27 datasets found

Construction of draft genomes for Thunnus orientalis and Euthynnus affinis

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...

Histones are a principal constituent of chromatin in eukaryotes and fundamental to our understanding of eukaryotic gene regulation. In archaea, histones are phylogenetically...

The Orthodenticle homeobox (Otx) gene is a conserved homeobox gene, crucial for patterning the anterior neural plate of vertebrate embryos. In the invertebrate chordate Ciona...

The ocean’s methane emission to the atmosphere is dominated by continental shelves where cold seeps are globally common features. Seeps emit methane into the hydrosphere, but...

The murine malaria parasite Plasmodium berghei is a robust and safe malaria model organism. The N15 phage-derivative, low-copy pJAZZ® vector system (from Lucigen) can carry...

a part of DNA spike based study confirming Enterobacteriaceae involvement in microbiome abundance

Nano3P-seq is a simple and robust method to accurately estimate transcript levels, tail lengths and tail nucleotide composition information in full-length individual reads, with...

Most genetic changes have negligible reversion rates. As most mutations that confer resistance to an adversary condition (e.g., drug treatment) also confer a growth defect in...

Validating pseudouridine mismatches in dRNA-seq through CMC-chemical reactivity

We used a molecular barcoding approach to quantify the fitness of ~60,000 randomly mutated variants of the Saccharomyces cerevisiae U3 snoRNA (the data were further used to...

Nucleosome organization is critical for gene regulation. In living cells, this organization is determined by multiple factors, including the action of chromatin remodelers,...

High-throughput sequencing data, including amplicon sequencing, barcode sequencing, single-cell transcriptome assays, RNA-seq, and EM-seq, generated in Ishiguro et al., 2024....

In this study we used nanopore direct RNA sequencing to evaluate RNA modifications

We develop a method, Single Molecule Structure sequencing (SMS-seq), that combines structural probing with native RNA sequencing to provide non-amplified, structural profiles of...

The replication of eukaryotic genomes is highly stochastic, making it difficult to determine the replication dynamics of individual molecules with existing methods. We now...

Development of MAP-C (mutation analysis in pools by chromosome conformation capture), which involves performing 3C on a pool of mutants (generated by programmed oligonucleotide...

Ligation by plant and fungal RNA ligases yields an internal 2'-phosphate group on each RNA ligation product. This work allowed us to define several unique signals produced by...

Transfer RNAs (tRNAs) are highly-modified small non-coding RNAs that play a pivotal role in protein translation. Dysregulation in tRNA abundances or their modifications can lead...

This project carries out the pilot CRISPR/Cas9 screens in the K562 background. Its goals are to confirm that positive controls work, and to assess the effects of experimental...