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...

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...

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 (n = 138) or familial (n = 8) CFM. This is identified as a highly significant burden of loss of function variants in SF3B2, which is the most prevalent genetic cause...

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...

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...

Previous study showed that exposure to arsenic, an environmental carcinogen, induces polyadenylation of canonical histone H3.1 mRNA. This study revealed that polyadenylation of H3.1 mRNA increases H3.1 protein, which results in displacement of histone variant H3.3 at active promoters, enhancers, and insulator regions. To investigate global changes in transcription induced by ectopic expression of polyadenylated...

The Allen Mouse Brain Atlas is a three-dimensional atlas of gene expression throughout the adult mouse brain. The atlas is separated into four key features:In Situ Hybridization (ISH) Data includes image data with cellular level resolution. To find gene expression data, search can be performed using Gene Search, Differential Search, Fine Structure Search, Bulk Search, and Human Differential Search.Reference...

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....

Basal forebrain cholinergic neuron (BFCN) degeneration is an indicator of Down syndrome (DS) and Alzheimer’s disease (AD). The Ts65Dn (Ts) mouse model recapitulates both cognitive and morphological deficits of DS and AD, including BFCN degeneration. Therefore, this study used Ts mice to understand mechanisms underlying BFCN degeneration to identify novel targets for therapeutic intervention. They performed...

Neurological dysfunction associated with Down syndrome (DS) is the concomitant basal forebrain cholinergic neuron (BFCN) degeneration and onset of Alzheimer’s disease (AD) pathology. Previously, single population RNA sequencing analysis in the Ts65Dn (Ts) mouse model of DS revealed that the mitochondrial oxidative phosphorylation pathway was significantly impacted, where a large subset of genes within...