Ce6b445c-d4cc-4e8f-b5e4-dc51440b12da - samples
Ontology highlight
ABSTRACT:
PROVIDER: EGAD00001010104 | EGA |
REPOSITORIES: EGA
Similar Datasets
Project description:Bacteriophage Immunoprecipitation Sequencing (PhIP-Seq) of LLD participants. Libraries and protocol were developed in the Weizmann Institute of Science. Two different libraries were used, containing microbial and other immunological peptides respectively.
| EGAS00001006999 | EGA
Project description:Objective: The purpose of this study was to observe changes in DNA methylation in service members who experienced PTSD. Methods: We compared DNA Methylation profiles in the blood of those with or without PTSD and also compared those with PTSD at both baseline and follow-up with those service members that only developed PTSD at follow-up (3-months after baseline). Blood was collected and analyzed at baseline and follow up. Results: In participants with PTSD, 10 genes were significantly hyper-methylated and 18 were significantly hypo-methylated. In the second analysis, participants that had PTSD at both time points did not present any differentially methylated gene regions. Interestingly, for individuals’ whose PTSD scores increased from baseline to follow-up, there were 8 hypo-methylated genes detected at the baseline.
2018-06-14 | GSE93673 | GEO
Project description:A growing body of evidence suggests interplay between the gut microbiota and the pathogenesis of nonalcoholic fatty liver disease (NAFLD). However, the role of the gut microbiome in early detection of NAFLD is unclear. Prospective studies are necessary for identifying reliable, microbiome markers for early NAFLD. We evaluated 2487 individuals in a community-based cohort who were followed up 4.6 years after initial clinical examination and biospecimen sampling. Metagenomic and metabolomic characterizations using stool and serum samples taken at baseline were performed for 90 participants who progressed to NAFLD and 90 controls who remained NAFLD free at the follow-up visit. Cases and controls were matched for gender, age, body mass index (BMI) at baseline and follow-up, and 4-year BMI change. Machine learning models integrating baseline microbial signatures (14 features) correctly classified participants (auROCs of 0.72 to 0.80) based on their NAFLD status and liver fat accumulation at the 4-year follow up, outperforming other prognostic clinical models (auROCs of 0.58 to 0.60). We confirmed the biological relevance of the microbiome features by testing their diagnostic ability in four external NAFLD case-control cohorts examined by biopsy or magnetic resonance spectroscopy, from Asia, Europe, and the United States. Our findings raise the possibility of using gut microbiota for early clinical warning of NAFLD development.
2022-07-11 | MTBLS2615 | MetaboLights
Project description:Blood transcriptional signatures may predate clinical diagnosis and detect subclinical incipient tuberculosis (TB) disease. To validate such blood signatures, close contacts of TB patients were recruited from multiple TB clinics in London. Close contacts of active TB were defined as individuals with a cumulative duration of exposure of greater than eight hours in a confined space to the index case prior to initiation of treatment. Known human immunodeficiency virus (HIV)-positive patients were excluded. At enrolment, interferon gamma release assays (IGRAs) were done using the QuantiFERON-TB Plus assay (Qiagen, Germany), and peripheral blood was collected into Tempus tubes for whole genome transcriptional profiling by RNA sequencing. Participants who progressed to active TB were identified by linkage with the national electronic TB register. Local case notes were reviewed to identify individuals who had received preventative treatment. This submission contains data from n=360 adult participants, of which n=9 progressed to TB during a median follow-up time of 1.9 years. The data were used for two publications: The first publication (Roe et al 2019) makes use of an initial subset of n=333 participants, of which n=6 progressed to TB during the median follow-up time of 346 days. In the second publication (Gupta et al 2019), we extended the dataset to n=360 participants and the median follow-up time to 1.9 years; n=3 initial non-progressors progressed to TB during this extended follow-up.
2019-08-29 | E-MTAB-6845 | biostudies-arrayexpress
Project description:Healthcare workers were recruited at St Bartholomew’s Hospital, London, UK in the week of lockdown in the United Kingdom (between 23rd and 31st March 2020). Participants underwent weekly evaluation using a questionnaire and biological sample collection (including serological assays) for up to 16 weeks when attending for work and self-declared as fit to attend work at each visit, with further follow up samples collected at 24 weeks. Blood RNA sequencing data was to be used to identify host-response biomarkers of early SARS-CoV-2 infection, to evaluate existing blood transcriptomic signatures of viral infection, and to describe the underlying biology during SARS-CoV-2 infection. This submission includes a total of 172 blood RNA samples from 99 participants. Of these, 114 samples (including 16 convalescent samples collected 6 months after infection) were obtained from 41 SARS-CoV-2 cases, with the remaining 58 from uninfected controls. Participants with available blood RNA samples who had PCR-confirmed SARS-CoV-2 infection during follow-up were included as ‘cases’. Those without evidence of SARS-CoV-2 infection on nasopharyngeal swabs and who remained seronegative by both Euroimmun anti S1 spike protein and Roche anti nucleocapsid protein throughout follow-up were included as uninfected controls. ‘Cases’ include all available RNA samples, including convalescent samples at week 24 of follow-up for a subset of participants. For uninfected controls, we included baseline samples only. Sample class denotes weekly interval to positive SARS-CoV-2 PCR; non-infected controls (NIC); convalescent samples (Conv)_.
2021-07-07 | E-MTAB-10022 | biostudies-arrayexpress
Project description:Oral lichen planus (OLP) is a poorly understood chronic inflammatory mucocutaneous disease and is associated with many systemic diseases, which may lead to the erosion of oral mucosa and bring physical and psychological disorders to patients. However, the pathogenesis and immune microenvironment of OLP with different clinical subtypes are unclear. therefore, this study established a clinical cohort of OLP with 1-year follow-up and obtained the clinical information and bulk RNA-seq files to explore the immune microenvironment and molecular mechanism of oral lichen planus with different clinical subtypes. Based on the erosion of oral mucosa in the biopsy, the participants of OLP were divided into two groups, non-erosive OLP (NEOLP) and erosive OLP (EOLP). According to whether erosion occurred in oral mucosa more than three times and a remission period of less than 3 months within a one-year follow-up, OLP was divided into two groups, recalcitrant erosive OLP (REOLP) and stable OLP (SOLP).
2023-08-01 | GSE213346 | GEO
Project description:Interventions: Group 1: The radioembolization in hepatic malignancies is a routine clinical procedure. Serum samples for growth factor determination from peripheral venous blood are taken at three points in time - before therapy, after the first radioembolization and before the second radioembolization.
Study procedure ends after the third blood sample has been taken.
The second therapy for SIRT and the follow-up examinations belong to the scope of routine clinical procedures/follow-up.
Primary outcome(s): Evaluation of growth hormone release as a prognostic marker for overall survival after local ablative radioembolization therapy (SIRT) of hepatic malignancies.
Study Design: Allocation: N/A: single arm study; Masking: Open (masking not used); Control: uncontrolled; Assignment: single; Study design purpose: basic science
| 2721073 | ecrin-mdr-crc
Project description:This CYCling Lynch patients for Exercise and Prevention (CYCLE-P) trial was a prospective, non-randomized controlled trial conducted at the Familial High-Risk Gastrointestinal and Cancer Prevention Clinic of The University of Texas MD Anderson Cancer Center. Twenty-one LS participants with a confirmed pathogenic mutation in one of four DNA mismatch repair (MMR) genes were enrolled between April 2018 and January 2019. Follow-up was conducted 1-year from the start of the intervention. Statistical analysis by both per-protocol and intention-to-treat was performed from March to May 2021.
2023-08-07 | GSE210011 | GEO