Investigation Title Transcription profiling of E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development Comment[Submitted Name] Comparison between E. coli K-12 BW25113 wt and E. coli K-12 BW25113 yjgK deleted mutant on 8 h biofilm cell development Experimental Design unknown_experiment_design_type transcription profiling by array Experimental Design Term Source REF EFO Comment[SecondaryAccession] GSE12701 Comment[ArrayExpressReleaseDate] 2009-02-09 Comment[AEMIAMESCORE] 4 Comment[ArrayExpressAccession] E-GEOD-12701 Comment[MAGETAB TimeStamp_Version] 2010-07-30 05:22:48 Last Changed Rev: 13058 Experimental Factor Name Experimental Factor Type Experimental Factor Term Source REF Person Last Name Kim Person First Name Younghoon Person Mid Initials Person Email Younghoon.Kim@chemail.tamu.edu Person Phone Person Fax Person Address Dr. Wood's Lab, Chemical Engineering, Texas A and M University, Room 502 Jack E. Brown building 3122 TAMU, College Station, 77843, USA Person Affiliation Texas A and M University Person Roles submitter Person Roles Term Source REF The MGED Ontology Quality Control Type Quality Control Term Source REF Replicate Type Replicate Term Source REF Normalization Type Normalization Term Source REF Date of Experiment Public Release Date 2009-02-09 PubMed ID Publication DOI Publication Author List Publication Title Publication Status Publication Status Term Source REF Experiment Description The role of six toxin-antitoxin (TA) systems on biofilm development was investigated (MazEF, RelBEF, ChpB, YefM-YoeB, DinJ-YafQ, and TomB-Hha). Although these TA systems were reported previously to not impact bacterial fitness, we found that biofilm formation is decreased by toxins and increased by anti-toxins, in part, through YjgK. Hence, one role of TA systems is to regulate biofilm formation. Experiment Overall Design: Strains: E. coli K-12 BW25113 wild-type and E. coli BW25113 yjgK deleted mutant Experiment Overall Design: Medium: LB Experiment Overall Design: Cells: biofilm cells on glass wool Experiment Overall Design: Time: 8 h Experiment Overall Design: Temperature: 37oC Protocol Name P-G12701-2 P-G12701-1 P-AFFY-6 Affymetrix:Protocol:ExpressionStat Protocol Type nucleic_acid_extraction labeling feature_extraction bioassay_data_transformation Protocol Description The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 8 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater (cat. no. 3110BX, Biospec), and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104) including an on-column DNase digestion with RNase-free DNase I (Qiagen). The total RNA samples were first converted into cDNA through a reverse transcription reaction with poly-A RNA controls spiked into the same reaction mixture to monitor the entire target labeling process. The cDNA was then digested with DNase I (Amersham Biosciences) to produce 50-200 bp fragments, which was checked by running the fragmented cDNA on a 2% agarose gel. The fragmented cDNA was labeled at the 3’ termini by the Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix, P/N 900181). Title: Affymetrix CEL analysis. Description: Title: Affymetrix CHP Analysis (ExpressionStat). Description: Protocol Parameters Protocol Hardware Protocol Software MicroArraySuite 5.0 MicroArraySuite 5.0 Protocol Contact Protocol Term Source REF The MGED Ontology SDRF File E-GEOD-12701.sdrf.txt Term Source Name The MGED Ontology ArrayExpress EFO The MGED Ontology Term Source File http://mged.sourceforge.net/ontologies/MGEDontology.php http://www.ebi.ac.uk/arrayexpress http://www.ebi.ac.uk/efo/ http://mged.sourceforge.net/ontologies/MGEDontology.php Term Source Version