Next, poly-adenylated RNA was purified using RNeasy Kit (Quiagen, Chatsworth, CA) according to the manufacturers instructions. Sample RNA and reference mRNA (Stratagene) were amplified using an Amino Allyl MessageAmp II aRNA kit (Ambion, Austin, TX).
|
Label |
Cy5
|
Label protocol |
not provided
|
|
|
|
Hybridization protocol |
(labeled with Cy5) and amplified Human Universal Reference RNA (labeled with Cy3) (Stratagene, La Jolla, CA) were competitively hybridized to HEEBO (human exon evidence-based oligonucleotide) microarrays as described (http://www.microarray.org/sfgf/heebo.do).
|
Scan protocol |
GenePix 4000A
|
Description |
Image: http://smd.stanford.edu/MicroArray/gifs/2007-07/75954.gif
|
Data processing |
Array data were filtered based on fluorescent hybridization signal 1.5-fold over local background in either the Cy5 or the Cy3 channel and if the data were technically adequate in 80% of experiments. Array data underwent LOWESS normalization, and the data were displayed as a log2 ratio of LOWESS-normalized Cy5/Cy3 ratio (span parameter=0.4)
|
|
|
Submission date |
Sep 20, 2011 |
Last update date |
Jan 12, 2012 |
Contact name |
David Fiorentino |
E-mail(s) |
fiorentino@stanford.edu
|
Phone |
650-498-6120
|
Fax |
650-723-7796
|
Organization name |
Stanford University
|
Department |
Dermatology
|
Lab |
Blake Wilbur Clinic, W0074
|
Street address |
900 Blake Wilbur Drive
|
City |
Stanford |
State/province |
CA |
ZIP/Postal code |
94305 |
Country |
USA |
|
|
Platform ID |
GPL9551 |
Series (1) |
GSE32245 |
Fiorentino 2006-7 dermatomyositis, lupus, control skin |
|
Data table header descriptions |
ID_REF |
ID_REF |
CH1I_MEAN |
Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale |
CH2I_MEAN |
Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale |
CH1B_MEDIAN |
The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background |
CH2B_MEDIAN |
The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background |
CH1D_MEAN |
The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel |
CH2D_MEAN |
.The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel |
CH1I_MEDIAN |
Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale |
CH2I_MEDIAN |
Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale |
CH1B_MEAN |
The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background |
CH2B_MEAN |
The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background |
CH1D_MEDIAN |
The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale |
CH2D_MEDIAN |
The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale |
CH1_PER_SAT |
The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale |
CH2_PER_SAT |
The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale |
CH1I_SD |
The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel |
CH2I_SD |
The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel |
CH1B_SD |
The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background |
CH2B_SD |
The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background |
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 |
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 |
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 |
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 |
SUM_MEAN |
The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale |
SUM_MEDIAN |
The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale |
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 |
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 |
RAT2_MEDIAN |
The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale |
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 |
PIX_RAT2_MEDIAN |
The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale |
RAT2_SD |
The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale |
TOT_SPIX |
The total number of feature pixels.; Type: integer; Scale: linear_scale |
TOT_BPIX |
The total number of background pixels.; Type: integer; Scale: linear_scale |
REGR |
The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale |
CORR |
The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale |
DIAMETER |
The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale |
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 |
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 |
TOP |
Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale |
BOT |
Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale |
LEFT |
Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale |
RIGHT |
Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale |
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 |
CH2IN_MEAN |
Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel |
CH2BN_MEDIAN |
Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background |
CH2DN_MEAN |
Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel |
RAT2N_MEAN |
Type: float; Scale: linear_scale |
CH2IN_MEDIAN |
Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale |
CH2DN_MEDIAN |
Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale |
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 |
RAT2N_MEDIAN |
Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale |
LOG_RAT2N_MEAN |
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 |
VALUE |
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 |