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).

• Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

  PMID 18776137 · PMC2584123 · Diabetes · 2008 · 6 claims · 7 setups

  Full-text index only

  Lymphocytes (but not monocytes) from type 1 diabetic patients show a distinct subset of genes with significantly increased H3K9me2 compared with healthy controls.

  blood pooled gene chip-chip conventional quantitative

• 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

  Full-text index only

  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

• Toxoplasma: the next 100years.

  PMID 18672085 · PMC2596634 · Microbes and infection · 2008 · 8 claims · 8 setups

  Full-text index only

  Micronemes, rhoptries, and dense granules are specialized secretory organelles that mediate T. gondii host cell invasion and remodeling

  gondii mammalian cdna affymetrix sage

• Sequencing the regulatory genome.

  PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

  Full-text index only

  Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

  interphase nine beta-globin drosophila nuclear digital chip

• TFAP2 paralogs facilitate chromatin access for MITF at pigmentation and cell proliferation genes.

  PMID 35580127 · PMC9159589 · PLoS genetics · 2022 · 8 claims · 8 setups

  Has reproduction · 95

  Pigmentation genes are only expressed in mitfa-expressing zebrafish melanocyte-lineage cells that also express tfap2 paralogs

  gfp+ sk-mel-28 tfap2a single-cell crispr atac-seq

• Architectural and evolutionary features of TE-derived TSSs shape tissue-specific promoter activity in the human genome.

  PMID 41620470 · PMC12963367 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  A three-step RAMPAGE-based pipeline can systematically identify TE-derived transcription start sites (TSSs) genome-wide, distinguishing them from autonomous TE transcription and background noise.

  biosamples same k562 genomic rampage rna-seq h3k4me3

• HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

  PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 66

  HTSstation is a web application suite coupling simple web forms to modular analysis pipelines for ChIP-seq, RNA-seq, 4C-seq and re-sequencing HTS applications, accessible at http://htsstation.epfl.ch.

  embryonic mycobacterium forebrain rna-seq re-sequencing 4c-seq

• ATACdb 2.0: a comprehensive chromatin accessibility database of human and mouse.

  PMID 41243977 · PMC12807738 · Nucleic acids research · 2026 · 8 claims · 8 setups

  Full-text index only

  ATACdb 2.0 expands data scale, adding mouse chromatin accessibility data and substantially expanding human samples, plus pseudo-bulk ATAC-seq profiles built from scATAC-seq data to increase cell type diversity

  geo scatac-ref bulk scatac-seq h3k27ac

• Epigenetic profiling of hematopoietic stem cells from male mice identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response.

  PMID 41720793 · PMC13035812 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Lifelong CR reduces white blood cell production and shifts hematopoiesis toward myeloid and thrombo-erythroid lineages while suppressing lymphoid output

  peripheral sorted young aged complete flow bulk

• Benchmarking component choices for unpaired single cell RNA and epigenomic integration.

  PMID 41987329 · PMC13192178 · Genome biology · 2026 · 7 claims · 8 setups

  Full-text index only

  Gene activity scores (GAS) show limited correlation with actual gene expression but effectively preserve cellular neighborhood structure and support clustering.

  e18 pbmc brain kidney scrna-seq share-seq gas

• Sequencing DNA methylation and hydroxymethylation at co-occurring chromatin features.

  PMID 41667493 · PMC13002996 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  6-base-CUT&Tag (6B-C&T) simultaneously maps G, A, T, C, 5mC, and 5hmC at antibody-targeted chromatin features on the same DNA fragment

  e14tg2a synthetic mescs mesc 6-base-cut&tag standard exonuclease

• Transcription and potential functions of a novel XIST isoform in male peripheral glia.

  PMID 41386982 · PMC12863056 · Genome research · 2026 · 8 claims · 8 setups

  Full-text index only

  XIST is robustly expressed in male peripheral glia, particularly nonmyelinating Schwann cells, across human heart and skeletal muscle tissue.

  heart skeletal atlas peripheral scrna-seq aggregated scatac-seq

• Mechanisms of gene regulation by SRCAP and H2A.Z.

  PMID 41792122 · PMC13087030 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Acute SRCAP degradation causes rapid, genome-wide replacement of H2A.Z by canonical H2A, with turnover fastest at active promoters/enhancers and slower at bivalent loci

  syat cut&run live h2a.z

• An Erg-driven transcriptional program controls B cell lymphopoiesis.

  PMID 32541654 · PMC7296042 · Nature communications · 2020 · 7 claims · 8 setups

  Has reproduction · 81

  Erg is essential for early B lymphoid differentiation

  erg b220+ prob wild-type lacz rna-seq flow

• CLAMP: predicting specific protein-mediated chromatin loops in diverse species with a chromatin accessibility language model.

  PMID 41555433 · PMC12903630 · Genome biology · 2026 · 8 claims · 8 setups

  Full-text index only

  CLAMP, a chromatin-accessibility language model, predicts protein-mediated chromatin loops across 10 species, 18 proteins, and 24 cell types with superior performance versus existing methods.

  species gm12878 types chromatin cross-protein cross-cell-type