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).

Publications 1.3k Datasets 392.5k Experiments 4

System / cell line: bidirectional ✕ Assay: rna-seq ✕ Clear

Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

PMID 40281430 · PMC12032694 · BMC genomics · 2025 · 7 claims · 8 setups

Full-text index only

A large repository of nascent run-on RNA-seq samples (DBNascent) was assembled and uniformly processed to identify sites of bidirectional transcription genome-wide.

bidirectional across high-quality nascent comparative eqtl
Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

PMID 38594607 · PMC11003151 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 8 setups

Has reproduction · 100

H3K27ac ChIP-seq and RNA-seq were used to construct eRNA expression profiles across multiple tissues in Enshi Black (ES) and Duroc pigs, revealing tissue-level eRNA regulatory landscapes

longissimus muscle snps pig h3k27ac strand-specific starr-seq
TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

PMID 25391375 · PMC4315292 · Genome research · 2015 · 8 claims · 8 setups

Has reproduction · 80

TP53 binding events fall into three distinct categories defined by the local chromatin environment: TSS (H3K4me3+), enhancer (H3K4me1+/H3K4me3-), and distal (H3K4me1-/H3K4me3-) peaks.

imr90 hct116 chip-seq rna-seq atac-seq
Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

PMID 38548265 · PMC11954816 · Journal of advanced research · 2025 · 8 claims · 8 setups

Has reproduction · 79

Meta-analysis confirmed a positive association between DED and DEP occurrence

patients taiwan biobank twb meta-analysis genome-wide score

Experiments

Atlas of nascent RNA transcripts reveals tissue-specific enhancer to gene linkages.

Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs.

TP53 engagement with the genome occurs in distinct local chromatin environments via pioneer factor activity.

Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.