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XHM: a system for detection of potential cross hybridizations in DNA microarrays

Kristian Flikka, Fekadu Yadetie, Astrid Laegreid, Inge Jonassen
2004 BMC Bioinformatics  
We have developed a tool called XHM (cross hybridization on microarrays) for assessment of the reliability of hybridization signals by detecting potential cross-hybridizations on DNA microarrays.  ...  Cross-hybridization among genes with high sequence similarities can be a source of error reducing the reliability of DNA microarray results.  ...  Acknowledgments We would like to thank Per Winge at Department of Biology, Norwegian University of Science and Technology (NTNU) for useful discussions on DNA hybridization.  ... 
doi:10.1186/1471-2105-5-117 pmid:15333145 pmcid:PMC517492 fatcat:fkviczgbpnavtfwn7how5g3j3e

Microbial Community Functional Structures in Wastewater Treatment Plants as Characterized by GeoChip [chapter]

XIAOHUI WANG, YU XIA, XIANGHUA WEN, YUNFENG YANG, JIZHONG ZHOU
2015 Bioremediation of Wastewater  
A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and  ...  Aims: To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure.  ...  Also, in our study, the DNA rather than cDNA from RNA was used for GeoChip hybridization.  ... 
doi:10.1201/b18618-11 fatcat:f3kblogaq5eetnal5z6iv5zgne

Microbial Community Functional Structures in Wastewater Treatment Plants as Characterized by GeoChip

Xiaohui Wang, Yu Xia, Xianghua Wen, Yunfeng Yang, Jizhong Zhou, Zhi Zhou
2014 PLoS ONE  
A comprehensive functional gene array named GeoChip 4.2 was used to determine the microbial functional genes involved in a variety of biogeochemical processes such as carbon, nitrogen, phosphorous and  ...  Aims: To investigate microbial community functional structures of activated sludge in wastewater treatment plants (WWTPs) and to understand the effects of environmental factors on their structure.  ...  Also, in our study, the DNA rather than cDNA from RNA was used for GeoChip hybridization.  ... 
doi:10.1371/journal.pone.0093422 pmid:24671164 pmcid:PMC3966879 fatcat:olcgrwznzzah7nglperfvqj4ea

The Zinc Finger Mutation C417R of I- B Kinase Impairs Lipopolysaccharide- and TNF-Mediated NF- B Activation through Inhibiting Phosphorylation of the I- B Kinase Activation Loop

F. Yang, J. Yamashita, E. Tang, H.-l. Wang, K. Guan, C.-Y. Wang
2004 Journal of Immunology  
Sun for providing mutant Jurkat T cells, and Dr. Brian Ashburner for plasmids.  ...  Aliquots (15 g) of RNA samples were separated on a 1.4% agarose-formaldehyde gel and transferred onto a nylon filter for 16 -24 h (Bio-Rad). RNA was cross-linked with a UV cross-linker (Promega).  ...  In contrast, the phosphorylation of the activation loop of IKK␤ induced by LPS was not detected in THP/IKK␥C417R cells.  ... 
doi:10.4049/jimmunol.172.4.2446 pmid:14764716 fatcat:35yxsbagrne77ai4k3ax4qusq4