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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,... -
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... -
Lamprey CTCF Binding Landscape and Hox Evolution
We identified lamprey homologs of CTCF, and performed ChIP-seq for the CTCF protein in the Arctic lamprey, Lethenteron camtschaticum. Using the same anti-CTCF antibody, ChIP-seq... -
Decode-seq: a practical approach to improve differential gene expression anal...
It is often the case that inadequate numbers of biological replicates are utilized in differential gene expression analysis. We describe an easy and effective RNA-seq approach... -
Transcriptome analysis of cytotrophoblasts and syncytiotrophoblasts derived f...
We tested the relevance of an established stem-cell-derived model of trophoblast development to Toxoplasma gondii infection. Human trophoblast stem cells were cultured under... -
Simplified ChIP-exo assays
Chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and its ultra-high resolution cousin ChIP-exo are methods that identify where proteins bind along any genome... -
Transcriptome assemblies 10 vertebrate species
2 types of content: a) Raw RNA-seq files from cell lines of 10 vertebrate species (human, mouse, cow, tasmanian devil, chicken, duck, zebra finch, xenopus, medaka and... -
Homo sapiens Targeted Locus (Loci)
Mutant allelic series for human p53 ORF -
Saturation_Genome_Editing_of_RAD51C
Saturation Genome Editing of RAD51C. This study aims to functionally characterize saturating-levels of mutation at the RAD51C locus. We will target the Coding Sequence (CDS) and... -
20Mammals
Definition of functional regulatory regions in the vast non-coding fractions of mammalian genomes remains a daunting challenge that underscores our limited understanding of... -
Principles of ER Co-Translational Translocation Revealed by Proximity-Specifi...
Localized protein synthesis is a fundamental mechanism for creating distinct subcellular environments. Here we developed a generalizable proximity-specific ribosome profiling... -
High-throughput identification of miRNA targets using CLASH (crosslinking, li...
Purpose: Identification of miRNA-mRNA interactions in human cells. Method: We used the CLASH technique with PTH-tagged AGO1 protein as a bait. Results: In 6 experiments we... -
Multiplexed high throughput screening identifies broadly-active rescuers of p...
The accumulation of misfolded proteins within intracellular aggregates is a distinctive feature observed within multiple neurodegenerative diseases (NDDs), yet the genes and... -
Analysis of transcriptomic dynamics during the compatible and incompatible in...
Leptosphaeria maculans (anamorph Phoma lingam), the causal agent of blackleg disease in Brassica napus, poses a continual threat to canola/rapeseed production The overall goal... -
Metagenomic next-generation sequencing for microbial pathogen
This study aims to detect pathogens in bronchoalveolar lavage fluid (BALF) from SCAP patients using both metagenomics extended-spectrum pathogenic microorganism sequencing... -
Cut-and-Run in situ factor profiling maps DNA binding and 3D contact sites at...
Unlike Chromatin Immunoprecipitation (ChIP), which fragments and solubilizes total chromatin, Cut-and-Run is performed in situ, allowing for both high-resolution chromatin... -
Bacterial communities associated to the toxigenic benthic dinoflagellate Pror...
Toxigenic benthic dinoflagellates of the genus Prorocentrum interact with bacteria. The nature of the interactions may avoid or trigger a benthic harmful algal bloom and/or be... -
Development of Platanus-allee and benchmarks of haplotype assemblers
Platanus-allee, a new de novo haplotype assembler, was developed and benchmarks of haplotype construction abilities of multiple tools were performed. The target samples were... -
Mining microbial metatranscriptomes for expression of antibiotic resistance g...
We use a novel approach (an analysis of metatranscriptomics data) to study antibiotic resistance, a topic that poses major health care concerns. We investigate resistance gene... -
rumen sample Raw sequence reads
rumen microbial diversity in Tan sheep