Project description:To reannotate the genome of Zymoseptoria tritici IPO323, RNA-Seq and Iso-Seq runs were performed on different growth media to provide new source of evidence for gene model predictors. New gene models were predicted and combined with existing annotation releases. Finally, selection of best gene models was done by congruence with evidence data like transcript assembled from RNA-Seq, Iso-Seq cDNA and fungal proteins from databases.

2023-07-04 | GSE218898 | GEO

Contradictory of gene expression signatures for clinical prognostic prediction caused by update of reference genome and annotation

Project description:Gene expression estimates detected by RNA-sequencing technology vary with the updates of reference genome and gene annotation, which might confound existing expression-based prognostic signatures, making them inapplicable to clinical practice. In this study, we proposed a method to decrease these effects and developed a qualitative signature for stage I lung adenocarcinoma, whose classification was based on within-sample relative expression orderings (REOs) of gene pairs. The signature was validated in 471 stage I samples derived from public RNA-sequencing and microarray data (both log-rank p < 0.001). Notably, our signature could effectively predict prognosis for 30 stage I patients with severely degraded FFPE tissues (log-rank p = 0.0177). More important, the risk classification was stable in the latest annotation. In summary, our signature would be a promising signature for clinical individualized application because of its excellent prognostic performance and classification robustness.

2020-01-13 | GSE143486 | GEO

Eruca reference genome

Project description:A de novo Eruca sativa reference genome assembly and annotation

| PRJEB50993 | ENA

Integrative genome annotation of Malassezia sympodialis

Project description:The skin commensal yeast Malassezia is associated with several skin disorders. To establish a reference resource, we sought to determine the complete genome sequence of Malassezia sympodialis and identify its protein-coding genes. A novel genome annotation workflow combining RNA sequencing, proteomics, and manual curation was developed to determine gene structures with high accuracy.

2016-12-20 | PXD003773 | Pride

Proteogenomic refinement of the Neomegalonema perideroedes genome annotation

Project description:Neomegalonema perideroedes (formerly Meganema perideroedes) str. G1 is the type strain and only described isolate of the genus Neomegalonema (formerly Meganema). N. perideroedes is distinguished by the ability to accumulate high amounts of polyhydroxyalkanoates and has been associated with bulking problems in wastewater treatment plants due to its filamentous morphology. In 2013, its genome was sequenced as part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA), which aims to improve the sequencing coverage of the poorly represented regions of the bacterial and archaeal branches of the tree of life. As N. perideroedes str. G1 is relatively distantly related to well described species – being the only sequenced member of its proposed family - the in silico prediction of genes by nucleotide homology to reference genes might be less reliable. The aim of this study was to improve the genome annotation by usage of proteomic data. Besides the identification of novel and overlooked genes, the N-terminal cleavage pattern and the differences between databases were considered. Proteogenomic approaches, such as is described here, complements the GEBA initiative well - by providing important refinement of reference genome annotations.

2019-03-20 | PXD008508 | Pride

Functional genomics of cattle through integration of multi-omics data

Project description:The cattle industry is the largest of the agricultural commodities in the United States and generated over $101 billion in farm cash receipts during 2016; 28% of all US farm cash receipts. Although the sequence of the bovine reference genome has been publicly available since 2009, annotation of functional genome elements is largely incomplete, resulting in limitations for exploiting the genome to phenome relationship. This project generate high-quality detailed transcript and miRNA status datasets from a comprehensive set of bovine tissues, developmental stages, and cells through a set of rationally selected assays.

2022-07-30 | E-MTAB-11699 | biostudies-arrayexpress

Systematic Discovery and Characterization of Chromatin States and Butyrate-induced Variations for Cattle Genome Functional Annotation [dataset 1]

Project description:In this study, we generated six RNA-seq data that were collected from Rumen Epithelial Primary Cells (REPC) before and after (24h) butytate treatment. By combining other types of data sets, inclduing six histone modifications, RNA polymerase II, CTCF-binding sites, DNA accessibility, and DNA methylation, we established the first global map of regulatory elements (15 chromatin states) and defined their coordinated activities in cattle. We, for the first time, were able to establish the correlation among nutritional elements, chromatin states, gene activities, and phenotypic outcomes.

2019-07-24 | GSE129416 | GEO

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