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Series GSE1854 Query DataSets for GSE1854
Status Public on Nov 03, 2004
Title Gene Expression Profiling of Host Response in Models of Acute HIV infection
Platform organism Homo sapiens
Sample organism Macaca fascicularis
Experiment type Expression profiling by array
Summary 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 Unpublished Data 7) Qualifier, value, source 2.2.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
Keywords: time-course
 
 
Contributor(s) Bosinger SE, Hosiawa KA, Cameron MJ, Persad D, Ran L, Xu L, Boulassel MR, Parenteau M, Fournier J, Rud EW, Kelvin DJ
Citation(s) 15557180
Submission date Oct 21, 2004
Last update date Mar 15, 2012
Contact name Steven Edward Bosinger
E-mail(s) sbosinge@uhnres.utoronto.ca
Phone 416-340-4800x6965
Fax 416-340-3619
URL http://www.transnet.ca
Organization name Toronto General Research Institute, University Health Network
Department Division of Experimental Therapeutics
Lab Laboratory of host responses
Street address 200 Elizabeth St.
City Toronto
State/province Ontario
ZIP/Postal code M5G 2C1
Country Canada
 
Platforms (2)
GPL350 UHN Microarray Centre - Human 19K 3 (Part A)
GPL351 UHN Microarray Centre - Human 19K 3 (Part B)
Samples (60)
GSM32400 chip#12243916
GSM32412 chip#12244224
GSM32413 chip#12243917
Relations
BioProject PRJNA90475

Acute HIV Infection: 1 to 5 Weeks Postinfection with SHIV89.6P header descriptions
GPL350 ID#
Gene:1 wk post-infection
Mean Log10 Ratio:1 wk post-infection
SD Log10 Ratio:1 wk post-infection
n:1 wk post-infection
Std. Error:1 wk post-infection
Lower Confidence Interval:1 wk post-infection
Upper Confidence Interval:1 wk post-infection
t:1 wk post-infection
df:1 wk post-infection
'p (2-tailed)':1 wk post-infection
Significance:1 wk post-infection
Mean Log10 Ratio: 2 wks post-infection
SD Log10 Ratio: 2 wks post-infection
n: 2 wks post-infection
Std. Error: 2 wks post-infection
Lower Confidence Interval: 2 wks post-infection
Upper Confidence Interval: 2 wks post-infection
t: 2 wks post-infection
df: 2 wks post-infection
p (2-tailed): 2 wks post-infection
Significance: 2 wks post-infection
Mean Log10 Ratio:4 wks post-infection
SD Log10 Ratio:4 wks post-infection
n:4 wks post-infection
Std. Error:4 wks post-infection
Lower Confidence Interval:4 wks post-infection
Upper Confidence Interval:4 wks post-infection
t:4 wks post-infection
df:4 wks post-infection
p (2-tailed):4 wks post-infection
Significance:4 wks post-infection
Mean Log10 Ratio:5 wks post-infection
SD Log10 Ratio:5 wks post-infection
n:5 wks post-infection
Std. Error:5 wks post-infection
Lower Confidence Interval:5 wks post-infection
Upper Confidence Interval:5 wks post-infection
t:5 wks post-infection
df:5 wks post-infection
p (2-tailed):5 wks post-infection
Significance:5 wks post-infection

