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).

• Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer.

  PMID 39018396 · PMC466953 · Science advances · 2024 · 8 claims · 8 setups

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  Primate-specific ERVs are a rich source of enhancers displaying cancer-specific activity across multiple tumor types

  cancer hct116 tcga colorectal atac-seq chip-seq bulk

• H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity.

  PMID 40764058 · PMC12487818 · Genome research · 2025 · 8 claims · 8 setups

  Has reproduction · 55

  H3K9 and H3K27 methylation regulate CTCF binding at distinct genomic regions, and their simultaneous loss induces drastic changes in CTCF binding

  imefs early ctcf h3k9me3 h3k9me2

• LBR and LAP2 mediate heterochromatin tethering to the nuclear periphery to preserve genome homeostasis.

  PMID 41735607 · PMC12992122 · Nature cell biology · 2026 · 7 claims · 8 setups

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  Combined downregulation of 12 abundant, ubiquitously expressed nuclear envelope proteins (si-11) causes global detachment of constitutive heterochromatin from the nuclear envelope and its relocation to the nuclear interior in multiple mammalian cell types

  hct116 rpe-1 nih immunofluorescence immunoblot sequencing

• TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells.

  PMID 23233547 · PMC3589534 · Genome research · 2013 · 8 claims · 8 setups

  Has reproduction · 78

  TRIM28 repression of ERVs protects cellular gene expression in early embryos from perturbation by cis-acting activators contained within these retroelements.

  embryonic trim28 mrna-seq trim28 h3k9me3

• Chromatin state dynamics during the Plasmodium falciparum intraerythrocytic development cycle.

  PMID 41501628 · PMC12870380 · BMC genomics · 2026 · 8 claims · 6 setups

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  ChromHMM integration of 7 histone marks/variants, ATAC-seq accessibility, and HP1 ChIP-seq across ring, trophozoite, and schizont stages defines 11 chromatin states as optimal for the P. falciparum genome at 200 bp resolution

  plasmodium chip-seq atac-seq chromhmm

• Predicting the effect of CRISPR-Cas9-based epigenome editing.

  PMID 41524535 · PMC12795505 · eLife · 2026 · 8 claims · 6 setups

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  Machine learning (CNN and ridge regression) models trained on histone PTM ChIP-seq and RNA-seq data from 13 ENCODE cell types accurately predict endogenous gene expression, with transcriptome-wide correlations of ~0.70-0.79 for most cell types

  hek293t k562 computational chip-seq rna-seq mnase-seq

• Targeting the epigenome and the integrated stress response to normalize colorectal cancer subclonal plasticity and progression.

  PMID 41963303 · PMC13181133 · Cell death & disease · 2026 · 8 claims · 8 setups

  Has reproduction · 68

  The integrated stress response (ISR) induces CRC cell plasticity, subclonal diversity, and tumor progression in stress-surviving cells

  ht29-derived ht29 nod rna-seq faire-qpcr chip-seq

• Progressive transformation of the HIV-1 reservoir cell profile over two decades of antiviral therapy.

  PMID 36596305 · PMC9839361 · Cell host & microbe · 2023 · 8 claims · 8 setups

  Has reproduction · 80

  After ~2 decades of ART, intact HIV-1 proviruses are predominantly integrated in heterochromatin, especially centromeric/peri-centromeric satellite and micro-satellite DNA

  pbmc single cd4 pbmc-derived flip-seq mip-seq prip-seq

• Gene Regulatory Interactions at Lamina-Associated Domains.

  PMID 36833261 · PMC9957430 · Genes · 2023 · 8 claims · 8 setups

  Has reproduction · 31

  Active genes in constitutive LADs (cLADs) reside in euchromatic regions with low LMNB1 and LMNA/C enrichment, i.e., are locally detached from the nuclear lamina

  adipose ascs mesenchymal chip-seq rna-seq atac-seq

• Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell-like cells.

  PMID 41371963 · PMC12758400 · Genome research · 2026 · 8 claims · 6 setups

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  GSC-like and CySC-like cells isolated from upd tumor testes are transcriptionally comparable to wild-type GSC/early-spermatogonia and CySC clusters, respectively

  upd gsc-like wild-type scrna-seq differential gene

• Multimodal epigenetic and enhancer network remodeling shape the transcriptional landscape of human beige adipocytes.

  PMID 41501500 · PMC12881478 · Communications biology · 2026 · 8 claims · 8 setups

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  The white adipocyte transcriptional program is tightly linked to promoter-level modulation of H3K27ac and chromatin accessibility.

  adipose asc-derived white ascs bulk atac-seq chip-seq

• Transient histone deacetylase inhibition induces cellular memory of gene expression and 3D genome folding.

  PMID 41639407 · PMC12900649 · Nature genetics · 2026 · 8 claims · 8 setups

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  Acute HDAC inhibition (TSA pulse) induces genome-wide H3K27 hyperacetylation and reorganizes the histone modification landscape, shifting more of the genome to an active state.

  e14 simulated mescs calibrated atac-seq bulk

• Feed-forward loops by NR5A2 ensure robust gene activation during pre-implantation development.

  PMID 41355514 · PMC12848575 · Development (Cambridge, England) · 2026 · 8 claims · 8 setups

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  NR5A2 chromatin binding is dynamic, changing genome-wide from the 2-cell to the morula stage, with peak numbers and target regions (e.g. SINE B1/Alu) shifting over developmental time

  2-cell embryonic 8-cell zygotes cut&tag chip-seq h3k27ac

• EIF5A Couples Translational Control With Transcriptional Reprogramming Through Chromocenter Reorganization During Spermiogenesis.

  PMID 41486816 · PMC12903998 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  eIF5A is highly expressed in spermatogenic cells, particularly spermatogonia and round spermatids, across human and mouse testis

  spermatogenic round testis testicular proteomics proteomic atac-seq

• Chamber-specific chromatin architecture guides functional interpretation of disease-associated Cis-regulatory elements in human cardiomyocytes.

  PMID 41526351 · PMC12796357 · Nature communications · 2026 · 8 claims · 8 setups

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  Cardiomyocyte (CM)-specific Hi-C data detect substantially more and stronger promoter-interacting domains (PIDs) for CM marker genes than bulk cardiac tissue Hi-C data

  non-failing cardiac nf-lv-cm biological hi-c fluorescence-activated chip-seq