Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• E3RC: A step-by-step computational protocol for exploring enhancer RNA expression and regulation using conventional RNA-seq data.

  PMID 40716058 · PMC12318280 · STAR protocols · 2025 · 6 claims · 3 setups

  Has reproduction · 62

  E3RC is a computational framework for identifying and quantifying eRNAs and characterizing their expression and transcriptional regulation using conventional RNA-seq data.

  preimplantation genome erna bulk computational motif

• TBP regulates transposable element expression in early mouse embryos.

  PMID 41862641 · PMC13144441 · The EMBO journal · 2026 · 8 claims · 6 setups

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  The general transcription factor TBP binds and activates MaLR transposable elements in mouse embryos

  single embryos computational embryonic rna-seq atac-seq motif

• The 3D genomics of lampbrush chromosomes highlights the role of active transcription in chromatin organization.

  PMID 41978268 · PMC13076225 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  Single-nucleus Hi-C reveals CTCF-independent contact domains with stable boundaries defined by convergently oriented transcription units (TUs)

  chicken computational oocytes single-nucleus nome-seq rna-seq