Hope A Townsend

2 weeks ago | bmcgenomics.biomedcentral.com | Rutendo F. Sigauke |Lynn Sanford |Zachary L. Maas |Taylor Jones |Jacob Stanley |Hope A Townsend | +2 more

Detailed methods can be found in the Supplementary Methods, which includes technical details, full citations for all data utilized, and version numbers for all software utilized. Mouse samples were mapped to the mm10 reference genome and human samples to the hg38 genome. Nascent RNA sequencing experiments were manually curated from the Gene Expression Omnibus (GEO) [25, 26] and the Sequence Read Archive (SRA) [27]. All treatment conditions were annotated with reference to the cell harvest time.

Nov 23, 2024 | biorxiv.org | Jacob Stanley |Hope A Townsend |Rutendo F. Sigauke |Mary Allen

AbstractTranscription by RNA polymerases is an exquisitely regulated step of the central dogma. Transcription is the primary determinant of cell-state, and most cellular perturbations impact transcription by altering polymerase activity. Thus, detecting changes in polymerase activity yields insight into most cellular processes. Nascent run-on sequencing provides a direct readout of polymerase activity, but no tools exist to model this activity at genes.

Jun 20, 2024 | biorxiv.org | Kaylee Rosenberger |Lauren A. Vanderlinden |Jun Inamo |Hope A Townsend

AbstractBackground: Understanding genetic underpinnings of immune-mediated inflammatory diseases is crucial to improve treatments. Single-cell RNA sequencing (scRNA-seq) identifies cell states expanded in disease, but often overlooks genetic causality due to cost and small genotyping cohorts. Conversely, large genome-wide association studies (GWAS) are commonly accessible.