Data table
GPL350 ID# Gene:1 wk post-infection Mean Log10 Ratio:1 wk post-infection SD Log10 Ratio:1 wk post-infection n:1 wk post-infection Std. Error:1 wk post-infection Lower Confidence Interval:1 wk post-infection Upper Confidence Interval:1 wk post-infection t:1 wk post-infection df:1 wk post-infection 'p (2-tailed)':1 wk post-infection Significance:1 wk post-infection Mean Log10 Ratio: 2 wks post-infection SD Log10 Ratio: 2 wks post-infection n: 2 wks post-infection Std. Error: 2 wks post-infection Lower Confidence Interval: 2 wks post-infection Upper Confidence Interval: 2 wks post-infection t: 2 wks post-infection df: 2 wks post-infection p (2-tailed): 2 wks post-infection Significance: 2 wks post-infection Mean Log10 Ratio:4 wks post-infection SD Log10 Ratio:4 wks post-infection n:4 wks post-infection Std. Error:4 wks post-infection Lower Confidence Interval:4 wks post-infection Upper Confidence Interval:4 wks post-infection t:4 wks post-infection df:4 wks post-infection p (2-tailed):4 wks post-infection Significance:4 wks post-infection Mean Log10 Ratio:5 wks post-infection SD Log10 Ratio:5 wks post-infection n:5 wks post-infection Std. Error:5 wks post-infection Lower Confidence Interval:5 wks post-infection Upper Confidence Interval:5 wks post-infection t:5 wks post-infection df:5 wks post-infection p (2-tailed):5 wks post-infection Significance:5 wks post-infection
1 26087:R37412:Hs.77490:glutathione S-transferase theta 1:GSTT1 -0.075963687 0.230614088 16 0.057653522 -0.19884926 0.046921886 -1.317589704 15 0.207411977 no -0.054705484 0.593951778 14 0.15874029 -0.420761249 0.311350281 -0.344622551 13 0.735889515 no -0.054381668 0.432602611 14 0.115617911 -0.320997049 0.212233712 -0.47035678 13 0.645893629 no 0.115900003 0.268804244 14 0.071840956 -0.049765538 0.281565545 1.613285926 13 0.130682635 no
3 25953:R37034:Hs.7045:GL004 protein:GL004 0.009141222 0.203955658 16 0.050988915 -0.099539077 0.117821521 0.179278619 15 0.860118148 no 0.336363049 0.504710346 14 0.134889514 0.025307272 0.647418826 2.493618956 13 0.026910591 no -0.051890423 0.271829824 14 0.072649576 -0.219420646 0.115639801 -0.714256372 13 0.487696176 no -0.133171133 0.206941052 16 0.051735263 -0.243442236 -0.02290003 -2.574088245 15 0.021161798 no
5 24501:T80479:In multiple clusters:: -0.013814706 0.345729672 16 0.086432418 -0.198041044 0.170411632 -0.159832462 15 0.87514546 no 0.155277279 0.532457182 14 0.142305168 -0.172879027 0.483433584 1.091156992 13 0.295014989 no -0.072567677 0.520313803 14 0.139059713 -0.39323995 0.248104597 -0.521845437 13 0.610554497 no 0.023710827 0.506193785 16 0.126548446 -0.246020802 0.293442455 0.18736561 15 0.853884856 no
7 23805:R38384:Hs.269222:mitogen-activated protein kinase 4:MAPK4 -0.201834389 0.340043415 16 0.085010854 -0.383030735 -0.020638044 -2.374219062 15 0.031364135 no -0.172332098 0.329005793 13 0.091249789 -0.388103563 0.043439366 -1.888575307 12 0.083354455 no -0.138412255 0.470198538 14 0.125665845 -0.428198214 0.151373703 -1.101430982 13 0.290684639 no -0.120140029 0.327688304 15 0.084608756 -0.311538332 0.071258275 -1.419947935 14 0.177507001 no
9 23790:T77410:Hs.145567:hypothetical protein:AF038169 -0.23846339 0.280794535 16 0.070198634 -0.388088236 -0.088838544 -3.396980497 15 0.003982381 yes -0.038838435 0.372013022 14 0.099424662 -0.268112118 0.190435247 -0.390631806 13 0.70239561 no -0.159482623 0.464729444 14 0.124204168 -0.445897948 0.126932703 -1.284035994 13 0.221542581 no 0.21904318 0.361754997 14 0.09668309 -0.003908425 0.441994785 2.265579019 13 0.041204051 no
11 22568:T74308:Hs.271980:mitogen-activated protein kinase 6:MAPK6 0.206158846 0.268218618 16 0.067054654 0.063235234 0.349082459 3.074489732 15 0.00770849 yes 0.361741168 0.269804553 14 0.0721083 0.19545913 0.528023206 5.016637031 13 0.000235921 yes 0.0315799 0.471203 14 0.125934299 -0.258825114 0.321984915 0.250764888 13 0.805915663 no -0.240259473 0.34038164 14 0.09097082 -0.45003856 -0.030480387 -2.641060878 13 0.02035489 no
13 25511:R11726:Hs.10574:solute carrier family 2, (facilitated glucose transporter) member 8:SLC2A8 0.015265842 0.142442195 15 0.036778417 -0.063616016 0.094147701 0.415076117 14 0.684377096 no -0.085040277 0.467779147 14 0.125019236 -0.373335152 0.203254598 -0.680217539 13 0.50830019 no -0.03246903 0.21275664 14 0.056861604 -0.163592124 0.098654064 -0.571018537 13 0.577725375 no -0.038132224 0.356690802 16 0.0891727 -0.228199336 0.151934888 -0.427622173 15 0.675001785 no
15 25361:R12142:Data not found:: 0.117247435 0.470598696 15 0.121508061 -0.143361436 0.377856306 0.964935447 14 0.35095034 no -0.026644506 0.34594124 13 0.095946837 -0.253522723 0.200233712 -0.277700721 12 0.785968569 no 0.058030197 0.325215328 14 0.086917452 -0.142401807 0.258462202 0.667647239 13 0.516036652 no -0.121646916 0.119163366 16 0.029790842 -0.185144591 -0.05814924 -4.083366207 15 0.000978722 yes
17 24004:R37846:Hs.78362:Human clone 23839 mRNA sequence: -0.136757661 0.215080315 16 0.053770079 -0.251365871 -0.022149451 -2.543378483 15 0.022491202 no -0.074089099 0.47754904 13 0.132448273 -0.387279498 0.239101299 -0.55938139 12 0.586190558 no -0.184367411 0.629708613 14 0.168296706 -0.572460311 0.203725489 -1.09549031 13 0.293182689 no 0.023759027 0.408742394 15 0.105536832 -0.214981874 0.262499928 0.22512545 14 0.825134596 no
19 23427:T77020:Hs.118947:Homo sapiens cDNA FLJ33090 fis, clone TRACH2000559: 0.022144492 0.169958594 16 0.042489649 -0.06842005 0.112709034 0.521173812 15 0.609854567 no -0.183273329 0.214511893 14 0.057330715 -0.315478195 -0.051068464 -3.196773834 13 0.007010999 yes -0.038166781 0.041568032 14 0.011109524 -0.063785388 -0.012548173 -3.435501038 13 0.004429726 yes -0.146516811 0.050257097 16 0.012564274 -0.173296928 -0.119736695 -11.66138283 15 6.39E-09 yes
21 22984:T75143:Hs.6473:Homo sapiens cDNA FLJ13992 fis, clone Y79AA1002139, weakly similar to DNAJ PROTEIN HOMOLOG 1: 0.027036404 0.217148294 16 0.054287074 -0.088673754 0.142746562 0.498026551 15 0.625687579 no -0.158687775 0.250797193 14 0.067028369 -0.313255472 -0.004120078 -2.367471816 13 0.034096511 no -0.057253565 0.043500011 14 0.011625867 -0.084062862 -0.030444268 -4.924670652 13 0.000277644 yes -0.139088786 0.044233159 16 0.01105829 -0.162658973 -0.1155186 -12.57778461 15 2.27E-09 yes
23 21842:T66194:Hs.2699:glypican 1:GPC1 -0.03560889 0.127292968 16 0.031823242 -0.103438525 0.032220745 -1.118958584 15 0.280757151 no -0.127254812 0.449216855 14 0.120058254 -0.404109644 0.149600019 -1.059942216 13 0.308467653 no 0.045446848 0.343076051 14 0.091690931 -0.165992819 0.256886515 0.495652597 13 0.628412713 no 0.017685469 0.18410751 16 0.046026877 -0.080418498 0.115789436 0.384242204 15 0.706191287 no
