GEO DataSets

(Submitter supplied) Halobacterium salinarum is an extreme halophilic archaeon adapted to total salinities upwards of 4 M. Here we studied gene expression in H. salinarum grown in ten ion composition media that vary in two major aspects of ion composition: [NaCl] and Mg:K ratio.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by genome tiling array

Platform:

GPL17005

20 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) Numerous lineage-specific expansions of the transcription factor B (TFB) family in archaea suggests an important role for expanded TFBs in encoding environment-specific gene regulatory programs. Given the characteristics of hypersaline lakes the unusually large numbers of TFBs in halophilic archaea further suggests that they might be especially important in rapid adaptation to the challenges of a dynamically changing environment. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL13426

28 Samples

Download data: TXT

(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) 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) 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) 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) 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) This SuperSeries is composed of the SubSeries listed below.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

200 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

170 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of gap was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of vng0019h was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of sop2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of kinA2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of zim was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of vng2334c was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of vng1296C was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of htr2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV

(Submitter supplied) A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of phoR was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. more...

Organism:

Halobacterium salinarum NRC-1

Type:

Expression profiling by array

Platform:

GPL3739

8 Samples

Download data: CSV