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Sample GSM380003 Query DataSets for GSM380003
Status Public on Mar 13, 2009
Title 6wk BDC_2_rep2
Sample type RNA
 
Channel 1
Source name NOD 2 wk old Pancreatic LN CD4 cells
Organism Mus musculus
Characteristics cell type: NOD 2 wk old Pancreatic LN CD4 cells
Extracted molecule total RNA
Extraction protocol Rubins 2003 - Trizol Extraction of Total RNA from PBMCs; 1. Make sure the area is clean and free of any RNases. Keep the samples cold or on ice as much as possible to prevent RNA degradation. Use only RNase free tubes and RNase free, aerosol-barrier pipette tips throughout the whole experiment. 2. Add 1mL of Trizol to the frozen PBMC pellet. 3. If the Trizol was added to the PBMCs before freezing, thaw the Trizol/PBMCs on the benchtop for 5-10 minutes. 4. Vortex and transfer to 1.5ml microfuge tubes if not already in them. 5. Add 0.2 mls chloroform per 1 ml Trizol. Vortex or shake vigorously and incubate at room temp. for 2-3 minutes. 6. Centrifuge at 12,000g for 15 minutes at 4C. 7. Transfer the aqueous phase to a fresh tube. (The volume will be about 60% of the volume of Trizol.) Note: If isolating DNA, save the organic phase. Add 1uL of 1ug/uL Linear Acrylamide if RNA yield is expected to be low. 8. Add 0.5 mLs of isopropanol per 1 ml Trizol used. Incubate at room temp. for 10 minutes. 9. Centrifuge at top speed (14,000rpm) for 10 minutes at 4C. 10. The RNA pellet will be visible at the bottom of the tube. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube. 11. WASH 1: Wash the pellet with 1 ml 70% EtOH. Centrifuge at top speed 14,000g for 5-7 minutes. 12. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube. 13. WASH 2: Wash the pellet with 1 ml 70% EtOH. Centrifuge at top speed 14,000g for 5-7 minutes. 14. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube. 15. Air dry pellet shortly, until no EtOH is visible (2-5 minutes). Do not overdry! 16. Resuspend the pellet in 20uls of DEPC H2O. Store at ?80C. 17. Check RNA quality and quantity by denaturing gel and OD spec (260nm and 260/280 ratio).; Protocol Type = Extract preparation; Performer: Qing,,Li
Rubins 2003 - Ambion Message Amp I; FIRST STRAND CDNA SYNTHESIS: In PCR reaction tube, mix: Amount Reagent 0.1 - 5ug Total RNA 1uL T7 Oligo (dT) primer 11uL Nuclease free water 70oC for 10 min in a thermocycler with lid on, but not clamped down. Centrifuge briefly. Prepare in a Master Mix and keep at room temperature: Amount Reagent 2uL 10X First Strand Buffer 1uL Ribonuclease Inhibitor 4uL dNTP Mix Gently pipette or flick to mix, and then centrifuge briefly. Incubate master mix at 42oC for 2 minutes prior to adding to reaction tubes. Add to the master mix: Amount Reagent 1uL Reverse Transcriptase Quickly transfer 8ul of above Master Mix to each RNA sample, mix by pipetting. 42oC for 2 hours in thermocycler with lid on, but not clamped down. Centrifuge briefly, place on ice, and immediately proceed to next step SECOND STRAND SYNTHESIS: Amount Reagent 63uL Nuclease free water 10uL 10X Second Strand Buffer 4uL dNTP Mix 2uL DNA Polymerase 1uL RNase H Add 80uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly. 16oC for 2 hours in thermocycler with lid completely off. DS cDNA CLEANUP: Preheat the 5mL bottle of water at 50oC for at least 10 minutes. Place filter cartridge in a 2mL tube and add 100ul of cDNA Binding Buffer. Incubate at room temperature for 5 min. Transfer 100uL reaction from strip-8 PCR tubes into 1.5ml Eppendorf tubes. Add 