The most general definition of transcriptome assumes that it is a complete set of RNA molecules (transcripts) that are formed in a given organism. In response to exogenous and endogenous stimuli, transcriptome undergoes constant qualitative and quantitative changes. Monitoring these changes can provide information on how the living organisms function and deal with the changing environmental con...

Rhinovirus detection in symptomatic and asymptomatic children: value of host transcriptome analysis Authors: Heinonen S, Jartti T, Garcia C, et al. Am J Respir Crit Care Med 2015; [In press DOI: 10.1164/rccm.201504-0749OC] Summary: The “transcriptome” represents the set of RNA expressed by genes in one cell or a population of cells. Transcriptome analysis could facilitate our understanding of h...

Upon germination, pollen forms a tube that elongates dramatically through female tissues to reach and fertilize ovules. While essential for the life cycle of higher plants, the genetic basis underlying most of the process is not well understood. We previously used a combination of flow cytometry sorting of viable hydrated pollen grains and GeneChip array analysis of one-third of the Arabidopsis...

Whole-genome and transcriptome sequencing were performed to identify potential therapeutic strategies in the absence of viable treatment options for a patient initially diagnosed with vulvar adenocarcinoma. Genomic events were prioritized by comparison against variant distributions in the TCGA pan-cancer data set and complemented with detailed transcriptome sequencing and copy-number analysis. ...

To identify sources of inter-subject variation in vaccine responses, we performed high-frequency sampling of human peripheral blood cells post-vaccination, followed by a novel systems biology analysis. Functional principal component analysis was used to examine time varying B cell vaccine responses. In subjects vaccinated within the previous three years, 90% of transcriptome variation was expla...

The carmine spider mite (CSM), Tetranychus cinnabarinus, is an important pest mite in agriculture, because it can develop insecticide resistance easily. To gain valuable gene information and molecular basis for the future insecticide resistance study of CSM, the first transcriptome analysis of CSM was conducted. A total of 45,016 contigs and 25,519 unigenes were generated from the de novo trans...

The Library of Integrated Cellular Signatures (LINCS) project provides comprehensive transcriptome profiling of human cell lines before and after chemical and genetic perturbations. Its L1000 platform utilizes 978 landmark genes to infer the transcript levels of 14,292 genes computationally. Here we conducted the L1000 data quality control analysis by using MCF7, PC3, and A375 cell lines as rep...

The findings of the FANTOM3/ Genome Network project have redefined the landscape of the mammalian transcriptome by introducing an extensive collection of novel cDNAs and millions of sequenced tags corresponding to 59and 39-ends of mRNAs. This issue of PLoS Genetics includes a special collection of articles that explore the transcriptome complexity being revealed by work on the FANTOM3 dataset. ...

To globally survey the changes in transcriptional landscape during terminal erythroid differentiation, we performed RNA sequencing (RNA-seq) on primary human CD34(+) cells after ex vivo differentiation from the earliest into the most mature erythroid cell stages. This analysis identified thousands of novel intergenic and intronic transcripts as well as novel alternative transcript isoforms. Aft...