With advances in molecular biology, various biological phenomena can now be explored at higher resolution using mRNA sequencing (RNA-Seq) and chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), two powerful high-throughput next-generation sequencing (NGS) technologies. While methods are used widely in mouse, human, etc., less information is available in other animal...

this study was done to gain insights into transcriptional regulation of negative energy balance (neb) assoctiated genes. overexpressed genes in neb were identified using microarray and rna-seq data and promoter analysis of these overexpressed genes was applied to identify novel transcription factors. moreever, string database was used to construct a regulatory network of identified transcriptio...

The genus Endornavirus is a double-stranded RNA virus that infects a wide range of hosts. In this study, we report on the de novo assembly of a bell pepper endornavirus genome sequence by RNA sequencing (RNA-Seq). Our result demonstrates the successful application of RNA-Seq to obtain a complete viral genome sequence from the transcriptome data.

Large volumes of high-throughput sequencing data have been submitted to the Sequencing Read Archive (SRA). The lack experimental metadata associated with makes reuse and understanding quality very difficult. In case RNA (RNA-Seq), which reveals presence quantity in a biological sample at any moment, it is necessary consider that gene expression responds over short time interval (several seconds...

Long non‑coding RNAs (lncRNAs) are ncRNA transcripts >200 nucleotides that important genetic regulators. LncRNAs can directly regulate mRNA through a lncRNA‑mRNA regulatory mode and also competitive binding to micro (mi)RNA, which is generally known as the endogenous RNA (ceRNA) network. The present study evaluated functional roles networks of lncRNAs in chronic glomerulonephritis (CGN). pro...

The transcription factor SOX9 plays an essential role in determining the fate of several cell types and is a master factor in regulation of chondrocyte development. Our aim was to determine which genes in the genome of chondrocytes are either directly or indirectly controlled by SOX9. We used RNA-Seq to identify genes whose expression levels were affected by SOX9 and used SOX9 ChIP-Seq to ident...

Gene expression is the most fundamental level at which the genotype leads to the phenotype of the organism. Enabled by ultra-high-throughput next-generation DNA sequencing, RNA-Seq involves shotgun sequencing of fragmented RNA transcripts by next-generation sequencing followed by in silico assembly, and is rapidly becoming the most popular method for gene expression analysis. Poly[A]+ RNA-Seq a...

In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq da...