Sequencing Protocols

To facilitate scalable profiling of single cells, engineers at the University of Washington have developed split-pool ligation-based transcriptome sequencing (SPLiT-seq), a single-cell RNA-seq (scRNA-seq) method that labels the cellular origin of RNA through combinatorial barcoding. SPLiT-seq is compatible with fixed ...

Sequencing the RNA in a biological sample can unlock a wealth of information, including the identity of bacteria and viruses, the nuances of alternative splicing or the transcriptional state of organisms. However, current methods have limitations due...

Researchers from the University of Cambridge introduce RNA G-quadruplex sequencing (rG4-seq), a transcriptome-wide RNA G-quadruplex (rG4) profiling method that couples rG4-mediated reverse transcriptase stalling with next-generation sequencing. Using rG4-seq on polyadenylated-enriched HeLa RNA, the researchers generated a global in vitro ...

Carefully designed control experiments provide a gold standard for benchmarking new platforms, protocols and pipelines in genomics research. RNA profiling control studies frequently use the mixture design, which takes two distinct samples and combines them in known proportions to induce ...

Transcription of eukaryotic genomes produces protein-coding mRNAs and diverse noncoding RNAs (ncRNAs), including enhancer RNAs (eRNAs). Most ncRNAs are rapidly degraded, difficult to detect, and thus far have not been mappable in their full range. Mapping of transient RNAs is ...

Massively parallel cDNA sequencing (RNA-seq) experiments are gradually superseding microarrays in quantitative gene expression profiling. However, many biologists are uncertain about the validity of cost-saving sample pooling strategies for their RNA-seq experiments. Researchers from Aarhus University sequenced RNA-pools and compared their ...

RNA sequencing (RNA-seq) enables characterization and quantification of individual transcriptomes as well as detection of patterns of allelic expression and alternative splicing. Current RNA-seq protocols depend on high-throughput short-read sequencing of cDNA. However, as ongoing advances are rapidly yielding increasing ...

by Natalie McDonald, PhD RNA in the cell is comprised of a variety of populations, including traditional poly-adenylated messenger RNA (polyA RNA), non-adenlyated RNA, which may be coding or regulatory, ribosomal RNA (rRNA) and small and micro RNA.  The first ...

To identify physiological targets of drugs and bioactive small molecules, researchers at The Rockefeller University developed an approach, named DrugTargetSeqR, which combines high-throughput sequencing, computational mutation discovery and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-based genome editing. They applied this ...

The introduction of RNA sequencing (RNA-seq), as a direct result of rapid progression of next-generation sequencing technologies, has revolutionized the world of transcriptomics. It enables quantification of the complete set of RNA with all its isoforms in a given cell, ...