Comment[ArrayExpressAccession]	E-GEOD-40304
MAGE-TAB Version	1.1						
Public Release Date	2013-05-01
Investigation Title	Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription						
Comment[Submitted Name]	Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription
Experiment Description	To fit within the confines of the cell, bacterial chromosomes are highly condensed into a structure called the nucleoid. Despite the high degree of compaction in the nucleoid, the genome remains accessible to essential biological processes, such as replication and transcription. Here, we present the first high-resolution chromosome conformation capture-based molecular analysis of the spatial organization of the Escherichia coli nucleoid during rapid growth in rich medium and following an induced amino acid starvation that promotes the stringent response. Our analyses identify the presence of origin and terminus domains in exponentially growing cells. Moreover, we observe an increased number of interactions within the origin domain and significant clustering of SeqA-binding sequences, suggesting a role for SeqA in clustering of newly replicated chromosomes. By contrast, ‘histone-like’ protein (i.e. Fis, IHF and H-NS) binding sites did not cluster, and their role in global nucleoid organization does not manifest through the mediation of chromosomal contacts. Finally, genes that were downregulated after induction of the stringent response were spatially clustered, indicating that transcription in E. coli occurs at transcription foci. A 4 chips study of exponentially growing wild type E. coli strain MG1655 grown in LB rich media or after induction of the stringent response by serine hydroxamate for 30 min. Two technical replicates, Three biological replicates mixed prior hybridization on the chip.						
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	cagliero	Cagliero	Grand	Jones	Jin	O'Sullivan	
Person First Name	cedric	Cedric	Ralph	Beatrix	Ding	Justin	
Person Mid Initials			S	M	J	M	
Person Email	geo@ncbi.nlm.nih.gov						
Person Affiliation	NCI/NIH						
Person Address	NCI/NIH, 1050 boyles street, frederick, USA						
Person Roles	submitter						
Protocol Name	P-GSE40304-1	P-GSE40304-5	P-GSE40304-6	P-GSE40304-2	P-GSE40304-3	P-GSE40304-4	P-GSE40304-7
Protocol Description	The raw data (.pair file) was subjected to RMA (Robust Multi-Array Analysis; Irizarry et al. Biostatistics 4(2):249), quantile normalization (Bolstad et al. Bioinformatics 19(2):185), and background correction as implemented in the NimbleScan software package, version 2.4.27 (Roche NimbleGen, Inc.). ID_REF =  VALUE = RMA-normalized, averaged gene-level signal intensity	Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.	Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.	serine hydroxamate 500 ug/ml is added to induce stringent response	Growth in LB at 37C until OD600 = 0.2	The total RNA is purified by a hot phenol method	Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.
Protocol Type	normalization data transformation protocol	labelling protocol	hybridization protocol	sample treatment protocol	growth protocol	nucleic acid extraction protocol	array scanning protocol
Experimental Factor Name	GROWTH CONDITION						
Experimental Factor Type	growth condition						
Comment[SecondaryAccession]	GSE40304						
Comment[GEOReleaseDate]	2013-05-01						
Comment[ArrayExpressSubmissionDate]	2012-08-22						
Comment[GEOLastUpdateDate]	2013-05-02						
Comment[AEExperimentType]	transcription profiling by array						
SDRF File	E-GEOD-40304.sdrf.txt