Ontology highlight
ABSTRACT:
PROVIDER: PRJNA670076 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12848985_1.fastq.gz | Fastqsanger.gz | |||
| SRR12848985_2.fastq.gz | Fastqsanger.gz | |||
| SRR12848986_1.fastq.gz | Fastqsanger.gz | |||
| SRR12848986_2.fastq.gz | Fastqsanger.gz | |||
| SRR12848987_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 10 |
Similar Datasets
Project description:To effectively monitor microbial populations in acidic environments and bioleaching systems, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the known genes associated with the acidophiles. This array contained 1,072 probes in which there were 571 related to 16S rRNA and 501 related to functional genes. Acid mine drainage (AMD) presents numerous problems to the aquatic life and surrounding ecosystems. However, little is known about the geographic distribution, diversity, composition, structure and function of AMD microbial communities. In this study, we analyzed the geographic distribution of AMD microbial communities from twenty sites using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes, and the results showed that AMD microbial communities were geographically distributed and had high variations among different sites. Then an AMD-specific microarray was used to further analyze nine AMD microbial communities, and showed that those nine AMD microbial communities had high variations measured by the number of detected genes, overlapping genes between samples, unique genes, and diversity indices. Statistical analyses indicated that the concentrations of Fe, S, Ca, Mg, Zn, Cu and pH had strong impacts on both phylogenetic and functional diversity, composition, and structure of AMD microbial communities. This study provides insights into our understanding of the geographic distribution, diversity, composition, structure and functional potential of AMD microbial communities and key environmental factors shaping them. This study investigated the geographic distribution of Acid Mine Drainages microbial communities using a 16S rRNA gene-based RFLP method and the diversity, composition and structure of AMD microbial communities phylogenetically and functionally using an AMD-specific microarray which contained 1,072 probes ( 571 related to 16S rRNA and 501 related to functional genes). The functional genes in the microarray were involved in carbon metabolism (158), nitrogen metabolism (72), sulfur metabolism (39), iron metabolism (68), DNA replication and repair (97), metal-resistance (27), membrane-relate gene (16), transposon (13) and IST sequence (11).
2011-03-08 | E-GEOD-27542 | biostudies-arrayexpress
Project description:To effectively monitor microbial populations in acidic environments and bioleaching systems, a comprehensive 50-mer-based oligonucleotide microarray was developed based on most of the known genes associated with the acidophiles. This array contained 1,072 probes in which there were 571 related to 16S rRNA and 501 related to functional genes. Acid mine drainage (AMD) presents numerous problems to the aquatic life and surrounding ecosystems. However, little is known about the geographic distribution, diversity, composition, structure and function of AMD microbial communities. In this study, we analyzed the geographic distribution of AMD microbial communities from twenty sites using restriction fragment length polymorphism (RFLP) analysis of 16S rRNA genes, and the results showed that AMD microbial communities were geographically distributed and had high variations among different sites. Then an AMD-specific microarray was used to further analyze nine AMD microbial communities, and showed that those nine AMD microbial communities had high variations measured by the number of detected genes, overlapping genes between samples, unique genes, and diversity indices. Statistical analyses indicated that the concentrations of Fe, S, Ca, Mg, Zn, Cu and pH had strong impacts on both phylogenetic and functional diversity, composition, and structure of AMD microbial communities. This study provides insights into our understanding of the geographic distribution, diversity, composition, structure and functional potential of AMD microbial communities and key environmental factors shaping them.
2011-03-08 | GSE27542 | GEO
Project description:Aquatic product microbial community diversity
| PRJNA382434 | ENA
Project description:The study investigated the impact of environment on the composition of the gut microbiota and mucosal immune development and function at gut surfaces in early and adult life. Piglets of similar genotype were reared in indoor and outdoor environments and in an experimental isolator facility. Mucosa-adherent microbial diversity in the pig ileum was characterized by sequence analysis of 16S rRNA gene libraries. Host-specific gene responses in gut ileal tissues to differences in microbial composition were investigated using Affymetrix microarray technology and Real-time PCR.
2009-12-01 | GSE15256 | GEO
Project description:Chemical modifications to the tails of histone proteins act as gene regulators that play a pivotal role in adaptive responses to environmental stress. Determining the short and long term kinetics of histone marks is essential for understanding their functions in adaptation. We used Caenorhabditis elegans as a model organism to study the histone modification kinetics in response to environmental stress, taking advantage of their ability to live in both terrestrial and aquatic environments. We investigated the multigenerational genome-wide dynamics of five histone marks (H3K4me3, H3K27me3, H4K20me1, H3K36me1, and H3K9me3) by maintaining P0 animals on terrestrial (agar plates), F1 in aquatic cultures, and F2 back on terrestrial environments. We determined the distributions of histone marks in the gene promoter regions and found that H4K20me1, H3K36me1, and H3K9me3 showed up to eleven-fold differences in density, whereas H3K4me3 and H3K27me3 remained highly constant during adaptation from terrestrial to aquatic environments. Furthermore, we predicted that up to five combinations of histone marks can co-occupy single gene promoters and confirmed the colocalization of these histone marks by structured illumination microscopy. The co-occupancy increases with environment changes and different co-occupancy patterns contribute to variances in gene expressions and thereby presents a supporting evidence for the histone code hypothesis.
2021-07-09 | GSE103775 | GEO
Project description:The diversity and environmental distribution of the nosZ gene, which encodes the enzyme responsible for the consumption of nitrous oxide, was investigated in marine and terrestrial environments using a functional gene microarray. The microbial communities represented by the nosZ gene probes showed strong biogeographical separation, with communities from surface ocean waters and agricultural soils significantly different from each other and from those in oceanic oxygen minimum zones. Atypical nosZ genes, usually associated with incomplete denitrification pathways, were detected in all the environments, including surface ocean waters. The abundance of nosZ genes, as estimated by quantitative PCR, was highest in the agricultural soils and lowest in surface ocean waters.
2018-10-19 | GSE121473 | GEO