rG4-seq – a new method for RNA G-quadruplex (rG4) transcriptome profiling
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 ...
RNA-seq mixology – designing realistic control experiments to compare protocols and analysis methods
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 ...
TT-seq maps the human transient transcriptome
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 ...
Researchers discourage sample pooling in RNA-Seq experiments
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 ...
High-Resolution Transcriptome Analysis with Long-Read RNA Sequencing
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 ...
Success in RNA-Seq – Sample Prep and Workflow considerations
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 ...
DrugTargetSeqR: a genomics- and CRISPR-Cas9-based method to analyze drug targets
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 ...
Step by Step – RNA-Seq
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, ...
RNA sequencing in situ
Writing in Science, Lee et al. report an exciting first step toward combining some of the best aspects of both methods to sequence RNA in single cells in situ. Their approach, called fluorescence in situ RNA sequencing (FISSEQ), effectively treats ...
Intro to the Iso-Seq Method: Full-length transcript sequencing
from the PacBio Blog With the recent launch of SMRT Analysis v2.2, we’re excited to introduce analysis software support for the new Iso-Seq™ method for sequencing full-length transcripts and gene isoforms, with no assembly required! Today we’ll take a deeper ...
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- BAP-seq – bioorthogonal masked acylating agents for proximity-dependent RNA labelling
- Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment
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