Cargando…

Identification of m(6)A residues at single-nucleotide resolution using eCLIP and an accessible custom analysis pipeline

Methylation at the N(6) position of adenosine (m(6)A) is one of the most abundant RNA modifications found in eukaryotes; however, accurate detection of specific m(6)A nucleotides within transcripts has been historically challenging due to m(6)A and unmodified adenosine having virtually indistinguish...

Descripción completa

Detalles Bibliográficos
Autores principales:	Roberts, Justin T., Porman, Allison M., Johnson, Aaron M.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Cold Spring Harbor Laboratory Press 2021
Materias:	Method
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7962486/ https://www.ncbi.nlm.nih.gov/pubmed/33376190 http://dx.doi.org/10.1261/rna.078543.120

Ejemplares similares

fSHAPE, fSHAPE-eCLIP, and SHAPE-eCLIP probe transcript regions that interact with specific proteins
por: Corley, Meredith, et al.
Publicado: (2021)

htseq-clip: a toolset for the preprocessing of eCLIP/iCLIP datasets
por: Sahadevan, Sudeep, et al.
Publicado: (2022)

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
por: Sugimoto, Yoichiro, et al.
Publicado: (2012)

Monitored eCLIP: high accuracy mapping of RNA-protein interactions
por: Hocq, Rémi, et al.
Publicado: (2018)

Letter to the Editor: Pandemic (COVID-19) Proctoring for eCLIPs Neurointervention
por: O'Kelly, Cian, et al.
Publicado: (2020)

Robust transcriptome-wide discovery of RNA binding protein binding sites with enhanced CLIP (eCLIP)
por: Van Nostrand, Eric L., et al.
Publicado: (2016)

Deconvolution of in vivo protein-RNA contacts using fractionated eCLIP-seq
por: Biancon, Giulia, et al.
Publicado: (2022)

Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP
por: Lorenz, Daniel A., et al.
Publicado: (2022)

A Virtual Comparison of the eCLIPs Device and Conventional Flow-Diverters as Treatment for Cerebral Bifurcation Aneurysms
por: Peach, T. W., et al.
Publicado: (2019)

Skipper analysis of eCLIP datasets enables sensitive detection of constrained translation factor binding sites
por: Boyle, Evan A., et al.
Publicado: (2023)

COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis
por: Warden, Charles D., et al.
Publicado: (2013)

PureCLIP: capturing target-specific protein–RNA interaction footprints from single-nucleotide CLIP-seq data
por: Krakau, Sabrina, et al.
Publicado: (2017)

ECLip-the European consortium on lipodystrophies: an update
por: Araújo-Vilar, David
Publicado: (2015)

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
por: Colquhoun, Rachel M., et al.
Publicado: (2021)

Revised iCLIP-seq Protocol for Profiling RNA–protein Interaction Sites at Individual Nucleotide Resolution in Living Cells
por: Nabeel-Shah, Syed, et al.
Publicado: (2023)

exRNA-eCLIP intersection analysis reveals a map of extracellular RNA binding proteins and associated RNAs across major human biofluids and carriers
por: LaPlante, Emily L., et al.
Publicado: (2023)

GoldCLIP: Gel-omitted Ligation-dependent CLIP
por: Gu, Jiaqi, et al.
Publicado: (2018)

eCLIPs bifurcation remodeling system for treatment of wide neck bifurcation aneurysms with extremely low dome-to-neck and aspect ratios: a multicenter experience
por: De Vries, Joost, et al.
Publicado: (2021)

SNVPhyl: a single nucleotide variant phylogenomics pipeline for microbial genomic epidemiology
por: Petkau, Aaron, et al.
Publicado: (2017)

CLUE: a bioinformatic and wet-lab pipeline for multiplexed cloning of custom sgRNA libraries
por: Becker, Martin, et al.
Publicado: (2020)

omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data
por: Drewe-Boss, Philipp, et al.
Publicado: (2018)

iCLIP: Protein–RNA interactions at nucleotide resolution
por: Huppertz, Ina, et al.
Publicado: (2014)

Fast decoding cell type–specific transcription factor binding landscape at single-nucleotide resolution
por: Li, Hongyang, et al.
Publicado: (2021)

Development of a high-resolution NGS-based HLA-typing and analysis pipeline
por: Wittig, Michael, et al.
Publicado: (2015)

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution
por: Windhager, Lukas, et al.
Publicado: (2012)

spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes
por: Hacker, William C, et al.
Publicado: (2023)

Phylogenetic Clustering by Linear Integer Programming (PhyCLIP)
por: Han, Alvin X, et al.
Publicado: (2019)

Probing N(6)-methyladenosine RNA modification status at single nucleotide resolution in mRNA and long noncoding RNA
por: Liu, Nian, et al.
Publicado: (2013)

DENT-seq for genome-wide strand-specific identification of DNA single-strand break sites with single-nucleotide resolution
por: Elacqua, Joshua J., et al.
Publicado: (2021)

Shortcut barcoding and early pooling for scalable multiplex single-cell reduced-representation CpG methylation sequencing at single nucleotide resolution
por: Mai, Liyao, et al.
Publicado: (2023)

A benchmark for RNA-seq quantification pipelines
por: Teng, Mingxiang, et al.
Publicado: (2016)

High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing
por: de Paz, Alexandra M, et al.
Publicado: (2018)

Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs
por: Katsantoni, Maria, et al.
Publicado: (2023)

Phased nucleotide inserts for sequencing low-diversity RNA samples from in vitro selection experiments
por: Bendixsen, Devin P., et al.
Publicado: (2020)

Nucleotide resolution profiling of m(3)C RNA modification by HAC-seq
por: Cui, Jia, et al.
Publicado: (2020)

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
por: Ha, Gavin, et al.
Publicado: (2012)

The Clip Approach: A Visual Methodology to Support the (Re)Construction of Life Narratives
por: Talsi, Riikka, et al.
Publicado: (2021)

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution
por: Konig, Julian, et al.
Publicado: (2011)

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
por: König, Julian, et al.
Publicado: (2010)

Accessible Region Conformation Capture (ARC-C) gives high-resolution insights into genome architecture and regulation
por: Huang, Ni, et al.
Publicado: (2022)

Cannot write session to /tmp/vufind_sessions/sess_3jglcl2rfj5evepip3fq7ll9tk