The Osteoarthritis Initiative (OAI) was a longitudinal cohort study which investigated the natural history of knee osteoarthritis across the spectrum of the disease through the collection of imaging, biochemical, genetic, and risk markers of knee OA. Measures included knee symptoms and function (evaluated using the West Ontario and McMaster Universities Arthritis Index (WOMAC) and the Knee injury and...

This dataset includes 330 Emirati adults participating in the UAE Healthy Future Study-Pilot (UAEHFS-pilot) who provided mouthwash samples. There were 225 non-smokers and 105 smokers who used cigarettes, dokha, shisha, or a combination of tobacco products. 101 of the 105 smokers were male. Tobacco use and frequency were assessed with a structured questionnaire and urine cotinine lab results. Gene...

NHEJ is the dominant double-strand break (DSB) repair pathway. During synapsis, the two DNA ends at a DSB are brought together into physical proximity for DNA repair. Using single-molecule FRET (smFRET), the study showed that both Ku and XRCC4:DNA ligase IV (X4L4) are necessary to achieve a flexible synapsis of blunt DNA ends. The addition of XLF causes a transition to a close synaptic state and the...

This dataset was compiled to determine a genome-wide long interspersed element-1 (LINE-1) insertion site mapping method for bulk DNA. This study has shown that transposon insertion profiling by sequencing (TIPseq) is a method that can be used for LINE-1 mapping in single cells. For the study, live GM12878 lymphoblastoid cells were obtained from Coriell Institute for Medical Research. The dataset contains...

Adenovirus is a nuclear replicating DNA virus that relies on the host cell machinery for productive infection. Processing and metabolism of cellular RNAs are regulated by METTL3, which catalyzes the addition of N6-methyladenosine (m6A) to messenger RNAs. Although m6A-modified adenoviral RNAs have been detected previously, the location and function of m6A within the infectious cycle is unknown. For...

This dataset was collected to study the genetic cause of craniofacial microsomia (CFM), which is the second most common congenital facial anomaly. In this study, they performed whole exome or genome sequencing of 146 kindreds with sporadic or familial CFM. Blood or saliva samples were collected from the proband and DNA was extracted from blood and saliva using standard procedures. This resulted in...

Smoldering multiple myeloma (SMM) is an asymptomatic plasma cell disorder. It is associated with a high-risk of progression to multiple myeloma (MM). For this study, they performed targeted sequencing on 82 patients. The results showed fewer NRAS and FAM46C mutations with SMM, which is consistent with their role as drivers of the transition to MM. They also analyzed the change in clonal structure over...

The data from this study displays the complexity of the varicella-zoster virus (VZV) transcriptome architecture. VZV causes varicella and reactivates later in life to cause herpes zoster. The VZV genome is known to produce multitudes of overlapping transcripts and distinct open reading frames (ORFs) have been studied as well. However, the architecture of the VZV transcriptome remains unknown. This...

This dataset was collected to show that direct RNA sequencing using nanopore arrays is an alternative to conventional RNA sequencing approaches, which are complicated by high gene density, overlapping reading frames, and complex splicing patterns. In direct RNA sequencing, individual polyadenylated RNAs are sequenced directly. For this study, direct RNA sequencing was used to profile the herpes simplex...

Arboviruses are caused by a group of viruses spread to people (host) by the bite of infected insects (vector). It is within these hosts that arboviruses replicate and undergo genomic evolution. However, how arboviruses evolve, are transmitted, or cause disease in nature remain unclear. Therefore, this study established a Zika virus (ZIKV) vector-borne transmission system in immunocompromised mice to...