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PROVIDER: PRJNA776122 | ENA |
REPOSITORIES: ENA
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Project description:Leeuwenhoekiella palythoae strain:F5 Genome sequencing
| PRJNA766805 | ENA
Project description:Leeuwenhoekiella palythoae overview
| PRJNA767132 | ENA
Project description:Leeuwenhoekiella palythoae DSM 19859 genome sequencing
| PRJNA303392 | ENA
Project description:modENCODE_submission_3082 This submission comes from a modENCODE project of Michael Snyder. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: We are identifying the DNA binding sites for 300 transcription factors in C. elegans. Each transcription factor gene is tagged with the same GFP fusion protein, permitting validation of the gene's correct spatio-temporal expression pattern in transgenic animals. Chromatin immunoprecipitation on each strain is peformed using an anti-GFP antibody, and any bound DNA is deep-sequenced using Solexa GA2 technology. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CHIP-seq. BIOLOGICAL SOURCE: Strain: OP193(official name : OP193 genotype : unc-119(ed3); wgIs193(sea-2::TY1 EGFP FLAG C; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The SEA-2::EGFP fusion protein is expressed in the correct sea-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SEA-2 transcription factor. made_by : ); Developmental Stage: L3; Genotype: unc-119(ed3); wgIs193(sea-2::TY1 EGFP FLAG C; unc-119); Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L3; Target gene sea-2; Strain OP193(official name : OP193 genotype : unc-119(ed3); wgIs193(sea-2::TY1 EGFP FLAG C; unc-119) outcross : 3 mutagen : Bombard tags : GFP::3xFlag description : This strain's transgene was constructed by Mihail Sarov at the Max Planck Institute for Cell Biology in Tubiginen using Tony Hyman's recombineering pipeline. The resulting plasmid was used for biolistic transformation of an unc-119(ed3) strain. The SEA-2::EGFP fusion protein is expressed in the correct sea-2 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the SEA-2 transcription factor. made_by : ); temp (temperature) 20 degree celsius
2012-05-07 | E-GEOD-37806 | biostudies-arrayexpress
Project description:The deep marine subsurface is one of the largest unexplored biospheres on Earth, where members of the phylum Chloroflexi are abundant and globally distributed. However, the deep-sea Chloroflexi have remained elusive to cultivation, hampering a more thorough understanding of their metabolisms. In this work, we have successfully isolated a representative of the phylum Chloroflexi, designated strain ZRK33, from deep-sea cold seep sediments. Phylogenetic analyses based on 16S rRNA genes, genomes, RpoB and EF-tu proteins indicated that strain ZRK33 represents a novel class within the phylum Chloroflexi, designated Sulfochloroflexia. We present a detailed description of the phenotypic traits, complete genome sequence and central metabolisms of the novel strain ZRK33. Notably, sulfate and thiosulfate could significantly promote the growth of the new isolate, possibly through accelerating the hydrolysis and uptake of saccharides. Thus, this result reveals that strain ZRK33 may play a crucial part in sulfur cycling in the deep-sea environments. Moreover, the putative genes associated with assimilatory and dissimilatory sulfate reduction are broadly distributed in the genomes of 27 metagenome-assembled genomes (MAGs) from deep-sea cold seep and hydrothermal vents sediments. Together, we propose that the deep marine subsurface Chloroflexi play key roles in sulfur cycling for the first time. This may concomitantly suggest an unsuspected availability of sulfur-containing compounds to allow for the high abundance of Chloroflexi in the deep sea.
2024-05-22 | PXD023380 | Pride
Project description:Light was a ubiquitous environmental stimulus. Deep-sea microorganisms were exposed to a pervasive blue light optical environment. The utilization of blue light by deep-sea microorganisms, especially non-photosynthetic microorganisms, and the downstream pathway after light reception were obscure. Under the enrichment condition surrounded by blue light, a potential novel species named Spongiibacter nanhainus CSC3.9 from the deep-sea cold seep was isolated. Its growth and metabolism under blue light were significantly better than other wavelengths of light. Six blue light sensing proteins, including four BLUF (Blue Light Using Flavin) and two bacteriophytochrome, were annotated in the genome of strain CSC3.9. Then, with the assist of proteomic analysis, we demonstrated that 15960-BLUF was a crucial blue light receptor that interfered with motor behavior through chemotaxis pathway by means of in vivo and in vitro verification. In addition, 15960-BLUF mediated part of the blue light to promote the growth of strain CSC3.9. Further, we summarized the functional BLUF proteins from isolated marine microorganisms, and the high abundance distribution of BLUF similar to the downstream unresponsive domain type in strain CSC3.9 was demonstrated. The widespread distribution of BLUF protein in marine bacteria implied the extensiveness of this regulatory mechanism, and wavelength variation of light was a potential means to isolate uncultured microorganisms. This was the first reported in deep-sea microorganisms that BLUF-dependent physiological response to blue light. It provided a new clue for the blue light adaptation of microorganisms in disphotic zone.
2022-01-18 | PXD028001 | Pride
Project description:Transcription rate (TR) analysis of W303-1a yeast strain growing in exponential phase in YPD subjected to terbutyl stress Keywords: time course Transcription rate analysis by means of GRO of three independent replicates the yeast strain growing in exponential phase. Each time point replicate has been hybridized on a different macroarray (F5-F10). A single DNA genomic hybridization from the same labeling reaction was done on the same macroarrays for normalization.
2008-05-23 | E-GEOD-9663 | biostudies-arrayexpress
Project description:Asian cultivated rice (Oryza sativa L.) consists of two major subspecies, indica and japonica. Inter-subspecific hybrids between indica and japonica, usually accompanying hybrid sterility, exhibit much more vigorous heterosis than intra-subspecific hybrids. f5 locus, also called S24 or Sb, confers significant effects on hybrid male sterility and segregation distortion. BC14F2 plants with f5-i/i, f5-j/j and f5-i/j genotype respectively, were used to dissect the underlying pathway of f5-caused hybrid male sterility via comparative transcriptome analysis. 350, 421, and 480 differentially expressed genes (DEGs) were identified from f5-i/j vs. f5-j/j, f5-j/j vs. f5-i/i, and f5-i/j vs. f5-i/i respectively. 145 DEGs demonstrated simultaneously differential expression in both f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i. Enrichment analysis with MapMan and AgriGO indicated that protein and DNA metabolism, and cell control related processes were enriched in the 145 DEGs. Stress and cell control related processes were enriched in the DEGs of f5-i/j vs. f5-j/j and f5-i/j vs. f5-i/i, whereas, these two processes were not enriched in the DEGs of f5-j/j vs. f5-i/i. Biotic and abiotic stress resistance genes were suppressed, which may result in pollen cell more sensitive to various stresses. The down regulation of ascorbate peroxidase (APX) may break the dynamic homeostasis of ROS (reactive oxygen species) and cause oxidative stress, which can damage cellular components. The expression of most of the heat shock protein (HSP) genes, which can protect proteins and cells from been destroyed, were also decreased. Based on these results, a model was proposed to summarize the underlying process for f5-caused rice hybrid male sterility. These results provide significant clues to further dissecting the molecular mechanism of f5-caused intersubspecific reproductive barrier.
2021-02-12 | GSE110483 | GEO