Figure 5. (a) Normalized transcriptome abundances of Lyso-PAF-AT, PAF-AH and PLA2 in all transcriptome samples. (b) Regression of the Lyso-PAF/PAF ratio and abundance of LysoPAF-AT in the same coral transcriptome and metabolome interaction samples. (c) Images of a damaged and undamaged coral from the SLIs dataset. (d ) Regression of the Lyso-PAF/PAF ratio compared with the increasing coral dama...

The Journal of Nematology now offers publication of Nematode Genome Announcements (NGA) and Nematode Transcriptome Announcements (NTA). These brief reports announce the sequencing and assembly of a nematode genome or transcriptome resource, along with basic technical information on DNA sequencing and bioinformatic methods used. This publishing initiative offers a new avenue to openly and concis...

We analyzed 10 genome expression data sets by large-scale cross-referencing against broad structural and functional categories. The data sets, generated by different techniques (e.g. SAGE and gene chips), provide various representations of the yeast transcriptome (the set of all yeast genes, weighted by transcript abundance). Our analysis enabled us to determine features more prevalent in the t...

Background In recent years, next generation high throughput sequencing technologies have proven to be useful tools for investigations concerning the genomics or transcriptomics also of non-model species. Consequently, ornithologists have adopted these technologies and the respective bioinformatics tools to survey the genomes and transcriptomes of a few avian non-model species. The Common Blackb...

1. Transcriptome Analysis Recent advances in sequencing, computational biology, and information science have brought great new opportunities in biological research. One of the opportunities is that researchers are able to apply a systematic approach towards understanding some of the objects or phenomena in molecular biology/genetics and modern medicine. Not long ago, such a systematic approach ...

A comprehensive picture of the transcriptome – the identity and amount of each individual RNA molecule, for each cell type and state has been a holy grail for biologists working on a wide range of topics. For example, analysis of the transcriptome of embryos provide new information about molecular mechanisms underlying cell differentiation and organism development [1]; transcriptome of cancer c...

Red Clover Transcriptome, Spatial Gene Expression Genomic resources for forage legume red clover are limited. Chakrabarti et al. report the construction of a de novo transcriptome assembly of red clover representing multiple tissue types. The transcriptome assembly was functionally annotated and transcripts encoding putative transcription factors were identified. Gene expression analysis reveal...

Background: Given the demonstrated utility of Third Generation Sequencing [Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT)] long reads in many studies, a comprehensive analysis and comparison of their data quality and applications is in high demand. Methods: Based on the transcriptome sequencing data from human embryonic stem cells, we analyzed multiple data features of PacB...

Evolutionary biologists are increasingly comparing gene expression patterns across species. Due to the way in which expression assays are normalized, such studies provide no direct information about expression per gene copy (dosage responses) or per cell and can give a misleading picture of genes that are differentially expressed. We describe an assay for estimating relative expression per cell...

Simple sequence repeat (SSR) or microsatellite markers, are a valuable tool for several purposes such as evaluation of genetic diversity, fingerprinting, marker assisted selection, and breeding. Recent developments in sequencing technologies and bioinformatics analyses provide new opportunity to produce a high number of less costly SSRs. Here, we used for the first time a wholegenome shotgun se...