Ultraconserved regions (UCRs) are DNA segments greater than 200 nucleotides in length with 100% sequence identity between humans, rats and mice (Bejerano et al., 2004). 481 UCRs have been described. Of these, 111 (known as “exonic” UCRs) coincide with human protein-coding genes, while 256 UCRs (termed “non-exonic”) do not appear to be transcribed at all. […]
The Updated Annotation of the 481 UCRs Read More »
UCRs and T-UCRs Ultraconserved regions (UCRs) are DNA segments greater than 200 nucleotides in length that are 100% identical among humans, rats, and mice. 481 UCRs have been described (Bejerano et al., 2004). As the original UCR annotations are based on an older (hg17) human genome assembly (Bejerano et al., 2004), we re-annotated all UCRs
The Relationship Between T-UCRs and Cancer Read More »
Tiling probes for 481 UCRs and their extended regions 481 UCR DNA segments are extended for 1 kb flanking each end of the UCR. Each extended UCR is tiled by sense and antisense strand-specific probes at 40 bp resolution. A total of 51,320 tiling probes, covering 481 UCRs and their extended regions, are printed onto
Probe Design Strategy of the Arraystar Human T-UCR Array Read More »
What are super enhancer lncRNAs? Super-enhancer lncRNA (SE-lncRNAs), emerging as a novel class of master RNA regulators, is a special set of long noncoding RNAs transcribed from super-enhancer genomic loci. SE-lncRNAs, together with super-enhancers, activate the nearby gene expression by mechanisms of transcription factor trapping, chromatin looping, chromatin modification, PolII loading, and release of transcriptional repressor (Fig. 1). Also, SE-lncRNAs are increasingly
What Are Super-Enhancer LncRNAs and Why Study Them? Read More »
Arraystar Super-Enhancer LncRNA Arrays are the first commercially available solution for sensitive and accurate SE-lncRNA profiling. The SE-lncRNAs are compiled on the foundation of Arraystar Gold standard & Reliable long non-coding RNA (lncRNA) collections and authoritative super-enhancer databases. “Super lncRNAs”, a special class of SE-lncRNA, are also included in the array contents. To experimentally observe,
Comprehensive and Powerful SE-LncRNA Collection Read More »
Super-enhancer lncRNAs have been demonstrated master regulatory functions in biology and diseases, such as myogenesis, cardiomyocyte differentiation, erythropoiesis, fibrosis in post-myocardial infarction, and cancers. The innovative Arraystar Super-enhancer LncRNA Arrays simultaneously profile the super-enhancer lncRNAs and their target genes. The detailed annotation, analysis and cross-references are provided to facilitate the in-depth study on SE-lncRNAs and
Detailed Annotation and Analysis of Super-Enhancer LncRNAs and Their Target Genes Read More »
Introduction In higher eukaryotic cells, multi-exon genes can produce transcript isoforms by alternative splicing, greatly increase the variations of the encoded proteins. Many alternatively spliced transcript isoforms play distinct roles in different tissues and developmental stages. The aberrant expression of these transcript isoforms can lead to phenotypical changes and associate with diseases [1]. Similarly, super-enhancer
Transcript-Specific Probes on the Super-Enhancer LncRNA Arrays Read More »
Super-enhancer lncRNAs are generally labile and short in half-lives. They can function at low copy numbers per cell to activate the target genes by cis-mechanism. For example, LncRNA-HOTTIP can activate the HOXA gene cluster with an average of less than one copy per cell. To accurately detect and quantify the transient, low level SE-lncRNAs, Arraystar
In RNA-seq, RPKM (Reads Per Kilobase of transcript per Million reads mapped) was introduced to normalize for differences in both library size and gene length. However, the RPKM calculation assumes that the total RNA content is the same across all samples. As a result, the RPKM value for a specific transcript reflects its relative abundance
Microarrays Are More Adept at Low Abundance RNA Profiling Read More »
Long non-coding RNAs (LncRNAs) often express and function at low abundance, buried in other classes of abundant RNAs (Fig. 1A and 1B)[1]. There are serious limitations of RNA-seq for lncRNA profiling. Poor quantification of lncRNAs due to the low abundance and the lack of completeness in lncRNA annotation For mere detection of the presence of
What Are the Limitations of RNA-seq for LncRNA Profiling? Read More »