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 study showed that long interspersed element-1 (LINE-1) ORF2p expression is almost undetectable in human cancers. LINE-1 is the major driver of mobile DNA activity in humans. When expressed, LINE-1 loci produce bicistronic transcripts encoding two proteins essential for retrotransposition, ORF1p and ORF2p. ORF2p expression is not well characterized in human tissues and cell lines. For the study,...

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...

This dataset showed that mitovesicles, extracellular vesicles (EVs) of mitochondrial origin, are altered in Down syndrome (DS). Mitochondrial dysfunction is a distinctive feature of aging and neurodegenerative disorders, such as DS and Alzheimer’s disease. For this study, a high-resolution density gradient separation of EVs isolated from murine and human DS and diploid control brains was used. Using...

Fragile X syndrome (FXS) is caused by changes in FMR1 gene, which leads to transcriptional silencing and loss of its protein product fragile X mental retardation protein (FMRP). For this study, proteomic experiments were performed to investigate the de novo translational profile in FXS model mice is altered at steady state and in response to metabotropic glutamate receptor (mGluR) stimulation. Altered...

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 present a spectral alignment method for the identification of protein modifications using high-resolution mass spectrometry proteomics. For this study, they used SAMPEI for spectral alignment-based modified peptide identification. SAMPEI is an open-source algorithm that is designed for the discovery of functional protein and peptide signaling modifications. Human OCI-AML2...

Tau is one of the major microtubule-associated proteins in neurons. Its main role is to stabilize microtubules, supporting cytoskeletal organization, and axonal transport. Tau may undergo pathological modifications and become hyperphosphorylated. This causes the protein to accumulate into toxic assemblies that collectively lead to neurodegeneration. In Alzheimer's disease, tau proteins change shape...

This study investigated the pathways important for Mycobacterium tuberculosis, bacteria that cause tuberculosis, pathogenesis. They searched the Mycobacterium tuberculosis (M. tuberculosis) genome for open reading frames and identified an operon, Rv3679-Rv3680. This operon is predicted to encode proteins with ATPase activity. Using structure prediction modeling, they found that Rv3679 and Rv3680 have...

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...