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).

• epiGBS2: Improvements and evaluation of highly multiplexed, epiGBS-based reduced representation bisulfite sequencing.

  PMID 35178872 · PMC9311447 · Molecular ecology resources · 2022 · 8 claims · 8 setups

  Has reproduction · 52

  epiGBS2 provides a laboratory protocol and revised bioinformatics pipeline for de novo cytosine methylation and SNP calling in species with or without a reference genome

  arabidopsis great epigbs2 demultiplexed epigbs2 pcr demultiplexing

• Environmental Drivers of Genetic Divergence in Two Corals From the Florida Keys.

  PMID 40589611 · PMC12206660 · Evolutionary applications · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  Temperature was not the most important driver of coral genetic divergence in the Florida Keys; depth and water chemistry were more important

  agaricia agaricites coral sites 2brad population hierarchical

• Specific Marker Gene Analysis for Primary Central Nervous System Lymphoma Based on Methylation Difference and Development of Detection Primers.

  PMID 41097902 · PMC12528802 · Brain and behavior · 2025 · 7 claims · 5 setups

  Has reproduction · 62

  450K microarray analysis identified 26 overlapping differential methylation sites distinguishing PCNSL from CNS and non-CNS groups

  tcga ccle clinical pcnsl 450k rrbs roc

• Improving genomic prediction accuracy for methane emission and feed efficiency in sheep: integrating rumen microbial PCA with host genomic variation using neural network GBLUP (NN-GBLUP).

  PMID 40676527 · PMC12273308 · Genetics, selection, evolution : GSE · 2025 · 6 claims · 8 setups

  Has reproduction · 85

  PCA effectively reduces the dimensionality of high-dimensional RMC data while retaining essential biological information.

  sheep rumen rmc genomic rumen snp

• Aberration in DNA methylation in B-cell lymphomas has a complex origin and increases with disease severity.

  PMID 23326238 · PMC3542081 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 49

  B-cell non-Hodgkin lymphomas display striking intra-tumor (intra-sample) and inter-patient (inter-sample) cytosine methylation heterogeneity that increases progressively with disease aggressiveness (NBC<NGC<FL<GCB<ABC).

  dlbcl normal same lymphoma help errbs massarray

• Commonalities in gene expression and methylation changes across two rat models of acquired epilepsy.

  PMID 41530481 · PMC12877007 · Scientific reports · 2026 · 7 claims · 8 setups

  Full-text index only

  71 genes show concordant (same-direction) expression changes and 94 genes show concordant methylation changes across both the kindling and kainic acid epilepsy models

  hippocampus sequencing reduced-representation rt-pcr

• Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

  PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups

  Has reproduction · 91

  A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)

  yeonsan ogye_1.1 locus tissues whole-genome genome structural

• Compression of structured high-throughput sequencing data.

  PMID 24260313 · PMC3832420 · PloS one · 2013 · 8 claims · 7 setups

  Has reproduction · 43

  Leveraging an explicit data schema (separate field encoding, field modeling, template compression, domain modeling) enables stronger compression of HTS alignment data than general-purpose compression of serialized bytes.

  benchmark ten rna-seq exome genome

• A cellular epigenetic classification system for glioblastoma.

  PMID 41499453 · PMC13128495 · Neuro-oncology · 2026 · 8 claims · 8 setups

  Full-text index only

  ITHresolveGBM, a hierarchical two-step NMF method, deconvolutes bulk GBM DNA methylation profiles into three non-malignant (immune, glial, neuronal) and three malignant components

  gbm healthy pseudo-bulk tcga illumina single-cell deconvolution

• Identification of cis-regulatory elements provides insights into tissue-specific gene regulation in the sheep genome.

  PMID 41839849 · PMC12992920 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  274,682 enhancers and 25,975 promoters were characterized across 24 tissues from an adult female sheep using ChIP-seq, ATAC-seq, CAGE-seq, RRBS, WGBS, and RNA-seq.

  tissues sheep pig chip-seq atac-seq cage-seq