250uL of cDNA binding buffer to each cDNA sample, mix by pipetting. Add the mix to the filter cartridge. Centrifuge for 1 min at 10,000 x g. Discard flow-through. Add 650ul of cDNA wash buffer. Centrifuge for 1 min. at 10,000 x g. Discard flow-through. Centrifuge again for 1 min at 10,000 x g to remove trace amounts of ethanol. Transfer filter cartridge to fresh 2mL tube Add 50uL of preheated water to the center of the column. Incubate at room temperature for 2 minutes. Centrifuge for 1 minute at 10,000 x g. Repeat elution with a second 50ul of preheated water. Centrifuge for 1 minute at 10,000 x g. Transfer to strip-8 PCR tubes and mark a line for 8uL Concentrate the purified cDNA to < 8uL by drying in a vacuum centrifuge on high heat. Resuspend cDNA up to 8uL with H20, mix well, and keep on ice or store at ?20oC. IN VITRO TRANSCRIPTION Prepare the following master mix: Amount Reagent 8uL T7 NTP mix (75 mM each) 2uL T7 10X Reaction Buffer 2uL T7 Enzyme Mix Add 12uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly. 37oC for 6 hours in hybridization oven. Add to each reaction: Amount Reagent 2uL DNaseI Gently pipette or flick to mix, and then centrifuge briefly. 37oC for 30min in hybridization oven aRNA PURIFICATION Preheat 5mL bottle of nuclease free water at 50oC for at least 10 minutes. Immediately before staring aRNA purification., equilibrate 1 filter cartridge per aRNA sample Place filter cartridge in a 2mL tube and add 100ul of aRNA Binding Buffer. Incubate at room temperature for 5 min. Add 78uL aRNA Elution Solution to each IVT mix to bring final volume up to 100uL. Add 350uL of aRNA Binding Buffer to each aRNA sample. Add 250uL of ACS grade 95% ethanol to each sample. Mix by pipetting or gentle vortexing. Apply entire sample to the equilibrated filter cartridge. Centrifuge for 1 minute at 10,000 x g. Discard flow-through but re-use tube. Add 650uL aRNA Wash Buffer to each filter. Centrifuge for 1 minute at 10,000 x g. Discard flow-through but re-use tube. Centrifuge again for 1 min at 10,000 x g Transfer cartridge to a fresh 2mL tube. Elute aRNA by adding 50uL preheated (50oC) water to center of column. Incubate at room temperature for 2 min. Centrifuge for 1 minute at 10,000 x g. Repeat elution with a second 50uL of preheated water. Centrifuge for 1 minute at 10,000 x g. Store aRNA at ?80oC.; Protocol Type = Amplification; Performer: Qing,,Li
Label Cy3
Label protocol Rubins 2003 - Labeling Amplified RNA - Direct Incorporation of Cy Dyes; Preparation of Fluorescent DNA Probe from Amplified mRNA 1. To anneal primer, mix 3-4ug of amplified mRNA with 10ug of random hexamer primer in a total volume of 15.4ul: mRNA 3-4ug pdN6 (5 ug/uL) 2uL ddH2O (DEPC) to 15.4 uL Total volume: 15.4 uL 2. Heat to 65oC for 10 min and cool on ice. 3. Add 14.6uL reaction mixture (Master Mix or separate) to each RNA/hexamer mix Reaction mixture 5X first-strand buffer 6.0uL 0.1M DTT 3.0uL Unlabeled dNTPs (low dTTP) 0.6uL Cy3 or Cy5 (1 mM, Amersham) 3.0uL Superscript II (200 U/uL, Gibco BRL) 2.0uL Total volume: 14.6uL 4. Incubate at 42oC for 1 hr. 5. Add 1 uL SSII (RT booster) to each sample. Incubate for an additional 1 hr. 6. Degrade RNA by addition 15uL of 0.1N NaOH and incubate at 65-70oC for 10 min. 7. Neutralize by addition of 15uL of 0.1N HCl. 8. Add 380uL of TE (10mM Tris, 1mM EDTA) to a Microcon YM-30 column. Next add the 60uL of Cy5 probe and the 60??l of Cy3 probe to the same Microcon. 