Ontology highlight
ABSTRACT:
PROVIDER: PRJNA526107 | ENA |
REPOSITORIES: ENA
Dataset's files
primary
| Action | DRS | |||
|---|---|---|---|---|
| SRR8699861.fastq.gz | Fastqsanger.gz | |||
| SRR8699862.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 2 of 2 |
Similar Datasets
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 (?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
2015-08-31 | E-GEOD-54599 | BioStudies
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. Overall design: 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 37ºC 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.
2009-09-08 | GSE13531 | GEO
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 37ºC 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 | ArrayExpress
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. Overall design: 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 37ºC 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.
2009-09-08 | GSE13529 | GEO
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 37ºC 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 | ArrayExpress
Project description:This SuperSeries is composed of the following subset Series: GSE7714: Halobacterium NRC-1 oxygen, light and phr1 perturbation GSE7715: Halobacterium NRC-1 oxygen, light and ura3 perturbation GSE7716: Halobacterium NRC-1 oxygen, light and phr1/phr2 perturbation GSE7717: Halobacterium NRC-1 oxygen, light and bop perturbation GSE7718: Halobacterium NRC-1 oxygen, light and phr2 perturbation GSE7719: Halobacterium NRC-1 oxygen, light and sop2 perturbation GSE7720: Halobacterium NRC-1 oxygen, light and afsQ2 perturbation GSE7721: Halobacterium NRC-1 oxygen, light and htlD perturbation GSE7722: Halobacterium NRC-1 oxygen, light and vng0750C perturbation GSE7723: Halobacterium NRC-1 oxygen, light and boa1 perturbation GSE7724: Halobacterium NRC-1 oxygen, light and ark perturbation GSE7725: Halobacterium NRC-1 oxygen, light and boa4 perturbation GSE7726: Halobacterium NRC-1 oxygen, light and htr1 perturbation GSE7727: Halobacterium NRC-1 oxygen, light and kinA2 perturbation GSE7728: Halobacterium NRC-1 oxygen, light and htr8 perturbation GSE7729: Halobacterium NRC-1 oxygen and light perturbation GSE7730: Halobacterium NRC-1 oxygen, light and phoR perturbation GSE7731: Halobacterium NRC-1 oxygen, light and htr2 perturbation GSE7732: Halobacterium NRC-1 oxygen, light and vng1296C perturbation GSE7733: Halobacterium NRC-1 oxygen, light and vng2334C perturbation GSE7734: Halobacterium NRC-1 oxygen, light and zim perturbation GSE7735: Halobacterium NRC-1 oxygen, light and kinA2 perturbation, experiment 2 GSE7736: Halobacterium NRC-1 oxygen, light and sop2 perturbation, experiment 2 GSE7737: Halobacterium NRC-1 oxygen, light and vng0019h perturbation GSE7738: Halobacterium NRC-1 oxygen, light and gap perturbation Refer to individual Series
2008-01-02 | E-GEOD-7740 | BioStudies
Project description:BACKGROUND: Archaea are prokaryotic organisms with simplified versions of eukaryotic transcription systems. Genes coding for the general transcription factors TBP and TFB are present in multiple copies in several Archaea, including Halobacterium sp. NRC-1. Multiple TBP and TFBs have been proposed to participate in transcription of genes via recognition and recruitment of RNA polymerase to different classes of promoters. RESULTS: We attempted to knock out all six TBP and seven TFB genes in Halobacterium sp. NRC-1 using the ura3-based gene deletion system. Knockouts were obtained for six out of thirteen genes, tbpCDF and tfbACG, indicating that they are not essential for cell viability under standard conditions. Screening of a population of 1,000 candidate mutants showed that genes which did not yield mutants contained less that 0.1% knockouts, strongly suggesting that they are essential. The transcriptomes of two mutants, Delta tbpD and DeltatfbA, were compared to the parental strain and showed coordinate down regulation of many genes. Over 500 out of 2,677 total genes were regulated in the Delta tbpD and DeltatfbA mutants with 363 regulated in both, indicating that over 10% of genes in both strains require the action of both TbpD and TfbA for normal transcription. Culturing studies on the Delta tbpD and DeltatfbA mutant strains showed them to grow more slowly than the wild-type at an elevated temperature, 49 degrees C, and they showed reduced viability at 56 degrees C, suggesting TbpD and TfbA are involved in the heat shock response. Alignment of TBP and TFB protein sequences suggested the expansion of the TBP gene family, especially in Halobacterium sp. NRC-1, and TFB gene family in representatives of five different genera of haloarchaea in which genome sequences are available. CONCLUSION: Six of thirteen TBP and TFB genes of Halobacterium sp. NRC-1 are non-essential under standard growth conditions. TbpD and TfbA coordinate the expression of over 10% of the genes in the NRC-1 genome. The Delta tbpD and DeltatfbA mutant strains are temperature sensitive, possibly as a result of down regulation of heat shock genes. Sequence alignments suggest the existence of several families of TBP and TFB transcription factors in Halobacterium which may function in transcription of different classes of genes.
2007-01-01 | S-EPMC2121645 | BioStudies
Project description:RNA-seq on rRNA depleted libraries from exponentially growing Halobacterium salinarum NRC-1 strains Δura3 and Δhlx2 Overall design: Differential gene expression in Δhlx2 mutant compared to parent strain
2017-06-07 | GSE99730 | GEO
Project description:A plethora of non-coding RNAs has been discovered using high-resolution transcriptomics tools, indicating that transcriptional and post-transcriptional regulation is much more complex than previously appreciated. Small RNAs associated with transcription start sites of annotated coding regions (TSSaRNAs) are pervasive in both eukaryotes and bacteria. Here, we provide evidence for existence of TSSaRNAs in several archaeal transcriptomes including: Halobacterium salinarum, Pyrococcus furiosus, Methanococcus maripaludis, and Sulfolobus solfataricus. We validated TSSaRNAs from the model archaeon Halobacterium salinarum NRC-1 by deep sequencing two independent small-RNA enriched (RNA-seq) and a primary-transcript enriched (dRNA-seq) strand-specific libraries. We identified 652 transcripts, of which 179 were shown to be primary transcripts (?7% of the annotated genome). Distinct growth-associated expression patterns between TSSaRNAs and their cognate genes were observed, indicating a possible role in environmental responses that may result from RNA polymerase with varying pausing rhythms. This work shows that TSSaRNAs are ubiquitous across all domains of life.
2014-01-01 | S-EPMC4169567 | BioStudies
Project description:The existence of sense overlapping transcripts that share regulatory and coding information in the same genomic sequence shows an additional level of prokaryotic gene expression complexity. Here we report the discovery of ncRNAs associated with IS1341-type transposase (tnpB) genes, at the 3'-end of such elements, with examples in archaea and bacteria. Focusing on the model haloarchaeon Halobacterium salinarum NRC-1, we show the existence of sense overlapping transcripts (sotRNAs) for all its IS1341-type transposases. Publicly available transcriptome compendium show condition-dependent differential regulation between sotRNAs and their cognate genes. These sotRNAs allowed us to find a UUCA tetraloop motif that is present in other archaea (ncRNA family HgcC) and in a H. salinarum intergenic ncRNA derived from a palindrome associated transposable elements (PATE). Overexpression of one sotRNA and the PATE-derived RNA harboring the tetraloop motif improved H. salinarum growth, indicating that these ncRNAs are functional.
2015-01-01 | S-EPMC4615843 | BioStudies