GEO DataSets

(Submitter supplied) Genome reorganization by large scale indels, gene displacements, and horizontal gene transfers allow an organism to re-organize genes into operons (“operonization”) and explore novel strategies for adapting to its changing environment. We have characterized the process of operonization by mapping and comparing transcriptome structures (TSs) of four phylogenetically diverse exptremophilic archaea: a hydrogenotrophic methanogen (Methanococcus maripaludis S2), an anaerobic thermophile (Pyrococcus furiosis DSM 3638), an acidophilic and aerobic thermophile (Sulfolobus solfataricus P2), and a photoheterotrophic halophile (Halobacterium salinarum NRC-1). more...

Organism:

Methanococcus maripaludis S2; Pyrococcus furiosus DSM 3638; Saccharolobus solfataricus P2

Type:

Expression profiling by genome tiling array

Platforms:

GPL11623 GPL11622 GPL11621

46 Samples

Download data: CSV

(Submitter supplied) Experimentally mapped transcriptome structure of Sulfolobus solfataricus P2 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 25 nt).

Organism:

Saccharolobus solfataricus P2

Type:

Expression profiling by genome tiling array

Platform:

GPL11623

16 Samples

Download data: CSV

(Submitter supplied) Experimentally mapped transcriptome structure of Pyrococcus furiosus DSM 3638 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 16 nt).

Organism:

Pyrococcus furiosus DSM 3638

Type:

Expression profiling by genome tiling array

Platform:

GPL11622

14 Samples

Download data: CSV

(Submitter supplied) Experimentally mapped transcriptome structure of Methanococcus maripaludis S2 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes tiled every 14 nt).

Organism:

Methanococcus maripaludis S2

Type:

Expression profiling by genome tiling array

Platform:

GPL11621

16 Samples

Download data: CSV

(Submitter supplied) Total RNA hybridizations of Halobacterium salinarum NRC-1 total RNA versus a strain overexpressing TFBd were compared to verify the transcriptome landscape changes. Comparison with TFBd binding sites localized using ChIP-chip data and MeDiChI algorithm (Reiss et al, 2008) allowed observation that TF-binding in the middle of coding sequences can also result in transcription initiation or termination internal to a single annotated protein-coding gene.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by genome tiling array

Platform:

GPL8468

2 Samples

Download data: PAIR

(Submitter supplied) A detailed map of genomic locations where TFs bind DNA and modulate transcription is essential to model mechanisms of gene regulation on a systems-scale. Chromatin immunoprecipitation of transcription complexes coupled to microarray (ChIP-chip (Ren et al, 2000)) or sequencing (ChIP-seq (Robertson et al, 2007)) is a commonly used approach to construct such maps. In ChIP-chip, the resolution to which the protein-DNA binding sites (TFBSs) can be identified is often limited by the genomic spacing of the probes in the array. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Genome binding/occupancy profiling by genome tiling array

Platform:

GPL8468

5 Samples

Download data: PAIR

(Submitter supplied) Despite knowledge of complex prokaryotic transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have played a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of ~64% of all genes including putative non-coding RNAs in Halobacterium salinarum NRC-1. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by genome tiling array; Expression profiling by array; Genome binding/occupancy profiling by array; Genome binding/occupancy profiling by genome tiling array

7 related Platforms

202 Samples

Download data: CSV, PAIR

(Submitter supplied) Conditional ChIP-chip for TFBd at different growth stages.

Organism:

Halobacterium salinarum NRC-1

Type:

Genome binding/occupancy profiling by array

Platform:

GPL4664

12 Samples

Download data: CSV

(Submitter supplied) Halobacterium salinarum NRC-1 was grown in CM media, at 37oC in a waterbath with agitation of 125 rpm under constant light. Analysis of transcriptional changes during growth, in addition to mapping of transcriptome structure under the same conditions, provided interesting insights about regulatory logic within prokaryotic coding regions.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

52 Samples

Download data: CSV

(Submitter supplied) Experimentally mapped transcriptome structure of H. salinarum NRC-1 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes with 40 nt overlap between contiguous probes). H. salinarum NRC-1 presents a number of interesting switches in metabolism during growth due to complex changes in EFs including pH, oxygen, nutrition, etc. While most single perturbations (radiation, oxygen, metals, etc.) affect the expression of only ~10% of all genes (Baliga et al, 2004; Kauret al , 2006; Whitehead et al, 2006), the changes during growth resulted in differential regulation of a significantly higher proportion of genes (~63%, 1,518 genes). more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by genome tiling array

Platform:

GPL7255

53 Samples

Download data: CSV

(Submitter supplied) To investigate the architecture of the E. coli K-12 transcriptome, we used two RNA-Seq technologies to analyze strand-specific transcription at single-nucleotide resolution. We analyzed the data by using an organizational schema to annotate the promoters and terminators that define transcription units across the genome. Our results showed that most (ca. two-thirds) operons have a single promoter and terminator, whereas one-third of operons contain multiple transcription units. more...

Organism:

Escherichia coli K-12

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17884

26 Samples

Download data: TXT, WIG

(Submitter supplied) Organisms of the third domain of life, the Archaea, share molecular characteristics both with bacteria and eukarya. These organisms attract scientific attention as research models for regulation and evolution of processes such as transcription, translation and RNA processing. We have reconstructed the primary transcriptome of Sulfolobus solfataricus P2, one of the most widely studied model archaeal organisms. more...

Organism:

Saccharolobus solfataricus P2

Type:

Expression profiling by high throughput sequencing

Platform:

GPL9463

8 Samples

Download data: TXT

(Submitter supplied) We set out to determine a) if histone in Halobacterium salinarum regulates transcription and b) whether the magnitude and extent of these changes matches those observed in organisms which use histone protein as their primary DNA packaging agent. To this end, gene expression data for a histone knock-out (Δura3ΔhpyA) strain versus parent (Δura3) were collected.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL14876

12 Samples

Download data: TXT

(Submitter supplied) To investigate the contribution of ribonucleases to post-transcriptional regulation of mRNA levels, we examined the fitness consequences and gene expression changes of ribonuclease mutants in the extreme halophilic archaeon Halobacterium salinarum NRC-1. H. salinarum NRC-1 is known to use a large repertoire of environment-specific transcriptional regulatory programs, which may be complemented by post-transcriptional regulatory mechanisms. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by genome tiling array

Platform:

GPL17005

8 Samples

Download data: TXT

(Submitter supplied) Coexpression of proteins in response to pathway-inducing signals is the founding paradigm of gene regulation. Yet, it remains unexplored whether the relative abundance of coregulated proteins requires precise tuning. Here we present large-scale analyses of protein stoichiometry and corresponding regulatory strategies for 21 pathways and 67-224 operons in divergent bacteria separated by 0.6-2 billion years. more...

Organism:

Caulobacter vibrioides; Bacillus subtilis subsp. subtilis str. 168; Escherichia coli str. K-12 substr. MG1655; Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759

Type:

Other

7 related Platforms

21 Samples

Download data: WIG

(Submitter supplied) High-resolution transcriptional profiling of E. coli across nine timepoints of growth in rich media (LB). Samples collected from lag phase to stationary phase of growth. High-resolution tiling array to detect conditional operon isoforms. Custom Agilent array designed to detect condition-specific transcriptional isoforms. Array designed for E coli K12 MG1655 genome. Tiled using 23bp sliding window. Includes >10,000 probes surrounding predicted operon break sites at 6 bp resolution.

Organism:

Escherichia coli str. K-12 substr. MG1655; Escherichia coli

Type:

Expression profiling by array

Platform:

GPL18392

8 Samples

Download data: TXT