9. WASH 1: Spin 7-8 min. at 14,000g (=RCF). Remove flow through and save to a separate tube. 10. WASH 2: Add 450ul 1X TE and spin 7-8 min. at 14,000g. Remove flow through and save to the separate tube. 11. WASH 3: Add to centricon: 1X TE 450uL 1ug/uL Cot1 human DNA (Gibco-BRL) 20 uL 10ug/uL polyA RNA (Sigma, #P9403) 2 uL 10ug/uL tRNA (Gibco-BRL, #15401-011) 2 uL Spin 7-10 min. at 14,000g. Look for nice concentration of the "colored probe" in the centricon. Try to concentrate to a volume of less than 25uL. This volume is attained when the center of the membrane is dry and the probe forms a ring of liquid at the edges of the membrane. Make sure not to dry the membrane completely! 12. Invert the centricon into a clean tube and spin briefly at 14,000 RPM to recover the probe.; Protocol Type = Labeling; Performer: Qing,,Li
 
Channel 2
Source name 6wk BDC_2_rep2 Pancreatic LN CD4 cells
Organism Mus musculus
Characteristics cell type: 6wk BDC_2_rep2 Pancreatic LN CD4 cells
Extracted molecule total RNA
Extraction protocol Rubins 2003 - Trizol Extraction of Total RNA from PBMCs; 1. Make sure the area is clean and free of any RNases. Keep the samples cold or on ice as much as possible to prevent RNA degradation. Use only RNase free tubes and RNase free, aerosol-barrier pipette tips throughout the whole experiment. 2. Add 1mL of Trizol to the frozen PBMC pellet. 3. If the Trizol was added to the PBMCs before freezing, thaw the Trizol/PBMCs on the benchtop for 5-10 minutes. 4. Vortex and transfer to 1.5ml microfuge tubes if not already in them. 5. Add 0.2 mls chloroform per 1 ml Trizol. Vortex or shake vigorously and incubate at room temp. for 2-3 minutes. 6. Centrifuge at 12,000g for 15 minutes at 4C. 7. Transfer the aqueous phase to a fresh tube. (The volume will be about 60% of the volume of Trizol.) Note: If isolating DNA, save the organic phase. Add 1uL of 1ug/uL Linear Acrylamide if RNA yield is expected to be low. 8. Add 0.5 mLs of isopropanol per 1 ml Trizol used. Incubate at room temp. for 10 minutes. 9. Centrifuge at top speed (14,000rpm) for 10 minutes at 4C. 10. The RNA pellet will be visible at the bottom of the tube. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube. 11. WASH 1: Wash the pellet with 1 ml 70% EtOH. Centrifuge at top speed 14,000g for 5-7 minutes. 12. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube. 13. WASH 2: Wash the pellet with 1 ml 70% EtOH. Centrifuge at top speed 14,000g for 5-7 minutes. 14. Use the vacuum to very carefully aspirate the supernatant. Alternatively, carefully suck off the supernatant with a pipette. Discard supernatant. Check that the pellet is visible at the bottom of the tube. 15. Air dry pellet shortly, until no EtOH is visible (2-5 minutes). Do not overdry! 16. Resuspend the pellet in 20uls of DEPC H2O. Store at ?80C. 17. Check RNA quality and quantity by denaturing gel and OD spec (260nm and 260/280 ratio).; Protocol Type = Extract preparation; Performer: Qing,,Li
Rubins 2003 - Ambion Message Amp I; FIRST STRAND CDNA SYNTHESIS: In PCR reaction tube, mix: Amount Reagent 0.1 - 5ug Total RNA 1uL T7 Oligo (dT) primer 11uL Nuclease free water 70oC for 10 min in a thermocycler with lid on, but not clamped down. Centrifuge briefly. Prepare in a Master Mix and keep at room temperature: Amount Reagent 2uL 10X First Strand Buffer 1uL Ribonuclease Inhibitor 4uL dNTP Mix Gently pipette or flick to mix, and then centrifuge briefly. Incubate master mix at 42oC for 2 minutes prior to adding to reaction tubes. Add to the master mix: Amount Reagent 1uL Reverse Transcriptase Quickly transfer 8ul of above Master Mix to each RNA sample, mix by pipetting. 