The Challenges and Solutions of Small RNA Profiling The Biases of Using TPM in Small RNA Sequencing Data Analysis Simultaneously Profile Multiple Small RNA Classes Accurately Direct End-labeling to Avoid the Biases From Sequencing Library Prep Small RNA-seq has been used for profiling microRNAs and other small RNAs. However, the use of small RNA-seq data to quantify […]
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Arraystar GlycoRNA Array Profiling Arraystar GlycoRNA Array combines methods of biochemical capture of glycoRNA and RNA detection by microarray to quantify and profile glycoRNA expression. The integration of these two advanced techniques leverages the strengths of both methods for high specificity, sensitivity, and accuracy. The array covers a wide range of glycosylated small RNA classes,
GlycoRNAs have emerged as a new area of study in cancer, cardiovascular, neurological, immune, and respiratory diseases, opening up new avenues into novel biomarker and therapeutic applications. Breast Cancer Surface glycoRNAs are inversely related with tumor malignancy and metastasis, i.e. breast non-cancer cells (MCF-10A) have the highest glycoRNA levels, followed by breast cancer cells (MCF-7), while breast
GlycoRNAs are glycosylated small non-coding RNAs, including small nuclear RNAs (snRNAs), ribosomal RNAs (rRNAs), small nucleolar RNAs (snoRNAs), transfer RNAs (tRNAs), Y-RNAs[1], and microRNAs [2]. Glycosylated mRNAs are not known. Particularly, the N-glycans on glycoRNAs are highly sialylated and fucosylated. GlycoRNAs are displayed on the cell surface and can bind Siglec receptors important in immune
Ultraconserved regions (UCRs) are DNA segments greater than 200 bp in length that are completely conserved among human, rat, and mouse (Bejerano et al., 2004). 481 UCRs have been identified, 225 of which are classified as transcribed (“exonic”) or possibly transcribed (“possibly exonic”) due to overlap with coding exons. Of the remaining 256 UCRs, termed
Case Studies of profiling T-UCR expression in Cancer Recent genome-wide expression studies show that a subset of ultraconserved regions (UCRs), known as transcribed ultraconserved regions (T-UCRs), are abnormally expressed in a number of human cancers, such as leukemia, colorectal carcinoma, and hepatocellular carcinoma (Braconi, et al., 2011; Calin, et al., 2007; Lujambio, et al., 2010). In addition, the
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.
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
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
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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
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