This study dataset contains data from 28 adult and pediatric patients who were recruited from NYU Langone's Inflammatory Bowel Disease (IBD) Center. Study inclusion and exclusion criteria are noted below. Inclusion criteria: Subjects must have a suspected diagnosis of ulcerative colitis or Crohn’s disease Controls must have no clinical suspicion of ulcerative colitis or Crohn’s disease Signed and...

To construct a fixed time-scaled phylogenetic tree, the investigators combined 828 viral genome sequences obtained from COVID-19 patients at NYU Langone Health between March and May 2020 with 1,899 background sequences that were contributed to the Nextstrain repository. A total of 2,727 SARS-CoV-2 genomic sequences are available in the dataset. The supporting R code included with the dataset will produce...

This dataset was collected to show that there is a decline in cytotoxic T cells and TCR clonality in organ transplant recipients (OTRs) with squamous cell carcinoma (SCC). In this study, 5 SCC tumor samples and 6 transplant-associated SCC (TSCC) tumor samples were analyzed. Among SCC samples, the male to female ratio was 3 to 2 and the mean patient age was 81 years. Among TSCC samples, the male to...

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...

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...

Investigators obtained high quality SARS-CoV-2 sequences from 132 vaccinated and 283 unvaccinated individuals who were seen at NYU Langone Health facilities between May 1, 2021 and August 3, 2021. Fully vaccinated individuals received either two doses of the BNT162b2 (Pfizer/BioNTech) or mRNA-1273 (Moderna) vaccines, or a single-dose of the COVID-19 Janssen vaccine. Breakthrough infections were defined...

Arsenic, an environmental carcinogen, exposure induces polyadenylation of canonical histone H3.1 mRNA. For this study, human bronchial epithelial cells were exposed to arsenic for in vitro experiments, while A/J mice were exposed to arsenic for in vivo experiments. The results showed that polyadenylation of H3.1 mRNA increases H3.1 protein, which results in displacement of histone variant H3.3 at active...

Ultraviolet radiation (UVR) from the sun is the major cause of skin cancer. However, genes and pathways altered by solar-simulated UVR (ssUVR), a mixture of UVA and UVB, still remains unclear. For this study, human HaCaT keratinocytes were exposed to a single dose or 5 repetitive doses of ssUVR. Analyses of gene expression profiles and functional annotation were performed at 24 hours after irradiation....

Lysosomal dysfunction plays a key role in the pathogenesis of Alzheimer’s disease (AD) and Parkinson’s disease (PD). In early onset of AD, there is loss of Presenilin-1 (PSEN1) function. The loss of PSEN1 function impedes ER to lysosome delivery of chloride channel-7 (ClC-7). In murine blastocysts with different PSEN1 genotypes, isoproterenol and related β2-adrenergic agonists was used to reverse lysosomal...