title: chip#12273988

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate
Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = lot #465

source_name: monkey C88015F pre-infected

source_name: monkey C88015F 5 wks post SHIV89.6P infection


title: chip#12273970

status: Public on Nov 03 2004

type: RNA

city: Toronto

first: Steven

middle: Edward

last: Bosinger

state: Ontario

address: 200 Elizabeth St.

department: Division of Experimental Therapeutics

country: Canada

institute: Toronto General Research Institute, University Health Network

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate
Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = lot #467

molecule: total RNA

organism: Macaca fascicularis

source_name: monkey C95067F pre-infected

source_name: monkey C95067F 5 wks post SHIV89.6P infection


title: chip#12272967

source_name: monkey C88015F 2 wks post SHIV89.6P infection


title: chip#12273451

source_name: monkey C94071M pre-infected

source_name: monkey C94071M 4 wks post SHIV89.6P infection


title: chip#12273938


title: chip#12274309

source_name: monkey C89115M pre-infected

source_name: monkey C89115M 4 wks post SHIV89.6P infection


title: chip#12273987


title: chip#12273969

source_name: monkey C94071M 1 wk post SHIV89.6P infection


title: chip#12273877

source_name: monkey C89115M 1 wk post SHIV89.6P infection


title: chip#12321755

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate
Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = lot #464


title: chip#12272953


title: chip#12274113

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate
Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = lot #466


title: chip#12321941


title: Human bladder smooth muscle cells - non-stretched replicate 4

status: Public on Nov 04 2004

city: Boston

first: Rosalyn

last: Adam

state: MA

address: 300 Longwood Avenue

department: Urology

country: USA

institute: Children's Hospital Boston

description: Primary culture smooth muscle cells are explanted from human bladder biopsies obtained from children during open surgery for ureteral reimplantation. Cells are propagated in DMEM/10% FBS and are used between passages 3 and 5. Cells are seeded on silicone elastomer bottomed culture dishes coated with type I collagen. Non-stretched cells are maintained under identical culture conditions to cells subjected to cyclic-stretch relaxation but do not receive  the stretch stimulus. Total RNA is extracted from control and stretched cells using Trizol reagent and reverse-transcribed using Superscript II reverse transcriptase and T7-oligo dT as first-strand primer. Following clean-up cDNA was used as template for synthesis of biotin-labeled cRNA. Labeled cRNA was fragmented prior to hybridization to HG-U133A.

organism: Homo sapiens

source_name: Human bladder smooth muscle cells


title: chip#12279287

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate
Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = lot #451

source_name: monkey C95067F 2 wks post SHIV89.6P infection


title: chip#12321970


title: chip#12274180


title: HNF1b_1a-

status: Public on Nov 05 2004

city: Essen

first: Ludger

last: Klein-Hitpass

address: Virchowstr. 173

department: Universitaetsklinikum

country: Germany

institute: Institut fuer Zellbiologie

description:
A rat insulinoma cell line (INS-1) was generated that contains a FRT site for FLP recombinase mediated site specific integration of specific genes. In addition, the line contains the tetracycline repressor allowing tetracycline (tet)  induction of the introduced gene. By comparing the gene expression profiles of uninduced and tet-induced cells, target genes of introduced transcription factors can be identified. This entry corresponds to the RNA isolated from uninduced INS-1 cell line #1a containing hepatocyte nuclear factor-1b (HNF1b).
Keywords = INS-1
Keywords = beta-cell
Keywords = HNF1b
Keywords = tetracycline
Keywords = FRT
Lot batch =

organism: Rattus norvegicus

source_name: INS-1 cell line #1a with non-induced HNF1b


title: chip#12279219


title: chip#12274194


title: chip#12273516

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate

Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = lot #464


title: chip#12273507


title: chip#12279199


title: chip#12313801

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate
Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = Array lot 451

source_name: monkey C94071M 4 wk post SHIV89.6P infection


title: chip#12273481


title: chip#12273897


title: chip#12321956


title: chip#12313886

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate

Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = lot #451

source_name: monkey C89115M 4 wk post SHIV89.6P infection


title: chip#122723944


title: chip#122723476


title: chip#12279224


title: chip#12279235


title: chip#12321911


title: chip#12273468

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate
Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = lot #450


title: chip#12244204

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate
Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = Array lot 403


