Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq Footprint analysis of assay for transposase-accessible chromatin via sequencing (ATAC-seq) enables base resolution mapping of regulatory elements but is often underpowered and prone to false positives...

Sharper footprints, cleaner insights? Yuxuan Lin at the University of Pennsylvania explores a new approach that corrects Tn5 bias for bulk & single-cell ATAC-seq, boosting the accuracy of transcription-factor binding 🔬
👉 www.biorxiv.org/content/10.1...
#SingleCell #Epigenomics #ATACseq

🚀 Excited to share SMART-PTA (miniaturized Primary Template Amplification) a high-throughput single-cell whole-genome amplification method that preserves clonal lineage information while enabling deep genomic and transcriptomic profiling.

🙏 A huge thank you to the incredible team behind this work—your dedication and brilliance made this possible! Special thanks @landau.bsky.social to for the opportunity to work in such an inspiring environment @nygenome.org @WeillCornell.

🙌 We hope D&D-seq becomes a valuable tool for the single-cell community. Explore the potential of this method to uncover gene regulation dynamics like never before! We’d love to hear your feedback and see how YOU apply it. #OpenScience

🧬 Breaking new ground with single-cell multiomics! 🔗 Linking genotypes and phenotypes using D&D-GoT-ChA in 15,807 PBMCs with IDH2R140Q mutation. Reduced CTCF binding in mutant cells alters insulation at CTCF sites.

🧬 By coupling D&D-seq with 10xGenomics scATAC assay, we were able to map transcription factor binding event in single cells. 🔬✨ D&D-seq achieves precise single-cell Protein:DNA profiling!

🧬 Why D&D-seq? Existing methods struggle to profile weak/transient DNA:Protein interactions in single cells. We engineered a cutting-edge approach combining nanobody-tethered cytosine base editing to fill this gap. #SingleCell #Innovation

Single-cell mapping of regulatory DNA:Protein interactions Gene expression is coordinated by a multitude of transcription factors (TFs), whose binding to the genome is directed through multiple interconnected epigenetic signals, including chromatin accessibil...

🧬 We’re excited to introduce D&D-seq, a single-cell technology that maps DNA:Protein interactions through molecular footprinting. Check it out here: biorxiv.org/content/10.1... #Genomics #Epigenetics