Project description:The ‘Genetic Epidemiology of Asthma in Costa Rica’ is a family-based cross-sectional cohort ascertained between February 2001 and August 2008 on a Hispanic population isolate from the Central Valley of Costa Rica. The study recruited children between 6 to 14 years of age with moderate persistent asthma.
Project description:This dataset consists of 20 metaproteomic analyses of the Western Atlantic Ocean aboard the R/V Knorr KN210-04 DeepDOM expedition in 2013. Samples were collected by McLane pumps on GFF or GF75 filters, split, and frozen until analyses. Expedition metadata and co-sampled datasets are available at: https://www.bco-dmo.org/deployment/59057
Project description:Data from multiple high throughput technologies such as RNA sequencing (RNA-Seq) and protein mass spectrometry (MS/MS) are often used to assist in predicting eukaryote genome features such as genes, splice variants, and single nucleotide variants (SNVs). The genomes of parasitic nematodes causing neglected tropical diseases are often poorly annotated. Angiostrongylus costaricensis, a nematode that causes an intestinal inflammatory disease known as abdominal angiostrongyliasis (AA), is one example. Currently, no drugs or treatments are available for AA, a public health problem in Latin America, especially in Costa Rica and Brazil. The available genome of A. costaricensis, specific to the Costa Rica strain, is a draft version not supported by transcript- or protein-level evidence. This study used RNA-Seq and MS/MS data to perform an in-depth annotation of the A. costaricensis genome. Our prediction supplemented the reference annotation with a) novel coding and non-coding genes; b) pieces of evidence of alternative splicing generating new proteoforms; c) a list of SNVs specific to the Brazilian strain (Crissiumal). To the best of our knowledge, this is the first time that a multi-omics approach has been used to improve the genome annotation of a parasitic nematode. We hope this supplemented genome annotation can assist the future development of drugs to treat AA caused by either Brazil strain (Crissiumal) or Costa Rica strain.
