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Sample GSM629173 Query DataSets for GSM629173
Status Public on Dec 07, 2010
Title 252978410075_B7A_CY5_ETP05_035_CY3.mev.refIsIB.out
Sample type genomic
 
Channel 1
Source name Genomic DNA purified from wild type bacteria
Organism Escherichia coli
Characteristics strain: ETP05-035
Biomaterial provider Philip R. Hardwidge,University of Kansas Medical Center, USA,James M. Fleckenstein,U. Tennessee Health Science Center, USA,Robert J. Belland,U. Tennessee Health Science Center , USA, Roy Curtiss, III,Arizona State University, USA, David H. Francis,South Dakota State University, USA, Oscar G. Gomez-Duarte University of Iowa Childrens' Hospital, USA,Robert P. Gormley,US Navy, USA, Rodney A. Moxley,University of Nebraska, USA, George P. Munson,University of Miami, USA Firdausi Qadri,Intl. Centre for Diarrhoeal Disease Research, Bangladesh, Stephen J. Savarino,US Navy, USA
Treatment protocol None
Growth protocol cells were grown in LB overnight at 37 degrees celcius.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated by lysozyme and proteinase K treatment.
Label Cy3
Label protocol 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen). Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).
 
Channel 2
Source name Genomic DNA purified from wild type bacteria
Organism Escherichia coli
Characteristics strain: B7A
Biomaterial provider Philip R. Hardwidge,University of Kansas Medical Center, USA,James M. Fleckenstein,U. Tennessee Health Science Center, USA,Robert J. Belland,U. Tennessee Health Science Center , USA, Roy Curtiss, III,Arizona State University, USA, David H. Francis,South Dakota State University, USA, Oscar G. Gomez-Duarte University of Iowa Childrens' Hospital, USA,Robert P. Gormley,US Navy, USA, Rodney A. Moxley,University of Nebraska, USA, George P. Munson,University of Miami, USA Firdausi Qadri,Intl. Centre for Diarrhoeal Disease Research, Bangladesh, Stephen J. Savarino,US Navy, USA
Treatment protocol None
Growth protocol cells were grown in LB overnight at 37 degrees celcius.
Extracted molecule genomic DNA
Extraction protocol Genomic DNA was isolated by lysozyme and proteinase K treatment.
Label Cy5
Label protocol 4ug of genomic DNA was labeled at 37 degree Celcius overnight using DNA polymerase I Klenow fragment (New England Biolabs), a 25X 2:1 amino allyl dUTP (Ambion) dNTP mix, and random hexamers (Invitrogen). Labeled DNA was purified with Qiaquick PCR purification kit (QIAGEN).The purified labelled DNA was then dye coupled with the appropriate cye dye (CY3/CY5).
 
 
Hybridization protocol Equal concentrations of DNA probe from the appropriate Cy3 and Cy5 labeled probes were combined, dried and then resuspended in hybridization buffer as defined by the Agilent Oligonucleotide Array-Based CGH protocol. Resuspended probes were denatured at 95 degree Celcius and held at 37 degree Celcius prior to hybridization. The probe mixture then was added to the Agilent microarray slide and allowed to hybridize for 24 hours rotating at 20 rpm in a hybridization oven at 65 degree Celcius. Hybridized slides were washed sequentially as defined by the Agilent Oligonucleotide Array-Based CGH protocol.
Scan protocol Scanned on Axon GenePix 4000 scanner. PMT values were optimized during scanning to balance channel intensities.
Data processing Procedures to calculate the value of log2 ratio:
1. Use Agilent software Feature Extraction to analyze spotted arrays.
2. Use TM4 suite software ExpressConverter to modify Agilent Feature Extraction file into *.mev.
3. Calculate the value of log2 ratio (Reference/Query) from the normalized .mev file:
3a). If both channels (QUERY_MEDIAN_INTENSITY and REF_MEDIAN_INTENSITY) are zero, assign the value "null".
3b). If one channel is zero and the other is not zero, substitute the zero with one (1) and then, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE
3c). If neither channel is zero, assign the log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY to VALUE.
 
Submission date Nov 24, 2010
Last update date Dec 06, 2010
Contact name John Braisted
E-mail(s) jbraisted@jcvi.org
Organization name J Craig Venter Institute
Department PFGRC
Lab PFGRC_EXTSW
Street address 9704 Medical Center Dr
City Rockville
State/province MD
ZIP/Postal code 20850
Country USA
 
Platform ID GPL10979
Series (1)
GSE25601 Novel gene discovery in up to 10 ETEC strains and production of species microarray. Discovery of conserved and unique ETEC genes by comparative genome hybridization studies.

Data table header descriptions
ID_REF
VALUE log2 ratio of QUERY_MEDIAN_INTENSITY/REF_MEDIAN_INTENSITY.
QUERY_MEDIAN_INTENSITY Query strain median intensity.
REF_MEDIAN_INTENSITY Reference strain median intensity.

Data table
ID_REF VALUE QUERY_MEDIAN_INTENSITY REF_MEDIAN_INTENSITY
1 0.367 49 38
2 0.406 53 40
3 0.389 55 42
4 0.376 61 47
5 0.278 57 47
6 0.490 66 47
7 0.631 79 51
8 0.602 85 56
9 0.515 70 49
10 0.503 68 48
11 0.694 89 55
12 0.461 19453 14128
13 1.116 2972 1371
14 0.725 12206 7384
15 0.784 10783 6264
16 -2.778 2206 15128
17 -0.043 17683 18212
18 0.253 17016 14275
19 -0.544 24216 35301
20 0.480 20448 14656

Total number of rows: 44961

Table truncated, full table size 982 Kbytes.




Supplementary file Size Download File type/resource
GSM629173_252978410075_B7A_CY5_ETP05_035_CY3.txt.gz 12.5 Mb (ftp)(http) TXT
Processed data included within Sample table

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