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Series GSE7045 Query DataSets for GSE7045
Status Public on Feb 23, 2007
Title ChIP-Chip of General Transcription factors in Halobacterium NRC-1
Organism Halobacterium salinarum NRC-1
Experiment type Genome binding/occupancy profiling by array
Summary Cells responding to dramatic environmental changes or undergoing a developmental switch typically change the expression of numerous genes. In bacteria sigma factors regulate much of this process while in eukaryotes four RNA polymerases and a multiplicity of generalized transcription factors (GTFs) are required. Here, using a systems approach, we provide experimental evidence (including protein-coIP, ChIP-Chip, GTF perturbation and knockout, and measurement of transcriptional changes in these genetically perturbed strains) for how archaea likely accomplish similar large-scale transcriptional segregation and modulation of physiological functions. We are able to associate GTFs to nearly half of all putative promoters and show evidence for at least 7 of the possible 42 functional GTF pairs. This report represents a significant contribution towards closing the gap in our understanding of gene regulation by GTFs for all three domains of life and provides an example for how to utilize various experimental techniques to rapidly learn significant portions of a global gene regulatory network of organisms for which little is previously known.
Keywords: ChIP-Chip
 
Overall design Halobacterium NRC-1 expressing Cmyc-tagged TFBs and TBPs were grown to an OD600 between 1 and 1.2. The cells were cross-linked with 1.2% formaldehyde, then lysed and DNA sheared via sonication. Next cleared cell lysate was subject to immunoprecipitation against an anti-myc antibody. Protein-DNA complexes were purified and DNA was isolated after protease and RNAase treatment. DNA was amplified using universal linkers, labeled directly using Kreatech 547 and 647 dyes. Samples were grown in biological duplicate. Each DNA sample was hybridized against 2 microarrays as dyefilps. At least two experiments (including biological duplicates) were carried out.
 
Contributor(s) Facciotti MT, Reiss DJ, Pan M, Kaur A, Vuthoori M, Bonneau R, Shannon P, Srivastava A, Donohoe SM, Hood LE, Baliga NS
Citation(s) 17360575
Submission date Feb 15, 2007
Last update date Mar 20, 2012
Contact name Marc Facciotti
E-mail(s) mfacciotti@systemsbiology.org
Organization name Institute for Systems Biology
Street address 1441 North 34th Street
City Seattle
State/province WA
ZIP/Postal code 98103
Country USA
 
Platforms (4)
GPL4661 ISB Halobacterium Whole Genome SpanKit Spotted Microarray v1.0
GPL4662 ISB Halobacterium Whole Genome SpanKit Spotted Microarray v1.1
GPL4663 ISB Halobacterium Whole Genome SpanKit Spotted Microarray v1.2
Samples (78)
GSM156606 IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium GTF growth curve experiment, Array 6965
GSM156607 IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium GTF growth curve experiment, Array 6966
GSM156608 IP fraction of ChIP-Chip sample from Cmyc tagged TFBd, Halobacterium GTF growth curve experiment, Array 6970
This SubSeries is part of SuperSeries:
GSE13150 Prevalence of transcription promoters within archaeal operons and coding sequences
Relations
BioProject PRJNA114681

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Supplementary data files not provided

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