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Genome-wide map of Pol II occupancy alteration on chromatin upon CDK12 and CD...
We performed ChIP-Seq on MV4 11 cells after 6 hours treatment of DMSO, 100nM and 200nM THZ531 to determine the location of Pol II with phosphorylated Ser2 occupancy Overall... -
Two distinct mechanisms for X chromosome dosage compensation in Anopheles and...
Heteromorphic sex chromosomes induce potentially deleterious gene expression imbalances that are frequently corrected by dosage compensation (DC). Three distinct molecular... -
The evolution of small RNA pathways across the arthropods
A comparison of somatic and germline small RNA pathways across the arthropods -
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... -
ITS or 16S amplicon sequencing of Drosophila spp. and their natural food sour...
Banana samples fed on by wild Drosophila spp. were collected, and the fungal or bacterial compositions of their microbiota was analyzed by ITS or 16S amplicon sequencing,... -
Comparative analysis of amplicon and metagenomic sequencing methods reveals k...
Background: The interplay between hosts and their associated microbiome is now recognized as a fundamental basis of the ecology, evolution and development of both players. These... -
DMS-MaPseq: A genome-wide or targeted approach for RNA structure probing in vivo
Here we present dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq), which encodes DMS modifications as mismatches using a thermostable group II intron reverse... -
Whole-genome sequencing of several dipteran insects Genome sequencing
The genomes of several insect species were sequenced and their X-chromosomes characterized. -
G4access identifies G-quadruplexes and their associations with open chromatin...
Metazoan promoters are highly enriched in secondary structure forming motifs, among which G-quadruplexes (G4s). We describe G4access, a novel approach to isolate and sequence... -
Tracking the origin and evolutionary dynamics of RNA editing in metazoans
Whole-genome DNA-seq and strand-specific RNA-seq on 18 species, including 14 metazoans and four unicellular eukaryotes closely related to metazoans. For each species, two to... -
Poly(A)-tail profiling reveals an embryonic switch in translational control
Poly(A) tails enhance the stability and translation of most eukaryotic messenger RNAs, but difficulties in globally measuring poly(A)-tail lengths have impeded greater... -
Whole genome mapping of DNA G-quadruplexes in multiple species by G4-seq
The identification of DNA G-quadruplexes (G4s) in the genome is important to study different biological processes in which these structures play a role, such as genome... -
Bottleneck_Sequencing_of_Animal_Tissue__WGS_
Study somatic mutation in animal tissues, including mutation burden accumulation through lifespan and mutational signatures. -
PulseNet Salmonella enterica Genome sequencing
Salmonella enterica genomes sequenced as part of PulseNet USA surveillance for foodborne disease -
Transcriptomic evolution across bilaterian tissues
We investigate tissue transcriptomic evolution across bilaterian animals by analyzing RNA-seq data from eight different tissues across twenty species. Overall design:... -
Small RNA sequencing of the 8 to 30-nucleotide window from various samples
RNA-sequencing (RNA-Seq) protocols and bioinformatic pipelines are designed to streamline downstream analyses on sequences believed to be the most important. Here, we have... -
High-resolution quantitative profiling of tRNA abundance and modification sta...
Measurements of cellular tRNA abundance are hampered by pervasive blocks to cDNA synthesis at modified nucleosides and the extensive similarity among tRNA genes. We overcome... -
Error correction tool benchmark
This project compares the performance of different hybrid error correction tools. -
Genome-wide evolutionary analysis of eukaryotic DNA methylation
Eukaryotic cytosine methylation represses transposable elements, but also occurs in bodies of active genes. The extent to which these processes are conserved is unclear, and... -
Origin and Evolution of Neural Microexons
Our study focuses on the origin of the neural microexon program.</p><p>We discover that neural microexon programs are present in non-vertebrate...