Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR29353000.fastq.gz | Fastqsanger.gz | |||
| SRR29353001.fastq.gz | Fastqsanger.gz | |||
| SRR29353002_1.fastq.gz | Fastqsanger.gz | |||
| SRR29353002_2.fastq.gz | Fastqsanger.gz | |||
| SRR29353015_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 312 |
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Project description:ChIP-seq against eGFP-pha-4 in mixed stage (embryonic) worms. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODE_Data_Use_Policy_for_External_Users_03-07-14.pdf
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Project description:Polyhydroxyalkanoates (PHAs) are bio-based, biodegradable polyesters that can be produced from organic-rich waste streams using mixed microbial cultures. To maximize PHA production, mixed microbial cultures may be enriched for PHA-producing bacteria with a high storage capacity through the imposition of cyclic, aerobic feast-famine conditions in a sequencing batch reactor (SBR). Though enrichment SBRs have been extensively investigated a bulk solutions-level, little evidence at the proteome level is available to describe the observed SBR behavior to guide future SBR optimization strategies. As such, the purpose of this investigation was to characterize proteome dynamics of a mixed microbial culture in an SBR operated under aerobic feast-famine conditions using fermented dairy manure as the feedstock for PHA production. At the beginning of the SBR cycle, excess PHA precursors were provided to the mixed microbial culture (i.e., feast), after which followed a long duration devoid of exogenous substrate (i.e., famine). Two-dimensional electrophoresis was used to separate protein mixtures during a complete SBR cycle, and proteins of interest were identified.
2017-01-31 | PXD003126 | Pride
Project description:PHA production mixed cultures Raw sequence reads
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Project description:It is a cost-effective production method to synthesize polyhydroxyalkanoate (PHA) through mixed bacterial consortium fermentation. Pseudomonas balearica R90 and Brevundimonas diminuta R79, which represent the species of abundance increase in the propylene oxide activated sludge, were selected as the model to study the interaction mechanism of PHA synthesis by co-culture between strains. RNA-Seq analysis showed that the expression of acs and phaA genes of R79 and R90 increased in the mixed culture group, which enhanced their ability of acetic acid utilization and poly-β-hydroxybutyrate (PHB) synthesis. So the dry cell weight and the yield of PHB in the mixed culture group was prominently higher than that in the pure culture group. In addition, two-component system genes, quorum- sensing genes, flagellar synthesis related genes and chemotaxis related genes in R90 were enriched at 4 days, so R90 could adapt to the domestication environment more quickly, making the proportion of R90 higher than that of R79 at 4 days. However, the acs gene expression of R79 was higher than that of R90. Therefore, R79 can make better utilize acetate in the domestication solution environment, thus occupying the final dominant position.
2022-10-29 | GSE216514 | GEO
Project description:A biohydrogen and polyhydroxyalkanoates(PHA)-producing natural photoheterotrophic mixed culture composed mainly by Rhodopseudomonas palustris and Clostridium sp was studied by a proteomic analysis under non-growth conditions (nitrogen-absence and organic acids). Proteins in C. pasteurianum were upregulated, particularly those related to stress response. In contrast, C. pasteurianum in the consortium did not present such proteins, showing the advantage of being part of it. Both cultures showed proteins involved in organic acid metabolism and biohydrogen production, such as lactate dehydrogenase, ferredoxins, and hydrogenases. Proteomes of R. palustris as single culture and in consortium showed that organic acids were redirect into central carbon pathways to generate reduced equivalents for biohydrogen production. Light-harvesting proteins and fatty acid metabolism linked to PHA accumulation were also upregulated. This study provides insights into how the proteomes of individual organisms and their consortium counterparts adapt to non-growth conditions, shedding light on how microbial interactions influence protein expression.
2025-02-06 | PXD057021 | Pride
Project description:Mixed species in three open PHA accumulating bioreaactors Raw sequence reads
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Project description:modENCODE_submission_3158 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: OP37 (official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] 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 PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim ); Developmental Stage: L2; Genotype: unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage L2; Target gene pha-4; Strain OP37 (official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] 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 PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim ); temp (temperature) 20 degree celsius
2011-03-31 | E-GEOD-26153 | biostudies-arrayexpress
Project description:modENCODE_submission_2598 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: OP37(made_by : R. Waterston and S. Kim 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 PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] official name : OP37 ); Developmental Stage: late embryo; Genotype: unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage late embryo; Target gene pha-4; Strain OP37(made_by : R. Waterston and S. Kim 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 PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. tags : GFP::3xFlag mutagen : Bombard outcross : 3 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] official name : OP37 ); temp (temperature) 20 degree celsius Series_type: CHIP-seq
2011-02-18 | E-GEOD-25798 | biostudies-arrayexpress
Project description:modENCODE_submission_3161 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: OP37 (official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] 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 PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim ); Developmental Stage: Young Adult; Genotype: unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG]; Sex: Hermaphrodite; EXPERIMENTAL FACTORS: Developmental Stage Young Adult; Target gene pha-4; Strain OP37 (official name : OP37 genotype : unc-119(ed3) III; wgIs37 [unc-119(+) pha-4::TY1::EGFP::3xFLAG] 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 PHA-4::EGFP fusion protein is expressed in the correct pha-4 spatio-temporal expression pattern. This strain was used for ChIP-seq experiments to map the in vivo binding sites for the PHA-4 transcription factor. made_by : R. Waterston and S. Kim ); temp (temperature) 20 degree celsius
2011-03-31 | E-GEOD-25799 | biostudies-arrayexpress