Ontology highlight
ABSTRACT:
PROVIDER: PRJNA715927 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR14018330_1.fastq.gz | Fastqsanger.gz | |||
| SRR14018331_1.fastq.gz | Fastqsanger.gz | |||
| SRR14018332_1.fastq.gz | Fastqsanger.gz | |||
| SRR14018332_2.fastq.gz | Fastqsanger.gz |
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Project description:A total of 52 patients were analyzed: 21 of them monoinfected with HCV and 31 coinfected with HIV (HCV/HIV). HCV patients were recruited from Hospital Italiano and Hospital José María Ramos Mejía from Buenos Aires, Argentina, and HCV/HIV patients from Hospital Universitario La Paz, Hospital Infanta Leonor, Hospital Universitario La Princesa, Hospital Puerta de Hierro, from Madrid, Spain. All samples were processed at the National Center for Microbiology (Madrid). Patients were naıve of treatment for HCV. CHC infection was defined by the presence of anti-HCV antibodies in serum and detectable HCV RNA in plasma samples in at least 2 separate occasions. All HIV+ patients had HIV antibodies, CD4+ T-cells counts ≥ 500 cel/mm3 for at least one year before sample collection, and undetectable HIV viral load since they received suppressive antiretroviral treatment (ART) for at least one year. Plasma extracellular vesicles isolation and RNA purification was performed using the ExoRNeasy Serum/Plasma Midi kit (QIAGEN, Cat #77044). EVs were phenol-lysed and total RNA was purified by ethanol-based membrane binding into spin columns. Quality and integrity were evaluated by the Bioanalyzer 2100 with Agilent RNA 6000 Nano kit (Agilent). Small RNA library synthesis and sequencing were performed at Centre for Genomic Regulation (CRG) at Barcelona (Spain). Small RNA libraries were constructed with Illumina’s TruSeq Small RNA kit v.4 (Illumina) and 50nts (1x50) were sequenced in an Illumina HiSeq2500, with a single read approach.
2023-02-27 | E-MTAB-11811 | biostudies-arrayexpress
Project description:Soil bacterial communities under long-term organic production in Buenos Aires, Argentina
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Project description:Organic management on soil bacteria, comparison of different type of soils in Buenos Aires, Argentina
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Project description:The transition period is the most critical stage in the lactation cycle of dairy cattle. During this period, cows are subjected to high levels of oxidative stress. One way of managing this stress is through mineral supplementation with antioxidant micronutrients. The aim of this study was to evaluate the gene expression of transition dairy cows supplemented with the antioxidant trace elements copper (Cu), zinc (Zn), manganese (Mn) and selenium (Se). The study was carried out in a commercial Holstein dairy farm located in General Belgrano, province of Buenos Aires, Argentina. Cows (n=200) were randomly assigned to either a supplemented or a control group. Blood samples were obtained seven days after calving and used to determine superoxide dismutase and glutathione peroxidase activity, antioxidant capacity and thiobarbituric acid reactive substances. Additionally, RNA-sequencing analysis was performed. The oxidative stress index differed significantly between groups, despite only two differentially expressed genes which codify for second messengers (adjusted p value < 0.05). This would suggest that trace mineral supplementation of transition dairy cows would not induce changes in gene expression profiles in pathways associated with oxidative stress and immune function, since their expression is already high in response to the high oxidative stress levels and the dietary changes associated with this period. Nevertheless, considering the role of these minerals as cofactors, a higher availability in the supplemented group would increase antioxidant enzyme activity.
2023-12-20 | GSE231491 | GEO
Project description:Gram negative bacilli Genome sequencing
| PRJNA353060 | ENA
Project description:<p>The Sjögren's International Collaborative Clinical Alliance (SICCA) is a multisite observational cohort study that recruited a large cohort of geographically diverse participants. Enrollment of participants began in late 2004 at five (one domestic and four international) sites, in which all groups used the same protocol-directed methods to provide uniform evaluations; collect oral, ocular, and rheumatologic data; and collect specimens. The sites were located at the University of Buenos Aires, Argentina; Peking Union Medical College, Beijing, China; Rigshopitalet (formerly at Glostrup Hospital), Copenhagen, Denmark; Kanazawa Medical University, Ishikawa, Japan; King's College, London, UK (joined in 2007); and the University of California, San Francisco (UCSF). In 2009, Aravind Eye Hospital, Madurai, India; Johns Hopkins University, Baltimore, MD; and University of Pennsylvania, Philadelphia, PA were added as additional SICCA sites. UCSF is the coordinating center for SICCA. All specimens and data collected for SICCA are housed at UCSF.</p> <p>To facilitate the research focused on understanding the genetics of Sjögren'sSjögren's syndrome, high-density SNP genotype data and SICCA clinical information are being made available to the research community. This includes participants recruited from all SICCA research groups (RG). These participants (3,382), blood relatives (439), and unrelated healthy controls (25) had their whole blood or saliva sample (Oragene) extracted for DNA for the GWAS at the UCSF DNA Bank. Eighty eight percent of the participants are women, most are of European or Asian ancestry and the median age is 55.</p> <p>To assess potential batch effects when doing case-control comparisons using planned external controls, 30 DNA samples from each of three studies were genotyped with SICCA DNA samples:</p> <ol> <li>The Genetic Architecture of Smoking and Smoking Cessation - <a href="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000404.v1.p1">Collaborative Genetic Study of Nicotine Dependence (COGEND)</a> - PI: Laura Bierut.</li> <li>NEI-Age-related disease study (AREDS) - <a href="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000429.v1.p1">Genetic Variation in Refractive Error Substudy</a> - PI: Dwight Stambolian.</li> <li>Controls from the National Institute of Mental Health's <a href="http://www.nimhgenetics.org/available_data/controls/">(NIMH's)</a> Human Genetics Initiative.</li> </ol> <ul><a href="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000021.v3.p2">Genome-Wide Association Study of Schizophrenia</a> - PI: Pablo V. Gejman.</ul> <ul><a href="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000167.v1.p1">Molecular Genetics of Schizophrenia - nonGAIN Sample</a> (MGS_nonGAIN) - PI: Pablo V. Gejman.</ul> <p>Genotyping was performed at the Johns Hopkins University Center for Inherited Disease Research (CIDR). Data quality control, dbGaP preparation and posting, and imputation to 1000 Genomes to increase SNP density was performed by the Center for Biomedical Statistics at the University of Washington. Data analysis was performed at UCSF using software PLINK, EIGENSOFT, and SNPTEST.</p>
| phs000672 | dbGaP
Project description:Soil bacterial communities of old fields and remnants of natural grasslands of the Inland Pampa, Buenos Aires, Argentina Metagenome
| PRJNA449773 | ENA