Lake water metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1022586 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27460650_1.fastq.gz | Fastqsanger.gz | |||
| SRR27460650_2.fastq.gz | Fastqsanger.gz | |||
| SRR27460651_1.fastq.gz | Fastqsanger.gz | |||
| SRR27460651_2.fastq.gz | Fastqsanger.gz | |||
| SRR27460652_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 199 |
Similar Datasets
Project description:Here, we applied a microarray-based metagenomics technology termed GeoChip 5.0 to examined functional gene structure of microbes in four lakes at low and high elevations of approximately 530 and 4,600 m a.s.l., respectively.
2021-02-03 | GSE156784 | GEO
Project description:Esophageal squamous cell carcinoma (ESCC) is an aggressive cancer with one of the highest world incidences in the Eastern Cape region of South Africa. Several genome wide studies have been performed on ESCC cohorts from Asian countries, North America, Malawi and other parts of the world but none has been conducted on ESCC tumors from South Africa to date, where the molecular pathology and etiology of this disease remains unclear. We report here tumor associated copy number changes observed in 51 ESCC patients’ samples from the Eastern Cape province of South Africa. We extracted tumor DNA from 51 archived ESCC specimens and interrogated tumor associated DNA copy number changes using Affymetrix® 500K SNP array technology. The Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm was applied to identify significant focal regions of gains and losses. Gains of the top recurrent cancer genes were validated by fluorescence in situ hybridization and their protein expression assessed by immunohistochemistry. Twenty-three significant focal gains were identified across samples. Gains involving the CCND1, MYC, EGFR and JAG1 loci recapitulated those described in studies on Asian and Malawian cohorts. The two most significant gains involved the chromosomal sub-bands 3q28, encompassing the TPRG1 gene and 11q13.3 including the CTTN, PPFIA1and SHANK2 genes. There was no significant homozygous loss and the most recurrent hemizygous deletion involved the B3GAT1 gene on chromosome11q25. Focal gains on 11q13.3 in 37% of cases (19/51), consistently involved CTTN and SHANK2 genes. Twelve of these cases (23,5%), had a broader region of gain that also included the CCND1, FGF19, FGF4 and FGF3 genes. SHANK2 and CTTN are co-amplified in several cancers, these proteins interact functionally together and are involved in cell motility. Immunohistochemistry confirmed both Shank2 (79%) and cortactin (69%) protein overexpression in samples with gains of these genes. In contrast, cyclin D1 (65%) was moderately expressed in samples with CCND1 DNA gain. This study reports copy number changes in a South African ESCC cohort and highlights similarities and differences with cohorts from Asia and Malawi. Our results strongly suggest a role for CTTN and SHANK2 in the pathogenesis of ESCC in South Africa.
2020-04-07 | GSE59105 | GEO
Project description:Gray leaf spot (GLS) disease of maize is caused by the fungus Cercospora zeina in African countries, such as South Africa. The plant material was from maize inbred line B73-QTL, which was introgressed with a QTL region for resistance to GLS from the maize inbred line CML444 (Berger et al (2014) BMC Genetics 15 60 www.biomedcentral.com/1471-2156/15/60 ). This QTL was named 10G2_GLS and 10H_GLS from two field trials in KwaZulu-Natal province, South Africa in that study. B73-QTL plants were planted in the field, and subjected to natural infection with C. zeina. This was the same field trial as B73 plants that were sampled for RNAseq and the data reported in Swart et al (2017) Mol Plant Microbe Interact 30 710-724 (2017)(GSE94442). Samples were collected from lower leaves with moderate GLS lesions and younger upper leaves of the same B73-QTL plants with very few immature GLS lesions. The first aim of the experiment was to compare the maize transcriptomes during C.zeina challenge between B73 (from GSE94442 data) and B73-QTL plants (this study). The second aim was to identify novel transcripts expressed from the QTL region, which may underlie the quantitative disease resistance to GLS. The third aim was to identify C. zeina genes expressed in planta during infection.
2020-02-14 | GSE137198 | GEO
Project description:The emergence and fast global spread of COVID-19 has presented one of the greatest public health challenges in modern times with no proven cure or vaccine. Africa is still early in this epidemic, therefore the extent of disease severity is not yet clear. We used a mathematical model to fit to the observed cases of COVID-19 in South Africa to estimate the basic reproductive number and critical vaccination coverage to control the disease for different hypothetical vaccine efficacy scenarios. We also estimated the percentage reduction in effective contacts due to the social distancing measures implemented. Early model estimates show that COVID-19 outbreak in South Africa had a basic reproductive number of 2.95 (95% credible interval [CrI] 2.83–3.33). A vaccine with 70% efficacy had the capacity to contain COVID-19 outbreak but at very higher vaccination coverage 94.44% (95% Crl 92.44–99.92%) with a vaccine of 100% efficacy requiring 66.10% (95% Crl 64.72–69.95%) coverage. Social distancing measures put in place have so far reduced the number of social contacts by 80.31% (95% Crl 79.76–80.85%). These findings suggest that a highly efficacious vaccine would have been required to contain COVID-19 in South Africa. Therefore, the current social distancing measures to reduce contacts will remain key in controlling the infection in the absence of vaccines and other therapeutics.
2024-09-02 | BIOMD0000000978 | BioModels
Project description:The consistent cold temperatures and large amount of precipitation in the Olympic and Cascade ranges of Washington State are thought to increase atmospheric deposition of contaminants in these high elevation locations. Total mercury and 28 organochlorine compounds were measured in composite, whole fish samples collected from 14 remote lakes in the Olympic, Mt. Rainer, and North Cascades National Parks. Mercury was detected in fish from all lakes sampled and ranged in concentration from 17 to 262 ug/kg wet weight. Only two organochlorines, total polychlorinated biphenyls (tPCB) and dichlorodiphenyldichloroethylene (DDE), were detected in fish tissues (concentrations <25 ug/kg wet weight). No organochlorines were detected in sediments (MRL ≈1-5 ug/kg), while median total and methyl mercury in sediments were 30.4 and 0.34 ug/kg (dry weight), respectively. Using a targeted rainbow trout cDNA microarray with known genes, we detected significant differences in liver transcriptional responses, including metabolic, endocrine, and immune-related genes, in fish collected from a contaminated lake compared to a lake with a lower contaminant load. Overall, our results suggest that local urban areas are contributing to the observed contaminant patterns, while the transcriptional changes point to a biological response associated with exposure to these contaminants in fish. Specifically, the gene expression pattern leads us to hypothesize a role for mercury in disrupting the metabolic and reproductive pathways in fish from high elevation lakes in western Washington. Keywords: High altitude lakes, mercury, salmonids, organochlorines
2007-05-01 | GSE6886 | GEO
Project description:Ground water Arsenic toxicity is the global problem and millions of people are exposed to elevated levels through drinking water than WHO permiscible limit of 10µg/L. The exposure is associated with various cancerous and non-cancerous diseases. It may alter the gene expression profile of invidual and suppress the activity of various genes giving rise to different diseases. Pakistan, a developing country in South Asian region, also have different areas reported to have elevated Ground water As. levels since 2005. The Present Study aimed to investigate Transcriptome profile of the exposed subjects in two districts of Punjab Province Pakistan. i.e Lahore and Kasur. The population was stratified into three exposure groups comprising Low, Medium and High exposure based on their urinary arsenic levels. We used Agilent Microarrays platform for Transcriptomics analysis and Linear mixed model was used to find differential gene expression associated with Arsenic exposure
2019-12-26 | GSE110852 | GEO