Comment[ArrayExpressAccession] E-GEOD-39530 MAGE-TAB Version 1.1 Public Release Date 2012-11-20 Investigation Title Developmental stage specific metabolic and transcriptional activity of chlamydial elementary bodies and reticulate bodies in an axenic medium Comment[Submitted Name] Developmental stage specific metabolic and transcriptional activity of chlamydial elementary bodies and reticulate bodies in an axenic medium Experiment Description Chlamydia trachomatis is a significant human pathogen yet their obligate intracellular nature severe restrictions upon research. Chlamydiae undergo a complex developmental cycle characterized by an infectious cell type known as the elementary body (EB) and an intracellular active replicative form called the reticulate body (RB). EBs have historically been described as metabolically dormant. A cell-free (axenic) culture system was developed which showed high levels of metabolic and biosynthetic activity from both EBs and RBs. EBs preferentially utilized glucose-6-phosphate as an energy source whereas RBs required ATP. Both developmental forms showed improved activity when incubated under microaerobic conditions. Incorporation of isotopically-labeled amino acids into proteins from both developmental forms indicated unique expression profiles which were confirmed by genome-wide transcriptional analysis. The described axenic culture system will greatly enhance biochemical and physiological analyses of chlamydiae. Chlamydia axenic metabolic activity Term Source Name ArrayExpress EFO Term Source File http://www.ebi.ac.uk/arrayexpress/ http://www.ebi.ac.uk/efo/efo.owl Person Last Name Sturdevant Omsland Sager Nair Sturdevant Hackstadt Person First Name Dan Anders Janet Vinod Daniel Ted Person Mid Initials E Person Email dsturdevant@niaid.nih.gov Person Affiliation NIH Person Phone 4063639248 Person Address NIH, -, Hamilton, MT, USA Person Roles submitter Protocol Name P-GSE39530-1 P-GSE39530-6 P-GSE39530-3 P-GSE39530-8 P-GSE39530-7 P-GSE39530-2 P-GSE39530-4 P-GSE39530-5 Protocol Description ID_REF = VALUE = Signal ABS_CALL = indicating whether the transcript was present (P), absent (A), or marginal (M) DETECTION P-VALUE = All cRNAs were hybridized to a custom Affymetrix GeneChip Chlamydia trachomatis serovar L2 (LGV 434) was propagated in HeLa 229 cells and purified by Renografin density gradient centrifugation. RBs were isolated 14-16 h post infection while EBs were isolated 43-45 h post infection. The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. MAS5.0 signal intensity GeneChips were scanned using the Affymetrix GeneChip Scanner 7GPlus. EBs and RBs were treated with axenic medium in the presence or absence of rifampicin for 3 hours. Total RNA was isolated by use of an RNeasy Mini Kit (Qiagen) recommended by a standard protocol. Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix). Protocol Type bioassay_data_transformation hybridization grow feature_extraction image_aquisition specified_biomaterial_action nucleic_acid_extraction labeling Experimental Factor Name ORGANISM PART Experimental Factor Type organism part Publication Title Developmental stage-specific metabolic and transcriptional activity of Chlamydia trachomatis in an axenic medium. Publication Author List Omsland A, Sager J, Nair V, Sturdevant DE, Hackstadt T PubMed ID 23129646 Publication DOI 10.1073/pnas.1212831109 Comment[SecondaryAccession] GSE39530 Comment[GEOReleaseDate] 2012-11-20 Comment[ArrayExpressSubmissionDate] 2012-07-20 Comment[GEOLastUpdateDate] 2012-11-20 Comment[AEExperimentType] transcription profiling by array SDRF File E-GEOD-39530.sdrf.txt