Browse
Submit Data
Databases
API
Help

Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Histone dosage and gene expression changes in Halobacterium salinarum

ABSTRACT: 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 (?ura3?hpyA) strain versus parent (?ura3) were collected. The histone deletion mutant and parent strain, at log and stationary phase, were compared to the common reference strain NRC-1 (log). There are three biological replicates each, plus dye-flips, for a total of 24 arrays

ORGANISM(S): Halobacterium sp. NRC-1

SUBMITTER: Keely Dulmage

PROVIDER: E-GEOD-54599 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

ACCESS DATA

Json Xml

Similar Datasets

Histone dosage and gene expression changes in Halobacterium salinarum

Project description: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.

2015-08-31 | GSE54599 | GEO

Halobacterium NRC-1 ura3 parent strain and VNG1451C deletion mutant in response to growth in rich medium

Project description:Gene regulatory networks play an important role in coordinating biochemical fluxes through diverse metabolic pathways. The modulation of enzyme levels enables efficient utilization of limited resources as organisms dynamically acclimate to nutritional fluctuations in their environment. Here we have identified and characterized a novel nutrient-responsive transcription factor from the halophilic archaea, VNG1451C. In this experiment we used whole-genome microarray analysis in the VNG1451C deletion mutant vs. H. salinarum NRC-1 ura3 parent strain in rich medium during growth to show that the expression of many metabolic genes is perturbed in the VNG1451C deletion mutant. Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in complex medium (CM; 250g/L NaCl, 20g/L MgSO4.7H2O, 3g/L sodium citrate, 2g/L KCl, 10g/L peptone) at 37ÂºC under full-spectrum white light. Biological replicate samples were removed throughout the growth curve at early log, mid log, late log, and stationary phase to measure genome-wide transcription.

2010-05-06 | E-GEOD-13531 | biostudies-arrayexpress

Halobacterium salinarum NRC-1

Project description:Halobacterium NRC-1 ura3 parent strain and VNG1451C deletion mutant in response to growth in rich medium

| PRJNA110081 | ENA

Halobacterium NRC-1 VNG1451C deletion mutant growth in defined medium with and without glucose

Project description:Gene regulatory networks play an important role in coordinating biochemical fluxes through diverse metabolic pathways. The modulation of enzyme levels enables efficient utilization of limited resources as organisms dynamically acclimate to nutritional fluctuations in their environment. Here we have identified and characterized a novel nutrient-responsive transcription factor from the halophilic archaea, VNG1451C. In this experiment we used whole-genome microarray analysis in the VNG1451C deletion mutant vs. H. salinarum NRC-1 ura3 parent strain in defined medium during growth with and without glucose to show that the expression of many metabolic genes is perturbed in the VNG1451C deletion mutant in response to this sugar. Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in complete defined medium (CDM; 20 amino acids at concentrations defined by Shand and Perez, 1999. NaCl 250g/L, MgSO4 20 g/L, KCl 1 g/L, NaH2PO4 0.167mM, Biotin 0.02mM, Thiamin 0.015mM, Folic acid 0.0113 mM, MnSO4 0.01mM, FeSO4, 0.01mM, glucose added at 10% w/v where indicated in sample files) at 37ÂºC under full-spectrum white light. Biological replicate samples were removed throughout the growth curve at early log, mid log, and stationary phase to measure genome-wide transcription.

2010-05-06 | E-GEOD-13529 | biostudies-arrayexpress

Transcriptome Comparison of phoU Homologies Genes Deletion strain and the Parent Strain in log-phase (6 h).

Project description:Purpose: To compare the transcriptome changes in phoU1(serp0956) or phoU2(serp0316)deletion strain with the parent strain SE1457 in log-phase (6 h) Methods: Total RNA was isolated and sequenced from the phoU1 deletion strain, phoU2 deletion strain and the parent strain SE1457 in log-phase (6 h) in triplicate using an illumina high-seq 2500. Raw data was analyzed using TopHat. Genes were considered changed which performed fold-change>=1.5 and FDR<=0.05. Changed genes were then filtered to reveal the downstream targets of phoU1 or phoU2 in log-phase (6 h). Results: The expression of 23 genes were significantly decreased and 69 genes was significantly increased in expression level due to the loss of phoU1 expression.The expression of 474 genes were significantly decreased and 471 genes were significantly increased in expression level due to the loss of phoU2 expression.

2017-10-03 | GSE97400 | GEO

Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (gene expression)

Project description:Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain Keywords: Gene expression comparisons in different yeast strains Each strain was grown in at least biological triplicate to log phase in rich (YPD) medium. Extracted total RNA was compared to that collected from the diploid S288C strain, DBY8268 (ura3-52/ura3-delta, ho/ho, GAL2/GAL2)

2010-06-19 | E-GEOD-10268 | biostudies-arrayexpress

H. salinarum NRC-1 vs TFB knockouts and synthetic TFB constructs

Project description:The purpose was to show that reprogrammed TFB variants are rewired into the gene regulatory network and create global transcriptional changes. Global transcriptional changes in ?ura3, ?tfbD and ?tfbE and all synthetic TFB variants (including vector control) in the ?tfbD genetic background were determined for cultures grown at 25°C and 37°C. Each synthetic TFB variant was controlled by either PtfbD or PtfbE promoters. Two temperatures (25C) vs (37C) were tested with three OD points representing early (0.2), mid (0.4) and late (0.8) log phases. Each sample was run twice with dye flip between sample and reference RNA

2011-08-14 | E-GEOD-31308 | biostudies-arrayexpress

Variations in stress sensitivity and genomic expression in diverse S. cerevisiae strains (CGH)

Project description:Gene expression variation was measured in 17 non-laboratory strains compared to the sequenced S288c lab strain Keywords: comparative genomic hybridizations (CGH) comparing different yeast strains Each strain was grown in at least biological triplicate to log phase in rich (YPD) medium. Extracted total RNA was compared to that collected from the diploid S288C strain, DBY8268 (ura3-52/ura3-delta, ho/ho, GAL2/GAL2)

2010-06-19 | E-GEOD-10267 | biostudies-arrayexpress

Transcription profiling of Saccharomyces cerevisiae pGAL1-MKS1, pGAL1-NNK1, and pGAL1-FMP48 overexpression

Project description:Analysis of the transcriptional effects of pGAL1-MKS1, pGAL1-NNK1, and pGAL1-FMP48 overexpression. BY4700 gal1::NAT ura3delta0 S. cerevisiae cells carrying a [pGAL1-MKS1-HA, URA3, CEN], [pGAL1-NNK1-HA, URA3, CEN], or [pGAL1-FMP48-HA, URA3, CEN] plasmid, or empty vector BG1805, were grown to early log phase, induced with 0.2% galactose, and harvested after 1.5 h and 6 h. RNA from a strain overexpressing MKS1, NNK1, or FMP48 was competitively hybridized with RNA from an identically treated strain carrying empty vector.<br><br>FMP48 = YGR052W. MKS1 = YNL076W. NNK1 = YKL171W.

2010-05-25 | E-MEXP-2171 | biostudies-arrayexpress

Halobacterium salinarum NRC-1

Project description:Halobacterium NRC-1 oxygen, light and ura3 perturbation

| PRJNA105561 | ENA