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).

• Looping specificity of Polycomb response elements requires GAF and a combination of looping factors that could form a code.

  PMID 42206359 · PMC13216745 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  High GAF occupancy is required for chromatin looping and gene regulation at PREs

  drosophila third gaf dac_tss cut&run micro-c hi-c

• 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

• The revolution of the biology of the genome.

  PMID 15040884 · PMC7091781 · Cell research · 2004 · 8 claims · 6 setups

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  Polyploidization and gene duplication are the major mechanisms increasing eukaryotic genome size.

  genome drosophila schizosaccharomyces gene est mount comparative

• Sequential RNA polymerase II activation drives human hematopoiesis.

  PMID 41520338 · PMC13067999 · Cell reports · 2026 · 7 claims · 7 setups

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  sciCUT&Tag2in1 enables simultaneous single-cell combinatorial-indexing profiling of Pol II occupancy (Ser5/Ser2-phospho CTD) together with histone modifications (H3K4me1-2-3 or H3K27me3) in up to 50,000 cells per experiment

  g-csf-mobilized cd34+ 10-donor lineage-depleted scicut&tag2in1 individual souporcell

• Single-cell transcriptomics and chromatin accessibility profiling elucidate the kidney-protective mechanism of mineralocorticoid receptor antagonists.

  PMID 37906287 · PMC10760974 · The Journal of clinical investigation · 2024 · 8 claims · 8 setups

  Has reproduction · 95

  Mineralocorticoid effects are established through open chromatin and target gene expression primarily in principal and connecting tubule cells, and to a lesser extent in distal convoluted tubule cells

  kidney live blood snrna-seq snatac-seq bulk

• Multi-modal dissection of cell-type specific TDP-43 pathology in the motor cortex.

  PMID 41803120 · PMC12982666 · Nature communications · 2026 · 7 claims · 4 setups

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  Mainly excitatory cortical neurons are affected by TDP-43 pathology in the ALS/ALS-FTD motor cortex

  post-mortem publicly als single-nucleus single-nucleus spatial genotyping

• Multiomics and deep learning dissect regulatory syntax in human development.

  PMID 41951735 · PMC13216069 · Nature · 2026 · 8 claims · 8 setups

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  The Human Development Multiomic Atlas (HDMA) is a single-cell atlas of chromatin accessibility and gene expression from 817,740 fetal cells across 12 organs, spanning 203 cell types

  fetal annotated embryo chrombpnet share-seq chromvar activity-by-contact

• ERG phase separation attenuates cellular senescence.

  PMID 41704762 · PMC12907116 · iScience · 2026 · 8 claims · 6 setups

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  Centenarian PBMCs exhibit a distinct, more functionally engaged chromatin accessibility landscape compared to controls and typical elderly individuals

  pbmcs atac-seq rna-seq cibersortx

• The rates of adult neurogenesis and oligodendrogenesis are linked to cell cycle regulation through p27-dependent gene repression of SOX2.

  PMID 36627412 · PMC9832098 · Cellular and molecular life sciences : CMLS · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  p27 restricts residual CDK activity after mitogen withdrawal to antagonize cell cycling, but is not essential for cell cycle exit per se

  sez-derived computational nsc npc atac-seq bulk lisa

• Single-Cell Hi-C Technologies and Computational Data Analysis.

  PMID 39887949 · PMC11884588 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025 · 8 claims · 8 setups

  Has reproduction · 80

  Thirteen scHi-C protocols currently exist: eight that capture chromatin interactions alone and five that combine scHi-C with other omics (methylation, RNA-seq, DNA-seq).

  oocytes mm9 mm10 snhi-c schi-c sci-hi-c

• Multiomics Analysis of Arboviral Capsid Targets in Mosquitoes Reveals a Proviral Function of the Chromatin-Remodeling Brahma Complex.

  PMID 41565204 · PMC12927048 · Molecular & cellular proteomics : MCP · 2026 · 7 claims · 8 setups

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  Capsids from 11 pathogenic arboviruses spanning 3 genera (Orthoflavivirus, Orthobunyavirus, Alphavirus) interact with distinct sets of Aedes aegypti host proteins, forming a multimodal PPI atlas.

  aag2 aag2-c3 ap-ms dsrna co-immunoprecipitation

• Integration of ATAC-seq and RNA-seq reveals temperature-responsive regulatory regions in Plasmodium falciparum asexual stages.

  PMID 41721429 · PMC13032594 · Parasites & vectors · 2026 · 8 claims · 6 setups

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  Low temperature (26 °C) induces 1083 differentially accessible regions (DARs) in the ring stage (1081 gains, 2 losses), enriched primarily in promoter regions ≤3 kb upstream of transcription start sites

  plasmodium rna-seq atac-seq qpcr

• B-lineage commitment is dependent on a reversible epigenetic switch.

  PMID 41266087 · PMC12863259 · Genes & development · 2026 · 8 claims · 8 setups

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  B-lymphoid commitment is mediated by a transcription factor-dose-dependent epigenetic switch that suppresses inherent T-lineage potential in early lymphoid progenitors

  bone expanded pax5 ebf1 combined atac-seq chip-seq

• Stress Responsive bZIP Transcription Factors ATF4 and BACH1 Cooperate With MAF-Family bZIP Protein NRL to Fine-Tune Rod Photoreceptor Gene Expression.

  PMID 42246540 · PMC13249099 · Investigative ophthalmology & visual science · 2026 · 8 claims · 7 setups

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  ATF4 and BACH1 are identified as bZIP protein interactors of NRL

  y2hgold hek293 p28 flow-sorted yeast co-immunoprecipitation immunofluorescence

• Profiling chromatin accessibility responses in human neutrophils with sensitive pathogen detection.

  PMID 34145026 · PMC8321655 · Life science alliance · 2021 · 8 claims · 6 setups

  Has reproduction · 54

  ATAC-seq reveals unique neutrophil chromatin architecture changes in response to different stimuli before transcriptional activation, possibly regulating downstream gene expression.

  peripheral neutrophils blood atac-seq qrt-pcr sytox

• A unified framework for correcting batch effects and integrating multi-omics data.

  PMID 41786846 · PMC13079841 · Scientific reports · 2026 · 7 claims · 6 setups

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  MoDAmix, a four-stage domain adaptation framework (pre-training, single-omics adversarial adaptation, multi-omics adversarial alignment, semi-supervised class alignment), unifies batch correction across multiple omics layers.

  brain aml same single-cell bulk k-means

• 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

• Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.

  PMID 41365655 · PMC12758391 · Genome research · 2026 · 8 claims · 3 setups

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  A factor-agnostic MNase-seq chromatin occupancy profiling (COP) approach can simultaneously capture genome-wide TF and nucleosome occupancy at near-nucleotide resolution from a single assay

  saccharomyces cerevisiae mnase-seq gene

• Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate causal variants in macular degeneration.

  PMID 41528844 · PMC12971065 · Cell reports · 2026 · 8 claims · 8 setups

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  Generated a single-cell gene expression and chromatin accessibility (multiome) atlas of human RPE and choroid from control and AMD eyes

  rpe-choroid rpe arpe-19 scatac-seq joint h3k27ac activity-by-contact

• Putting proteins in one place.

  PMID 12790144 · PMC1316915 · Environmental health perspectives · 2003 · 8 claims · 7 setups

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  Rapamycin inhibits TOR, causing the silencing protein Sir3 to detach from chromatin at stress-response genes, triggering a coordinated multigene stress response that halts cancer cell proliferation

  saccharomyces yeast vascular skin chemical chromatin microarray