title: chip#12321915


title: chip#12313895


title: chip#12278808

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate

Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = lot #450


title: chip#12243536

description:
Experiment Design 1) Experiment Type normal vs diseased comparison, time course 2) Experimental Factor response to viral infection - SHIV89.6P 3) Number of hybridizations 60 4) Common Reference No 5) Quality Control Steps 4 technical replicate hybridizations per animal (3 replicate hybridizations for C89115M, C95067F) dual spotting of gene per array multiple spotting of select genes per array 2 biological replicates (2 different animals) per time point dye swaps 6) Experiment Description 4 cynomolgus monkeys (Macaca fascicularis) were infected with TCID50 of SHIV89.6P. Whole blood RNA was collected at 0, 1, 2, 4 and 5 weeks post-infection. Post-infection samples were competitively hybridized with pre-infected samples for each individual animal. Unpublished Data 7) Qualifier, value, source 2.2. Samples: samples used, extract preparation and labeling 2.2.1. Biosource properties 1) Organism (NCBI taxonomy) Macaca fascicularis 2) Contact details for sample Dr Erling W Rud Animal Resources Division, Health Canada. Sir Frederick Banting Research Centre Building 22, Room C308, postal locator 2203E Tunneys' Pasture Ottawa,Ontario, Canada K1A 0L2 Tel:(613) 957-8049 FAX:(613) 941-6625 erling_rud@hc-sc.gc.ca 3) Cell Type not applicable 4) Sex C88015F - female C89115M - male C94071M - male C95067F - female 5) Age C88015F - 13 years C89115M - 12 years C94071M - 7 years C95067F - 6 years 6) Developmental Stage adult 7) Organism Part peripheral whole blood 8) Strain or line not applicable 9) Genetic variation not applicable 10) Individual number C88015F, C89115M, C94071M & C95067F 11) Individual genetic characteristics not applicable 12) Disease state normal, AIDS 13) Targeted cell type blood 14) Cell line not applicable 2.2.2. Biomaterial manipulation 1) Growth conditions not applicable 2) In vivo treatments description - 4 cynomolgus monkeys (Macaca fascicularis) were infected intravenously with TCID50 of SHIV89.6P. 10 ml of peripheral blood was drawn at -2, 0, 1, 2, 4 and 5 weeks post-infection. 3) In vitro treatment not applicable 4) Treatment type infection 5) Compound not applicable 6) Separation technique not applicable 2.2.3. Hybridization extract preparation 1) Extraction method PAXgene peripheral blood RNA preparation 10 ml of peripheral blood was drawn from each animal directly into 4 PAXgene Blood RNA Tubes (QIAGEN #762125) according to manufacturer's protocol (http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/PaxgeneBloodRNAtube.pdf) Total RNA was purified using PAXgene Blood RNA kit (QIAGEN # 762134) according to manufacturer's protocol http://www.qiagen.com/literature/Handbooks/PDF/DNA_RNA_isolation_clinical/INT/PAXgene_Blood_RNA/1017455PAXgeneBloodRNA_prot.pdf) 2) Nucleic acid type total RNA 3) Amplification Method Total RNA was amplified using the Ambion MessageAmp aRNA kit (#1750), an Eberwine based method, with slight modifications to the manufacturer's protocol (http://www.transnet.ca/Amplification%20Protocol.htm). 2.2.3. Sample labeling 1) Amount of nucleic acid labeled 6 micrograms of aRNA was labeled with Cy3/Cy5 for hybridization 2) Label used Cy5 & Cy3 3) Label incorporation method aRNA was labelled by reverse transcription using the standard protocol of the Ontario Cancer Institute with slight modifications (http://www.transnet.ca/Hybridization%20Protocol_2.htm) 2.2.5. Spiking controls 1) Spiking control feature OCI Human 19k3-part1 OCI Human 19k3-part2 2) Spike type and qualifier not applicable 3) Qualifier, value, source not applicable 2.3. Hybridization procedure and parameters 2) Hybridization Protocol Protocol - (http://www.transnet.ca/Hybridization%20Protocol_2.htm) Solution Hybridization buffer: DIG solution (Roche cat.