Robin Dowell

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.

May 29, 2024 | nature.com | Sana D. Karam |Robin Dowell

AbstractDynamic regulation of gene expression is fundamental for cellular adaptation to exogenous stressors. P-TEFb-mediated pause-release of RNA polymerase II (Pol II) is a conserved regulatory mechanism for synchronous transcriptional induction in response to heat shock, but this pro-survival role has not been examined in the applied context of cancer therapy.