42oC for 2 hours in thermocycler with lid on, but not clamped down. Centrifuge briefly, place on ice, and immediately proceed to next step SECOND STRAND SYNTHESIS: Amount Reagent 63uL Nuclease free water 10uL 10X Second Strand Buffer 4uL dNTP Mix 2uL DNA Polymerase 1uL RNase H Add 80uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly. 16oC for 2 hours in thermocycler with lid completely off. DS cDNA CLEANUP: Preheat the 5mL bottle of water at 50oC for at least 10 minutes. Place filter cartridge in a 2mL tube and add 100ul of cDNA Binding Buffer. Incubate at room temperature for 5 min. Transfer 100uL reaction from strip-8 PCR tubes into 1.5ml Eppendorf tubes. Add 250uL of cDNA binding buffer to each cDNA sample, mix by pipetting. Add the mix to the filter cartridge. Centrifuge for 1 min at 10,000 x g. Discard flow-through. Add 650ul of cDNA wash buffer. Centrifuge for 1 min. at 10,000 x g. Discard flow-through. Centrifuge again for 1 min at 10,000 x g to remove trace amounts of ethanol. Transfer filter cartridge to fresh 2mL tube Add 50uL of preheated water to the center of the column. Incubate at room temperature for 2 minutes. Centrifuge for 1 minute at 10,000 x g. Repeat elution with a second 50ul of preheated water. Centrifuge for 1 minute at 10,000 x g. Transfer to strip-8 PCR tubes and mark a line for 8uL Concentrate the purified cDNA to < 8uL by drying in a vacuum centrifuge on high heat. Resuspend cDNA up to 8uL with H20, mix well, and keep on ice or store at ?20oC. IN VITRO TRANSCRIPTION Prepare the following master mix: Amount Reagent 8uL T7 NTP mix (75 mM each) 2uL T7 10X Reaction Buffer 2uL T7 Enzyme Mix Add 12uL to each tube. Gently pipette or flick to mix, and then centrifuge briefly. 37oC for 6 hours in hybridization oven. Add to each reaction: Amount Reagent 2uL DNaseI Gently pipette or flick to mix, and then centrifuge briefly. 37oC for 30min in hybridization oven aRNA PURIFICATION Preheat 5mL bottle of nuclease free water at 50oC for at least 10 minutes. Immediately before staring aRNA purification., equilibrate 1 filter cartridge per aRNA sample Place filter cartridge in a 2mL tube and add 100ul of aRNA Binding Buffer. Incubate at room temperature for 5 min. Add 78uL aRNA Elution Solution to each IVT mix to bring final volume up to 100uL. Add 350uL of aRNA Binding Buffer to each aRNA sample. Add 250uL of ACS grade 95% ethanol to each sample. Mix by pipetting or gentle vortexing. Apply entire sample to the equilibrated filter cartridge. Centrifuge for 1 minute at 10,000 x g. Discard flow-through but re-use tube. Add 650uL aRNA Wash Buffer to each filter. Centrifuge for 1 minute at 10,000 x g. Discard flow-through but re-use tube. Centrifuge again for 1 min at 10,000 x g Transfer cartridge to a fresh 2mL tube. Elute aRNA by adding 50uL preheated (50oC) water to center of column. Incubate at room temperature for 2 min. Centrifuge for 1 minute at 10,000 x g. Repeat elution with a second 50uL of preheated water. Centrifuge for 1 minute at 10,000 x g. Store aRNA at ?80oC.; Protocol Type = Amplification; Performer: Qing,,Li
Label Cy5
