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...

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. Live GM12878 lymphoblastoid cells were used for this study. The dataset contains sequencing data as well as supplementary...

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 fluorescence resonance energy transfer (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...

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...

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...

This study characterized gut microbiome in pre-treatment stool using 16S rRNA gene and shotgun metagenome sequencing in melanoma patients undergoing immunotherapy. Transcriptional expression of metagenomic pathways was confirmed with metatranscriptome sequencing. Metatranscriptomics is important for determining expression of metagenomic functions in the microbial community. They also examined associations...

Long interspersed element-1 (LINE-1) is an autonomous retroelement that utilizes copy and paste mechanism to propagate themselves throughout the genome through a process called retrotransposition. The LINE-1 bicistronic mRNA codes for two proteins, ORF1p and ORF2. While LINE-1 transcription is usually repressed in most healthy somatic cells, ORF1p expression has been observed in tumors, including prostate...

Generation R is an ongoing prospective cohort study of child development from the prenatal period through young adulthood in a multi-ethnic population recruited from the Rotterdam, Netherlands metropolitan area. The study enrolled 9,778 mothers with a delivery date between April 2002 and January 2006; they had 9,749 live births. The primary objective of the study is to identify early environmental...

This study showed that basal-like breast cancer (BLBC) is sensitive to suppression of iron-sulfur cluster (ISC) biosynthesis and identified DNA polymerase epsilon (POLE) as an ISC-containing protein that underlies this phenotype. This dataset includes RNA sequencing data and data underlying figures. The publication also contains supplementary data, which includes data for short hairpin RNA (shRNA)...