Comment[ArrayExpressAccession]	E-GEOD-6221
Public Release Date	2008-05-07
Investigation Title	Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris 								
Comment[Submitted Name]	Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris 
Experiment Description	To address the question of how photosynthetic bacterium Rhodopseudomonas palustris metabolize lignin derived compound p-coumarate, transcriptomics and quantitative proteomics were combined to characterize gene expression profiles at both the mRNA level and protein level in Rhodopseudomonas palustris grown with succinate, benzoate, and p-coumarate as the carbon source. Transcriptome profiles among Rhodopseudomonas palustris cells grown with succinate, benzoate, and p-coumarate as the carbon source were compared.								
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Term Source Name	EFO
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Term Source File	http://efo.svn.sourceforge.net/viewvc/efo/trunk/src/efoinowl/efo.owl								
Person Last Name	Oda	Pan	Oda	Pelletier	Zhang	Lankford	Samatova	Harwood	Hettich
Person First Name	Yasuhiro 	Chongle	Yasuhiro	Dale	Bing	Patricia	Nagiza	Caroline	Robert
Person Mid Initials				A		K	F	S	L
Person Email	yasuhiro@u.washington.edu								
Person Affiliation	University of Washington								
Person Phone	206-221-2798								
Person Fax	206-543-8297								
Person Address	Department of Microbiology, University of Washington, Box 357242, 1705 N.E. Pacific Street, HSB K-327, Seattle, WA, USA								
Person Roles	submitter								
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Protocol Name	P-GSE6221-1	P-GSE6221-5	P-GSE6221-4	P-GSE6221-2	P-GSE6221-3	P-GSE6221-6			
Protocol Description	ID_REF = <br>VALUE = Signal intensity<br>ABS_CALL = Detection	As recommended by the manufacturer (Affymetrix)	As recommended by the manufacturer (Affymetrix)	Rhodopseudomonas palustris cells were disrupted by treatment with by bead beating and RNA was purified with the RNeasy Mini kit (Qiagen) including DNase treatment on the column.	As recommended by the manufacturer (Affymetrix)	The Affymetrix Microarray Suite was used for initial data acquisition and processing. 			
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Protocol Type	bioassay_data_transformation	image_aquisition	hybridization	nucleic_acid_extraction	labeling	feature_extraction			
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Publication Title	Characterization of anaerobic catabolism of p-coumarate in Rhodopseudomonas palustris by integrating transcriptomics and quantitative proteomics.								
Publication Author List	Pan C, Oda Y, Lankford PK, Zhang B, Samatova NF, Pelletier DA, Harwood CS, Hettich RL								
PubMed ID	18156135								
Publication DOI	10.1074/mcp.M700147-MCP200								
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Comment[SecondaryAccession]	GSE6221								
Comment[GEOLastUpdateDate]	2008-05-07
Comment[GEOReleaseDate]	2008-05-06
Comment[ArrayExpressSubmissionDate]	2006-11-02
SDRF File	E-GEOD-6221.sdrf.txt