#1603558) supplemented with 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA Blocking agent not applicable Slide blocking not applicable Probe blocking: 0.45 ug/ul yeast tRNA, 0.45 ug/ul salmon sperm DNA during hybridization Wash procedure 3x15 min with 1xSSC, 0.1% SDS at 50 degrees Celsius, 3 fast washes in 1xSSC at 50 degrees Celsius Quantity of labelled target used all material generated from 6 ug amplified RNA per sample Time 18 hr (overnight) hybridization Concentration 0.2 ug/ul of aRNA per hybridization Volume 60 ul Temperature 30 degrees Celsius Description of the hybridization chamber hybridizations were incubated in a microscope slide box stored within a tissue culture incubator Qualifier, value, source not applicable 2.4. Measurements 2.4.1. Raw data Scanning protocol Scanning hardware: Scanarray Express Microarray Scanner, Packard Biosciences Scanning software: Scanarray Express Microarray Analysis System v1.1 Build #9 Scan Parameters Laser power: see individual image files in section 2.4.1 Spatial resolution:10 microns PMT gain: 60% 2.4.2. Image analysis and quantitation Image analysis software: Quantarray v.3.0, Packard BioSciences Availability: No longer commercially available Quantitation Parameters: Array Pattern: Spot rows: 25 Spot columns: 24 Spot spacing (vertical): 170 microns Spot spacing (horizontal): 170 microns Interstitial spacing: Off Array rows: 8 Array columns: 4 Array spacing (vertical): 4500 microns Array spacing (horizontal): 4500 microns Auto-adjustable Grid: Grid elasticity: 50/100 Spot elasticity: 50/100 Quantitation: Method: Fixed Circle Crosstalk correction: No Normalized to brightest: No Background subtraction: No Gene database file: for OCI Human 19k3-part1- H19k3a.qa (attached) for OCI Human 19k3-part2- H19k3b.qa (attached) Fixed circle quantitation parameters: Spot diameter: 60 microns Inner background diameter: 180 microns Outer background diameter: 200 microns Signal low percentile: 45 Signal high percentile: 95 Background low percentile: 5 Background high percentile: 55 Quantification output: Mean Intensity Quality Criteria Confidence calculation: Minimum Tolerance and weight: None selected Replicates: Combine replicates: no 2.4.3. Normalized and summarized data Data processing protocol Background subtraction and normalization Background subtraction and normalization was performed using the Quantarray Normalization Excel macro on individual quantitation output files. Each channel was background subtracted using the equation: ch Bkg. Subtr. Intensity = ch intensity - ch Bkg. Normalization strategy: total array Normalization algorithm: log ratio median centering Median log ratio = median(log2(ch1 Bkg. Subtr. Intensity) - log2(ch2 Bkg. Subtr. Intensity)) Normalization factor = 2^ median log ratio Normalized ch2 intensity = ch2 intensity*Normalization factor Statistical Analysis The background subtracted normalized intensities were used for statistical analysis. All spot intensities for within-chip, repeat hybridization, fluor-flip hybridization and biological replicates for each time point post-infection were compiled and tested for significance testing using the software package ArrayStat v.1.0, Imaging Research. ArrayStat parameters: Model selection: Manual Model selected: Proportional model with offsets Outlier detection: yes Threshold detection: Manual Threshold detected: p<0.01 Minimum No. of replicates: 12 (for 1 & 5 wks PI), 11 (for 2 & 4 wks PI) Conditions: Dependent Random Error Estimation Method: Small Sample Test: t-test Normalization: By median Nominal alpha: 0.05 Multiple Test correction: False Discovery Rate

Keywords = SHIV89.6P
Keywords = HIV
Keywords = nonhuman primate
Keywords = cDNA microarray
Keywords = time course
Lot batch = Array lot 403


title: chip#12243542


title: chip#12244261


title: chip#12244218


title: chip#12278816


title: B_Kin_3

city: Columbus

first: David

middle: Lawrence

last: Newsom

state: OH

department: Human Cancer Genetics

institute: Comprehensive Cancer Center

description:
K562 cell line treated for 24 hours with one micromolar imatinib. RNA was extracted using a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA and included half the standard level of Affymetrix RNA spike in controls.
Keywords = Human, leukemia, mock treated

source_name: K562 Cell line


title: chip#12278771

source_name: monkey C88015F pre-infected


title: chip#12251773


title: chip#12244217


title: chip#12278751


title: chip#12244224

source_name: monkey C88015F 5 wks post SHIV89.6P infection


title: chip#12324506


title: B_Kin_1


title: B_Ctrl_2

description:
K562 cell line was mock treated.  RNA was extracted using Trizol plus Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 8ug of total RNA and included suggested level of Affymetrix RNA spike controls.
Keywords = Human, leukemia, mock treated

source_name: K562 cell line


title: B_Ctrl_3


title: B_Ctrl_1