NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM379994 Query DataSets for GSM379994
Status Public on Mar 13, 2009
Title 6wk BDC_1_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_1_rep2 Pancreatic LN CD4 cells
Organism Mus musculus
Characteristics cell type: 6wk BDC_1_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//68829.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 25122 40841 157 55 24965 40786 29555 45915 160 62 29398 45860 0 0 8962 11432 27 33 100 100 100 100 65751 75258 .612 1.634 1.56 2.3 1.61 3.27 60 447 1.62 .99 80 1910 6200 27 35 54 62 0 44874 60 44814 1.795 50450 50389 .557 1.714 .844 .777
2 25074 40340 160 57 24914 40283 30192 45887 163 65 30032 45830 0 0 9735 12911 29 34 100 100 100 100 65197 75862 .618 1.617 1.526 2.37 1.59 3.3 64 395 1.61 .99 90 2060 6200 26 35 68 77 0 44324 63 44261 1.777 50419 50356 .563 1.677 .829 .746
3 238 120 161 54 77 66 238 119 162 59 77 65 0 0 27 25 22 21 96 100 90 78 143 142 1.167 .857 .844 .97 .88 .53 51 392 .5 .98 80 2200 6190 26 34 83 91 0 132 59 73 .942 131 71 1.062 .928 -.087 -.109
4 26275 61809 158 54 26117 61755 29047 65535 158 60 28889 65481 0 72 5887 8727 22 25 100 100 100 100 87872 94370 .423 2.365 2.267 2.48 2.27 .59 60 421 2.34 .99 80 2350 6190 26 34 98 106 -100 67913 59 67854 2.598 72007 71948 .385 2.49 1.377 1.316
5 30165 18743 157 54 30008 18689 31965 19156 157 59 31808 19102 0 0 6309 3356 21 37 100 100 100 100 48697 50910 1.606 .623 .601 .64 .62 .16 60 398 .62 1 80 2500 6190 26 34 113 121 0 20594 59 20535 .684 21048 20989 1.461 .66 -.547 -.6
6 21960 24115 154 54 21806 24061 23580 25219 157 60 23426 25165 0 0 4370 3896 39 51 100 100 100 100 45867 48591 .906 1.103 1.074 1.12 1.09 .2 60 412 1.1 1 80 2650 6190 26 34 128 136 0 26497 59 26437 1.212 27710 27650 .825 1.18 .278 .239
7 29678 33160 155 54 29523 33106 32396 34293 155 58 32241 34239 0 0 7522 6337 21 17 100 100 100 100 62629 66480 .892 1.121 1.062 1.21 1.08 .53 60 429 1.11 .99 80 2800 6190 26 34 143 151 0 36435 59 36376 1.232 37680 37620 .812 1.167 .301 .223
8 29887 60495 153 55 29734 60440 33309 65535 159 67 33156 65480 0 81 9213 12242 36 43 100 100 100 100 90174 98636 .492 2.033 1.975 2.32 2 1.35 64 443 2.02 .99 90 2960 6190 25 34 158 167 -100 66470 60 66409 2.233 72007 71947 .448 2.17 1.159 1.118
9 2362 2787 151 52 2211 2735 2514 2852 156 63 2363 2800 0 0 594 708 37 48 100 100 100 100 4946 5163 .808 1.237 1.185 1.35 1.23 .71 60 430 1.18 .99 80 3110 6190 26 34 174 182 0 3062 57 3005 1.359 3134 3077 .736 1.302 .443 .381
10 26359 52050 150 51 26209 51999 28158 55713 151 57 28008 55662 0 0 6201 9401 25 27 100 100 100 100 78208 83670 .504 1.984 1.987 2.26 2 1.85 60 430 1.99 .99 80 3260 6190 26 34 189 197 0 57190 56 57134 2.18 61215 61159 .459 2.184 1.124 1.127
11 340 234 148 49 192 185 346 229 149 51 198 180 0 0 59 60 17 13 100 100 100 100 377 378 1.038 .964 .909 1.01 .97 .37 60 422 .68 .99 80 3410 6190 26 34 204 212 0 257 54 203 1.059 252 198 .945 .999 .082 -.002
12 2295 1887 147 50 2148 1837 2402 1946 148 50 2255 1896 0 0 368 366 17 10 100 100 100 100 3985 4151 1.169 .855 .841 .84 .87 .1 51 412 .83 1 80 3560 6180 25 33 219 227 0 2073 55 2018 .94 2138 2083 1.064 .924 -.09 -.114
13 919 1076 144 49 775 1027 970 1104 145 49 826 1055 0 0 266 289 18 12 99 100 97 100 1802 1881 .755 1.325 1.277 1.79 1.28 2.45 69 423 1.15 .99 90 3710 6180 24 33 233 242 0 1182 54 1128 1.456 1213 1159 .687 1.403 .542 .489
14 168 71 146 51 22 20 169 65 146 52 23 14 0 0 21 31 17 12 63 56 21 23 42 37 1.1 .909 .609 1.1 .68 1.35 52 437 .41 .75 80 3880 6190 26 34 251 259 -50 78 56 22 .999 71 15 1.001 .669 -.002 -.58
15 22861 51925 147 53 22714 51872 26903 61179 147 57 26756 61126 0 12 9370 17307 17 17 100 100 100 100 74586 87882 .438 2.284 2.285 3.1 2.33 3.06 69 383 2.26 .99 90 4010 6180 24 33 263 272 0 57053 58 56995 2.509 67221 67163 .399 2.51 1.327 1.328
16 4311 3037 143 49 4168 2988 4693 3247 144 51 4550 3198 0 0 1329 846 18 14 100 100 100 100 7156 7748 1.395 .717 .703 .77 .72 .38 64 426 .7 .99 90 4170 6190 25 34 279 288 0 3337 54 3283 .788 3568 3514 1.27 .772 -.344 -.373
17 267 137 142 50 125 87 265 131 143 51 123 81 0 0 43 35 17 10 98 100 97 98 212 204 1.437 .696 .659 .76 .68 .38 60 419 .51 .98 80 4320 6190 26 34 295 303 0 151 55 96 .765 144 89 1.308 .724 -.387 -.467
18 7750 6128 142 49 7608 6079 8089 6572 142 48 7947 6523 0 0 1832 1647 17 9 100 100 100 100 13687 14470 1.252 .799 .821 .79 .82 .16 60 450 .8 1 80 4470 6180 25 33 310 318 0 6733 54 6679 .878 7221 7167 1.139 .902 -.188 -.149
19 169 63 137 48 32 15 166 60 138 48 29 12 0 0 30 18 17 10 63 57 46 24 47 41 2.133 .469 .414 .84 .41 1.47 80 402 .37 .92 100 4650 6200 26 36 327 337 0 69 53 16 .515 66 13 1.942 .455 -.957 -1.137
20 174 71 139 48 35 23 173 68 140 50 34 20 0 0 26 20 23 17 68 63 33 20 58 54 1.522 .657 .588 1.02 .63 1.3 60 392 .41 .91 80 4790 6190 26 34 342 350 0 78 53 25 .722 75 22 1.385 .646 -.47 -.63

Total number of rows: 38784

Table truncated, full table size 7927 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap