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Sample GSM1082987 Query DataSets for GSM1082987
Status Public on Dec 01, 2013
Title Rickettsia rickettsii transcriptome - ch2: G1 replicate 2; ch1: G2 replicate 2
Sample type RNA
 
Channel 1
Source name Temperature G2 Cy3
Organism Rickettsia rickettsii
Characteristics strain: str. Taiaçu
tissue: Pool of internal organs of 7 Amblyomma aureolatum female infected ticks
group: G2; incubated at 35C for 3 days
Treatment protocol Right after molting to adult, not fed females of A. aureolatum were incubated at 35oC and 93% relative humidity (RH) for 3 days
Growth protocol Ticks were mainteined for 3 days at incubator conditons described above
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Invitrap TwinSpin Cell Mini Kit (Stratec) and reverse transcribed using MessageAmp II Bacteria RNA Amplification Kit (Ambion)
Label Cy3
Label protocol Agilent's Genomic DNA ULS Labeling Kit
 
Channel 2
Source name Temperature G1 Cy5
Organism Rickettsia rickettsii
Characteristics strain: str. Taiaçu
tissue: Pool of internal organs of 7 Amblyomma aureolatum female infected ticks
group: G1; incubated at 25C for 3 days
Treatment protocol Right after molting to adult, not fed females of A. aureolatum were incubated at 25oC and 93% relative humidity (RH) for 3 days
Growth protocol Ticks were mainteined for 3 days at incubator conditons described above
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using Invitrap TwinSpin Cell Mini Kit (Stratec) and reverse transcribed using MessageAmp II Bacteria RNA Amplification Kit (Ambion)
Label Cy5
Label protocol Agilent's Genomic DNA ULS Labeling Kit
 
 
Hybridization protocol Two-Color Microarray-Based Gene Expression Analysis Protocol
Scan protocol Fluorescent array images were collected for both Cy3 and Cy5 with a High-Resolution C Scanner (Agilent Technologies) using Agilent Settings and image intensity data were extracted with Feature Extraction 10.5 Software using Agilent Settings
Description R. rickettsii under 35oC X R. rickettsii under 25oC, experiment 4
Data processing Raw and background corrected data
 
Submission date Feb 14, 2013
Last update date Dec 01, 2013
Contact name Maria Fernanda Galletti
E-mail(s) [email protected]
Organization name Universidade de São Paulo - Instituto de Ciências Biomédicas - Departamento de Parasitologia
Department Department of Parasitology
Lab Bioquemistry and Immunology of Arthropods
Street address Av. Prof. Lineu Prestes, 1374 sala 39
City São Paulo
State/province São Paulo
ZIP/Postal code 05508-900
Country Brazil
 
Platform ID GPL16681
Series (2)
GSE44316 Rickettsia rickettsii transcriptome - Elevation of temperature response
GSE44349 Natural blood feeding and temperature shift modulate the global transcriptional profile of Rickettsia rickettsii.

Data table header descriptions
ID_REF ID column of the reference platform
gSignal Raw Median Signal of feature in green channel
rSignal Raw Median Signal of feature in red channel
gProcessedSignal Dye-normalized signal after surrogate algorithm,green channel,used for computation of log ratio.
rProcessedSignal Dye-normalized signal after surrogate algorithm,red channel,used for computation of log ratio.
VALUE log(gProcessedSignal/rProcessedSignal) representing (test/control)
INV_VALUE log(rProcessedSignal/gProcessedSignal)

Data table
ID_REF gSignal rSignal gProcessedSignal rProcessedSignal VALUE INV_VALUE
1 5.331303e+004 6.552900e+004 4.371090e+005 3.305745e+005 0.12132 -1.213204144e-001
2 1.371290e+002 1.717742e+002 6.081118e+001 1.227290e+002 -0.304964 3.049637518e-001
3 1.421333e+002 1.659167e+002 6.224846e+001 9.159600e+001 0.000000000e+000 0.000000000e+000
4 1.555938e+002 1.921250e+002 5.659007e+001 2.987692e+002 -0.722596 7.225955037e-001
5 2.142031e+002 2.421719e+002 3.561534e+002 6.827886e+002 -0.282649 2.826492006e-001
6 2.728636e+002 3.305606e+002 6.924539e+002 1.324088e+003 -0.281526 2.815259375e-001
7 2.746563e+002 2.780938e+002 6.998868e+002 9.467069e+002 -0.131188 1.311877360e-001
8 2.611905e+002 2.837460e+002 6.254658e+002 9.961065e+002 -0.202102 2.021021770e-001
9 1.584762e+002 1.889524e+002 6.384117e+001 3.094472e+002 -0.685486 6.854857339e-001
10 1.344576e+002 1.383051e+002 6.077489e+001 9.135597e+001 0.000000000e+000 0.000000000e+000
11 1.793492e+002 1.980476e+002 1.733892e+002 4.008235e+002 -0.363931 3.639312040e-001
12 2.030313e+002 2.025781e+002 3.013572e+002 4.339100e+002 -0.158318 1.583180461e-001
13 1.923607e+002 2.022623e+002 2.461630e+002 4.401470e+002 -0.252375 2.523749848e-001
14 1.364355e+002 1.462419e+002 5.977042e+001 9.118854e+001 0.000000000e+000 0.000000000e+000
15 4.295077e+002 4.911846e+002 1.533661e+003 2.550306e+003 -0.220863 2.208629230e-001
16 1.792540e+002 1.885397e+002 1.823761e+002 3.549221e+002 -0.289165 2.891652238e-001
17 1.533846e+002 1.441385e+002 6.455727e+001 9.195931e+001 0.000000000e+000 0.000000000e+000
18 2.011803e+002 1.841803e+002 2.978173e+002 3.263469e+002 -0.0397296 3.972959206e-002
19 1.402698e+002 1.384603e+002 5.847982e+001 9.096871e+001 0.000000000e+000 0.000000000e+000
20 1.461791e+002 1.617761e+002 5.584342e+001 1.477599e+002 -0.422584 4.225844690e-001

Total number of rows: 15744

Table truncated, full table size 1398 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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