25 30084:R14795:Data not found:: -0.262572358 0.358131772 16 0.089532943 -0.453407309 -0.071737408 -2.932689906 15 0.010288962 yes 0.384915169 0.453998884 14 0.121336306 0.105113147 0.664717192 3.172300058 13 0.007349243 yes -0.007621822 0.326377414 14 0.087228033 -0.208770027 0.193526382 -0.087378131 13 0.931702555 no 0.46487245 0.32372858 14 0.086520102 0.265356736 0.664388164 5.372999314 13 0.000126881 yes
27 30081:R14792:Hs.351990:ESTs, Highly similar to CH60_HUMAN 60 KDA HEAT SHOCK PROTEIN, MITOCHONDRIAL PRECURSOR [H.sapiens]: -0.299399365 0.466003815 16 0.116500954 -0.54771527 -0.05108346 -2.569930592 15 0.02133727 no 0.011781634 0.630433808 13 0.174850878 -0.401674994 0.425238262 0.067381039 12 0.947388039 no -0.178325057 0.735179393 14 0.196484958 -0.631420181 0.274770068 -0.907576127 13 0.380618492 no 0.06256107 0.210941811 15 0.054464941 -0.060647188 0.185769327 1.148648433 14 0.269948546 no
29 30295:R14809:Hs.108771:ESTs: -0.16112805 0.343548439 16 0.08588711 -0.344192091 0.021935991 -1.876044615 15 0.080245881 no -0.002633702 0.381969761 14 0.102085713 -0.238043778 0.232776374 -0.025798928 13 0.97980954 no -0.151983148 0.444443994 14 0.118782654 -0.425896439 0.121930143 -1.27950625 13 0.223083843 no 0.064706375 0.351112752 14 0.09383883 -0.151686355 0.281099105 0.689547973 13 0.502601972 no
31 27922:R40487:Hs.21239:KIAA0985 protein:KIAA0985 -0.175378623 0.370158181 15 0.095574431 -0.380365391 0.029608145 -1.834995202 14 0.087839683 no 0.009660054 0.492172816 14 0.131538718 -0.293668774 0.312988882 0.073438865 13 0.942574843 no -0.162399053 0.653339299 14 0.174612272 -0.565055675 0.240257569 -0.930055205 13 0.369291927 no -0.080020294 0.406988187 14 0.108772168 -0.330849364 0.170808775 -0.735668834 13 0.474997044 no
33 27826:R13074:Hs.21245:ESTs: -0.192914087 0.418773091 14 0.111921816 -0.434706471 0.048878297 -1.723650431 13 0.108454301 no -0.15856951 0.448176919 14 0.11978032 -0.434783423 0.117644403 -1.323836085 13 0.208365043 no -0.178557813 0.473297466 14 0.126494068 -0.470253658 0.113138032 -1.411590404 13 0.181555239 no 0.134764853 0.498820747 14 0.133315452 -0.172661131 0.442190838 1.010871964 13 0.330523423 no
35 26782:R39119:Hs.113210:ESTs: 0.02764536 0.115783041 16 0.02894576 -0.034051067 0.089341788 0.955074593 15 0.354679695 no -0.159979962 0.226059129 14 0.060416844 -0.299301453 -0.020658471 -2.647936439 13 0.020090462 no -0.06041297 0.100764377 14 0.026930412 -0.122514612 0.001688673 -2.243299093 13 0.04293518 no -0.120469526 0.163133325 16 0.040783331 -0.207397138 -0.033541913 -2.95389127 15 0.009855172 yes
37 29754:R41661:Hs.13390:KIAA1889 protein:KIAA1889 -0.310612089 0.370039266 16 0.092509816 -0.507792095 -0.113432083 -3.357612205 15 0.004317393 yes -0.079908476 0.426913548 14 0.114097445 -0.343017656 0.183200704 -0.700352896 13 0.496050713 no -0.21284314 0.672268526 14 0.179671321 -0.62716595 0.201479669 -1.184625007 13 0.257371777 no -0.037805976 0.330674883 15 0.085379888 -0.2309487 0.155336749 -0.442797205 14 0.664677239 no
39 29841:R15138:Hs.165570:Homo sapiens clone 25052 mRNA sequence: -0.156215887 0.449251564 16 0.112312891 -0.395605147 0.083173374 -1.39089899 15 0.184545934 no 0.073588623 0.368762274 13 0.102276253 -0.168256285 0.315433531 0.719508401 12 0.485605049 no -0.195713817 0.51392781 11 0.154955065 -0.540975218 0.149547583 -1.263035948 10 0.235230714 no n/a n/a n/a n/a n/a n/a n/a n/a n/a n/a

Total number of rows: 19201

Table truncated, full table size 8221 Kbytes.




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Supplementary data files not provided

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