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Determination of isoform-specific RNA structure with nanopore long reads
Current methods for determening RNA structure with short-read sequencing cannot capture most differences between distinct transcript isoforms. Here, we present RNA structure... -
RNA oxidation HOCl
RNA oxidation by hypochlorous acid (HOCl) is of major interest in vitro as well as in vivo settings. Conducting a thorough analysis of HOCl oxidation of ribonucleosides,... -
The Genomics of Speciation in Campylobacter
For further information on this study please see http://www.sanger.ac.uk/resources/downloads/bacteria/campylobacter-jejuni.html This data is part of a pre-publication release.... -
TENT5 cytoplasmic non-canonical poly(A) polymerases regulate the innate immun...
In this study, we aimed to identify mRNAs that are polyadenylated by TENT5 non-canonical poly(A) polymerases in Caenorhabditis elegans and murine macrophages using genome-wide... -
Humans and other commonly used model organisms are resistant to cycloheximide...
Ribosome profiling measures genome-wide translation dynamics at sub-codon resolution. Cycloheximide (CHX), a widely used translation inhibitor to arrest ribosomes in these... -
Genome-wide analysis of DNA replication and double strand breaks by TrAEL-seq
We have designed a methodology for capture of DNA 3’ ends that allows mapping of resected DNA breaks, stalled replication forks and also normal replication fork progression.... -
m1A marks translation initiation sites in human and mouse messenger RNA [Sequ...
We developed a novel approach, m1A-seq, for high-resolution mapping of the transcriptome-wide m1A landscape, based on antibody-mediated capture followed by massively parallel... -
High-resolution nucleosome positioning from ATAC-seq chromatin accessibility ...
We describe the NucleoATAC algorithm for high-resolution nucleosome positioning and occupancy determination using ATAC-seq. Overall design: ATAC-seq was performed on... -
Pseudouridine-chemical probes-Nanopore direct RNA sequencing
Validating pseudouridine mismatches in dRNA-seq through CMC-chemical reactivity -
Isolation and analysis of rereplicated DNA by Rerep-seq
Changes in gene copy number contribute to genomic instability, the onset and progression of cancer, developmental abnormalities, and adaptive potential. The origins of gene... -
Transcriptome-wide mapping reveals widespread dynamic regulated pseudouridyla...
Pseudouridine is the most abundant modification occurring on RNA, yet with the exception of a few well-studied RNA molecules little is known about the modified positions and... -
Critical assessment of DNA adenine methylation in eukaryotes using quantitati...
The discovery of N6-methyldeoxyadenine (6mA) across eukaryotes led to a search for additional epigenetic mechanisms. However, some studies have highlighted confounding factors... -
Nano-DMS-MaP allows isoform specific RNA structure determination
Genome-wide measurements of RNA structure can be obtained using reagents that react with unpaired bases, leading to adducts that can be identified by mutational profiling on... -
SncRNA sequencing of zoo animals
In this study we analyzed the blood sncRNA profiles of mostly uncharacterized zoo animals and related them to known RNA profiles. -
ChIP-seq of adenovirus core protein VII
To determine whether adenovirus core protein VII preferentially binds specific host chromatin regions, we performed native chromatin immunoprecipitation of protein VII-bound... -
RNA sequencing of host transcriptome of human foreskin fibroblast cells infec...
The purpose of these data is to determine if the impact bradyzoites have on the host transcripton is dependent on the export of parasite effector proteins via Myr1. We found... -
Massively parallel characterization of CYP2C9 variant enzyme activity and abu...
CYP2C9 encodes a cytochrome P450 enzyme responsible for metabolizing up to 15% of small molecule drugs, and CYP2C9 variants can alter the safety and efficacy of these... -
MRT-ModSeq - Rapid detection of RNA modifications with MarathonRT
The study aimed to characterize the mutational signatures produced by MarathonRT upon reverse transcription of modified cellular RNAs and use the signatures of validated... -
Paired nicking by nCas9 induced large-scale segmental duplication of the genome.
Structural variations (SVs) on the genome can result in various sporadic diseases, while they are recognized to contribute to genetic evolution. However, the technologies to... -
Mus musculus Homo sapiens Raw sequence reads
Endogenous retroviruses (ERVs) are transposable elements that cause host genome instability and usually play deleterious roles such as tumorigenesis. Recent advances also...