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Sample GSM628941 Query DataSets for GSM628941
Status Public on Dec 07, 2010
Title 252978410061_B7A_CY5_COCAR07_40_CY3.mev.refIsIB.out
Sample type genomic
 
Channel 1
Source name Genomic DNA purified from wild type bacteria
Organism Escherichia coli
Characteristics strain: cocar 07-40
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 23, 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 0.427 39 29
2 0.485 42 30
3 0.568 43 29
4 0.358 41 32
5 0.392 42 32
6 0.438 42 31
7 0.585 48 32
8 0.447 45 33
9 0.631 48 31
10 0.515 50 35
11 0.492 45 32
12 0.230 22582 19251
13 0.766 1845 1085
14 0.315 7540 6059
15 0.461 7949 5774
16 -3.686 1858 23914
17 -0.218 21895 25473
18 -0.111 19577 21144
19 -1.028 21784 44428
20 0.378 17321 13331

Total number of rows: 44961

Table truncated, full table size 984 Kbytes.




Supplementary file Size Download File type/resource
GSM628941_252978410061_B7A_CY5_COCAR07_40_CY3.txt.gz 12.6 Mb (ftp)(http) TXT
Processed data included within Sample table

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