Label protocol Rubins 2003 - Labeling Amplified RNA - Direct Incorporation of Cy Dyes; Preparation of Fluorescent DNA Probe from Amplified mRNA 1. To anneal primer, mix 3-4ug of amplified mRNA with 10ug of random hexamer primer in a total volume of 15.4ul: mRNA 3-4ug pdN6 (5 ug/uL) 2uL ddH2O (DEPC) to 15.4 uL Total volume: 15.4 uL 2. Heat to 65oC for 10 min and cool on ice. 3. Add 14.6uL reaction mixture (Master Mix or separate) to each RNA/hexamer mix Reaction mixture 5X first-strand buffer 6.0uL 0.1M DTT 3.0uL Unlabeled dNTPs (low dTTP) 0.6uL Cy3 or Cy5 (1 mM, Amersham) 3.0uL Superscript II (200 U/uL, Gibco BRL) 2.0uL Total volume: 14.6uL 4. Incubate at 42oC for 1 hr. 5. Add 1 uL SSII (RT booster) to each sample. Incubate for an additional 1 hr. 6. Degrade RNA by addition 15uL of 0.1N NaOH and incubate at 65-70oC for 10 min. 7. Neutralize by addition of 15uL of 0.1N HCl. 8. Add 380uL of TE (10mM Tris, 1mM EDTA) to a Microcon YM-30 column. Next add the 60uL of Cy5 probe and the 60??l of Cy3 probe to the same Microcon. 9. WASH 1: Spin 7-8 min. at 14,000g (=RCF). Remove flow through and save to a separate tube. 10. WASH 2: Add 450ul 1X TE and spin 7-8 min. at 14,000g. Remove flow through and save to the separate tube. 11. WASH 3: Add to centricon: 1X TE 450uL 1ug/uL Cot1 human DNA (Gibco-BRL) 20 uL 10ug/uL polyA RNA (Sigma, #P9403) 2 uL 10ug/uL tRNA (Gibco-BRL, #15401-011) 2 uL Spin 7-10 min. at 14,000g. Look for nice concentration of the "colored probe" in the centricon. Try to concentrate to a volume of less than 25uL. This volume is attained when the center of the membrane is dry and the probe forms a ring of liquid at the edges of the membrane. Make sure not to dry the membrane completely! 12. Invert the centricon into a clean tube and spin briefly at 14,000 RPM to recover the probe.; Protocol Type = Labeling; Performer: Qing,,Li
 
 
Hybridization protocol not provided
Scan protocol Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = GenePix Results 3; Parameter Image Origin = 1330, 5890; Software: type: feature extraction; Performer: Qing,,Li
Description Simple annotation: Diabetes, CD4
Image: http://smd.stanford.edu/MicroArray/gifs//68830.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Mar 12, 2009
Last update date Mar 12, 2009
Contact name Hugh O McDevitt
E-mail(s) ughmcd@stanford.edu
Organization name Stanford University School of Medicine
Department Departments of Microbiology and Immunology and Medicine
Street address -
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL8291
Series (1)
GSE15213 IFN-alpha induced gene expression profile in NOD/BDC2.5 and NOD mice.

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

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 16509 34292 147 53 16362 34239 19733 37992 148 58 19586 37939 0 0 6927 8882 23 20 100 100 100 100 50601 57525 .478 2.093 1.937 4.55 2 8.14 60 454 2.05 .99 80 1910 6240 31 39 54 62 0 30368 47 30321 1.853 33645 33598 .54 1.715 .89 .779
2 15803 32274 146 55 15657 32219 18482 36441 149 63 18336 36386 0 0 6527 9856 28 55 100 100 99 100 47876 54722 .486 2.058 1.984 3.28 1.96 5.94 69 383 2.02 .99 90 2060 6230 29 38 68 77 0 28581 49 28532 1.822 32271 32222 .549 1.757 .866 .813
3 227 147 144 54 83 93 221 133 154 69 77 79 0 0 40 59 48 74 80 62 33 8 176 156 .892 1.12 1.026 1.26 1.05 .78 60 399 .64 .96 80 2210 6230 30 38 84 92 0 130 48 82 .992 118 70 1.008 .909 -.011 -.138
4 14464 43443 146 55 14318 43388 15791 45768 157 76 15645 45713 0 0 5411 15287 55 75 100 100 100 100 57706 61358 .33 3.03 2.922 3.39 3.03 1.7 64 411 3.01 .99 90 2360 6230 29 38 98 107 0 38472 49 38423 2.684 40531 40482 .373 2.588 1.424 1.372
5 19160 13118 142 53 19018 13065 21996 14582 152 66 21854 14529 0 0 6296 4432 50 61 100 100 100 100 32083 36383 1.456 .687 .665 .73 .67 .48 69 395 .69 .99 90 2510 6220 28 37 113 122 0 11617 47 11570 .608 12913 12866 1.644 .589 -.717 -.764
