Rutendo F. Sigauke

3 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.

1 month ago | genomebiology.biomedcentral.com | Taylor Jones |Rutendo F. Sigauke |Lynn Sanford |Dylan J. Taatjes |Mary Allen |Robin Dowell

The stand-alone TF Profiler application can be found on github (https://github.com/Dowell-Lab/TF_profiler) and Zenodo [76]. TF Profiler takes an annotation file for bidirectional regions from a nascent sequencing experiment and derives a TF activity profile. This includes generating simulated sequences based on the base composition of the regions provided, scanning for PSSM hits within the genome and statistically assessing TF enrichment and depletion.

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.