Transcriptomics on Maragkakis Lab

SenCat: Redefining human cell senescence through multiomic profiling of multiple senescent primary cell types

Mon, 01 Jun 2026 00:00:00 +0000

Summary

SenCat is a comprehensive multiomic atlas of human cell senescence generated by profiling multiple primary cell types induced to senescence through distinct triggers. Integrated analysis of transcriptome, epigenome, and proteome data across cell types and senescence inducers redefines the core features of the senescent state and identifies cell-type-specific and universal senescence signatures.

Transcript-guided targeted cell enrichment for scalable single-nucleus RNA sequencing

Wed, 11 Mar 2026 00:00:00 +0000

Summary

This study introduces a method for transcript-guided targeted enrichment of specific cell populations prior to single-nucleus RNA sequencing. By selecting nuclei based on expression of specific transcripts, the approach achieves deep profiling of rare cell types at scale, enabling discovery of cell-type-specific transcriptional programs that would be missed by unbiased approaches.

TERA-Seq: True end-to-end sequencing of native RNA molecules for transcriptome characterization

Tue, 24 Aug 2021 00:00:00 +0000

Summary

TERA-Seq is a method that combines chemical ligation of adapters to both RNA ends with nanopore direct RNA sequencing to capture complete native RNA molecules from the 5’ cap to the 3’ poly(A) tail. This enables simultaneous characterization of RNA modifications, poly(A) tail length, and transcript boundaries at single-molecule resolution.

CLIPSeqTools — a novel bioinformatics CLIP-seq analysis suite

Fri, 01 Jan 2016 00:00:00 +0000

Summary

CLIPSeqTools is a modular bioinformatics pipeline for the analysis of CLIP-seq data, providing tools for read processing, peak calling, motif analysis, and visualization. The suite enables comprehensive characterization of RNA-binding protein interaction sites across the transcriptome.