Project description:Enhanced cross-linking immunoprecipitation (eCLIP) featuring a size-matched input control has been recently applied to profile the binding sites of more than one hundred RNA binding proteins (RBPs). However computational pipelines and quality control metrics needed to process CLIP data at scale have yet to be well defined. Here, we describe our ENCODE eCLIP processing pipeline (https://github.com/YeoLab/eclip), enabling users to go from raw reads to processed peaks that are enriched above paired input, reproducible across biological replicates, and can be directly compared against the public ENCODE eCLIP resource. In particular, we discuss processing steps designed to address common artifacts, including properly quantifying unique RNA fragments bound by both unique genomic- and repetitive element-mapped reads. Using manual quality annotation of 350 ENCODE eCLIP experiments, we develop metrics for quality assessment of eCLIP experiments prior to and after sequencing, including library yield, number of unique fragments in the library, total binding relative information, and biological reproducibility. In particular, we quantify the commonly believed linkage between depth of sequencing and peak discovery, and derive methods for estimating required sequencing depth based on pre-sequencing metrics. Finally we provide recommendations for the common question of integrating RBP binding information with RNA-seq to generate splicing maps representing the positional effect of binding on alternative splicing. These pipelines and QC metrics enable large-scale processing and analysis of eCLIP data, and will help to standardize rigorous analysis of RBP binding data.

2018-06-08 | GSE107766 | GEO

Best practices for eCLIP experiments and analysis [poor quality]

2018-06-08 | GSE107767 | GEO

Best practices for differential accessibility analysis in single-cell epigenomics

Project description:This submission is a dataset of single-nucleus multi-omics of uninjured and injured spinal cords of mice harvested and profiled using 10x Multiome ATAC + Gene Expression kit.

2024-04-30 | GSE230765 | GEO

SCAI/HRS Expert Consensus Statement on Transcatheter Left Atrial Appendage Closure.

Project description:Exclusion of the left atrial appendage to reduce thromboembolic risk related to atrial fibrillation was first performed surgically in 1949. Over the past 2 decades, the field of transcatheter endovascular left atrial appendage closure (LAAC) has rapidly expanded, with a myriad of devices approved or in clinical development. The number of LAAC procedures performed in the United States and worldwide has increased exponentially since the Food and Drug Administration approval of the WATCHMAN (Boston Scientific) device in 2015. The Society for Cardiovascular Angiography & Interventions (SCAI) has previously published statements in 2015 and 2016 providing societal overview of the technology and institutional and operator requirements for LAAC. Since then, results from several important clinical trials and registries have been published, technical expertise and clinical practice have matured over time, and the device and imaging technologies have evolved. Therefore, SCAI prioritized the development of an updated consensus statement to provide recommendations on contemporary, evidence-based best practices for transcatheter LAAC focusing on endovascular devices.

| S-EPMC11307869 | biostudies-literature

SCAI Expert Consensus Statement on the Management of Calcified Coronary Lesions.

Project description:The prevalence of calcification in obstructive coronary artery disease is on the rise. Percutaneous coronary intervention of these calcified lesions is associated with increased short-term and long-term risks. To optimize percutaneous coronary intervention results, there is an expanding array of treatment modalities geared toward calcium modification prior to stent implantation. The Society for Cardiovascular Angiography and Interventions, herein, puts forth an expert consensus document regarding methods to identify types of calcified coronary lesions, a central algorithm to help guide use of the various calcium modification strategies, tips for when using each treatment modality, and a look at future studies and trials for treating this challenging lesion subset.

| S-EPMC11307856 | biostudies-literature

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