6 13924 15884 143 53 13781 15831 15212 17218 149 61 15069 17165 0 0 3137 3572 40 41 100 100 100 100 29612 32234 .871 1.149 1.139 1.19 1.15 .43 60 404 1.15 .99 80 2660 6230 30 38 129 137 0 14066 47 14019 1.017 15248 15201 .983 1.009 .025 .013
7 18007 21256 143 54 17864 21202 20253 23413 145 58 20110 23359 0 0 5371 6722 29 33 100 100 100 100 39066 43469 .843 1.187 1.162 1.38 1.15 1.51 69 390 1.18 .99 90 2810 6220 28 37 143 152 0 18824 48 18776 1.051 20734 20686 .951 1.029 .072 .041
8 18208 50027 140 52 18068 49975 20521 55924 147 65 20381 55872 0 0 6147 14413 37 41 100 100 100 100 68043 76253 .362 2.766 2.741 3.31 2.78 3.57 69 390 2.73 .99 90 2960 6220 28 37 158 167 0 44302 46 44256 2.449 49525 49479 .408 2.428 1.292 1.28
9 1921 1940 138 50 1783 1890 2030 2017 144 58 1892 1967 0 0 373 534 34 37 100 100 100 100 3673 3859 .943 1.06 1.04 1.05 1.08 .27 60 421 1.02 .99 80 3110 6220 29 37 174 182 0 1718 44 1674 .939 1786 1742 1.065 .921 -.091 -.119
10 16931 34375 136 51 16795 34324 18969 38851 137 55 18833 38800 0 0 5629 9621 20 21 100 100 100 100 51119 57633 .489 2.044 2.06 2.96 2.04 5.43 69 420 2.02 .99 90 3260 6220 28 37 188 197 0 30441 45 30396 1.81 34405 34360 .553 1.824 .856 .867
11 302 202 131 48 171 154 303 199 132 49 172 151 0 0 41 83 16 12 100 100 100 97 325 323 1.11 .901 .878 .88 .86 .41 60 430 .67 .97 80 3420 6220 29 37 205 213 0 179 43 136 .798 176 134 1.254 .777 -.326 -.363
12 2156 1873 134 48 2022 1825 2238 1913 134 48 2104 1865 0 0 304 276 16 10 100 100 100 100 3847 3969 1.108 .903 .886 .91 .9 .19 51 417 .87 .99 80 3560 6220 29 37 219 227 0 1659 43 1616 .799 1694 1652 1.251 .785 -.323 -.349
13 633 617 134 46 499 571 626 612 136 48 492 566 0 0 115 189 38 12 100 100 100 100 1070 1058 .874 1.144 1.15 1.12 1.11 .29 60 391 .98 .99 80 3720 6220 29 37 235 243 0 546 41 506 1.013 542 501 .987 1.019 .019 .027
14 151 63 133 48 18 15 151 61 138 50 18 13 0 0 21 15 42 17 13 42 0 15 33 31 1.2 .833 .722 1.35 .64 1.98 84 306 .42 .91 110 3870 6240 29 40 248 259 0 56 43 13 .738 54 12 1.355 .64 -.438 -.645
15 15738 38297 138 50 15600 38247 18237 44344 139 55 18099 44294 0 0 6112 12100 19 20 100 100 100 100 53847 62393 .408 2.452 2.447 3.12 2.44 3 70 384 2.43 .98 90 4020 6220 28 37 264 273 0 33915 44 33870 2.171 39270 39225 .461 2.167 1.118 1.116
16 4659 3192 133 47 4526 3145 4615 3217 133 49 4482 3170 0 0 606 641 16 11 100 100 100 100 7671 7652 1.439 .695 .707 .68 .72 .12 60 430 .7 .99 80 4170 6220 29 37 280 288 0 2827 42 2785 .615 2849 2807 1.625 .626 -.7 -.675
17 262 143 134 47 128 96 267 142 134 48 133 95 0 0 43 35 16 10 100 100 100 100 224 228 1.333 .75 .714 .77 .72 .27 60 431 .54 .98 80 4320 6220 29 37 295 303 0 127 42 85 .664 126 84 1.506 .633 -.59 -.661
18 6976 6228 135 48 6841 6180 7120 6240 136 48 6985 6192 0 0 1169 1376 16 9 100 100 100 100 13021 13177 1.107 .903 .886 .9 .92 .18 60 461 .91 .99 80 4470 6220 29 37 310 318 0 5515 43 5473 .8 5526 5483 1.25 .785 -.322 -.349
19 170 77 131 49 39 28 172 71 131 50 41 22 0 0 33 43 16 17 75 65 58 25 67 63 1.393 .718 .537 .93 .56 1.27 79 399 .46 .91 100 4650 6230 29 39 327 337 0 68 43 25 .636 63 19 1.573 .475 -.653 -1.073
20 159 70 132 47 27 23 158 61 133 48 26 14 0 0 24 45 16 10 69 64 43 38 50 40 1.174 .852 .538 1.05 .64 1.57 61 422 .44 .84 90 4800 6200 26 35 342 351 0 62 42 20 .754 54 12 1.326 .477 -.407 -1.068

Total number of rows: 38784

Table truncated, full table size 7937 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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