These expression measurements were based on RNA sequencing of adult individuals, typically one male and one female per species.
For example, predicted microRNA chr16:62121639-62121678:- was based on RNA sequences found in ESC and its expression clusters with mir-302a, with which it shares a seed sequence (cluster 2, see Figure S7).
To identify clusters of high sequence-structure similarity, we apply a clustering procedure based on RNA sequence-structure alignment.
This new annotation based on RNA sequencing includes 17 new coding sequences (Table 2).
In mutations identified from complete genome or exome sequences, corresponding transcriptome analysis based on RNA sequencing (RNA-Seq) is performed to corroborate variants predicted to alter splicing.
We systematically calculated the enrichment levels of histone modifications in the gene body of all the P. falciparum genes at trophozoite stage and compared them with relative gene expression categorized based on RNA sequencing (Fig. 3a).
This database provides estimates of gene expression levels across 10 human tissues (colon, heart, hypothalamus, kidney, liver, lung, ovary, skeletal muscle, spleen, and testes) and is based on RNA sequencing, which provides a less biased estimate of gene expression than probe-based technologies.
OperomeDB represents one of the first attempts to provide a comprehensive resource for operon structures in microbial genomes based on RNA-sequencing data, providing a one stop portal for understanding the genome organization in the context of transcriptional regulation in a condition-specific manner.
Our framework for lincRNA candidate selection for genetic analysis, based on RNA-sequencing catalogs and genomic studies, has led us to unexplored roles for lincRNAs in brain development.
A close to 2-fold increase in expression of the X-chromosome is supported by a number of studies (Gupta et al. 2006; Nguyen and Disteche 2006; Yildirim et al. 2012), but has recently been challenged by claims based on RNA-sequencing (RNA-seq) analyses that there is no global increase in X-chromosomal gene expression (Xiong et al. 2010).
Studies have explored these "junk DNA" based on RNA deep sequencing and genome-wide analysis that the "junk DNA" was not derived from any known genes and does not encode any protein [ 4, 5].
