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).

• chromIDEAS reveals epigenetic dynamics via multi-dimensional clustering of chromatin states.

  PMID 41816913 · PMC12980073 · Nucleic acids research · 2026 · 8 claims · 8 setups

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  chromIDEAS groups chromatin states into functionally coherent clusters by jointly analyzing epigenetic composition and genomic distribution

  thp1 cd34+ chromideas chip-seq atac-seq

• Systematic clustering algorithm for chromatin accessibility data and its application to hematopoietic cells.

  PMID 33253153 · PMC7728210 · PLoS computational biology · 2020 · 7 claims · 5 setups

  Has reproduction · 90

  A systematic clustering algorithm for ATAC-seq data can be built by binarizing the genome into open/closed chromatin (1/0) strings and computing Hamming distances between samples for hierarchical clustering.

  monocytes natural hematopoietic leukemia atac-seq hierarchical

• 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

• 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

• Precise modulation of BRG1 levels reveals features of mSWI/SNF dosage sensitivity.

  PMID 40846763 · PMC12425804 · Nature genetics · 2025 · 8 claims · 8 setups

  Has reproduction · 75

  BRG1 binding to chromatin exhibits a linear, dose-dependent response to BRG1 protein levels, independent of TF or histone-modification co-occupancy

  brg1-fkbp12-f36v brg1-knock-in mes snf2h-fkbp12-f36v western cut&run atac-seq

• iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm.

  PMID 41499218 · PMC12777978 · Briefings in bioinformatics · 2026 · 7 claims · 8 setups

  Has reproduction · 53

  iceDP uses the Density Peak clustering algorithm plus a distribution test and fold change filter to identify NHCCs from Hi-C interaction matrices while removing false positives

  olfactory embryonic tc-797 islet hi-c h3k27ac micro-c

• Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus.

  PMID 35710138 · PMC9296009 · Genes & development · 2022 · 8 claims · 7 setups

  Has reproduction · 81

  Sox2 transcriptional activation is traced almost entirely to two key transcription factor-bound regions (SRR107 and SRR111) within the SCR

  escs esc sequence compiled allele-specific chip-seq motif

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

  PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 80

  BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

  lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr

• Engineered apoptotic nucleases for chromatin research.

  PMID 17626049 · PMC1935020 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  Inserting TEVP cleavage sites immediately downstream of the two caspase-3 sites in DFF45 (I1I2 mutant) makes DFF40 nuclease activity exclusively dependent on TEVP cleavage (DFF-T)

  recombinant cerevisiae coli western plasmid serial

• CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data.

  PMID 41734268 · PMC12987762 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 5 setups

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  CIRCE re-implements the Cicero co-accessibility algorithm in Python, producing near-identical results while running much faster and using far less memory

  bmmc pbmc foetal cis-regulatory enhancer-promoter scalability

• Phosphorylation of SF3B1 by CDK11 orchestrates spliceosome activation via SNIP1-dependent RES complex recruitment.

  PMID 41904131 · PMC13194972 · Nature communications · 2026 · 8 claims · 7 setups

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  CDK11 inhibitor OTS964 traps the spliceosome in a previously uncharacterized intermediate (B_OTS964) that has the NTR complex integrated but the NTC complex not yet associated.

  hct116 gst-sf3b1 ip-mass subcellular iclip-seq

• SOX2 phosphorylation during mitosis limits genomic damage.

  PMID 41213799 · PMC12863253 · Genes & development · 2026 · 8 claims · 8 setups

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  SOX2 (but not SOX9) remains dynamically bound to mitotic chromatin throughout all mitotic stages in neural stem cells

  sox2-halo nscs flag-wt-sox2 live-cell immunocytochemistry frap

• Short activation domains control chromatin association of transcription factors.

  PMID 41511382 · PMC12788797 · eLife · 2026 · 8 claims · 8 setups

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  Short activation domains (39-60 aa, only 5-7% of the synthetic TF) dominate the chromatin-bound fraction of a synthetic transcription factor.

  u2os synthetic single-molecule flow fluorescence

• 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

• Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations.

  PMID 41530870 · PMC12888741 · Genome medicine · 2026 · 8 claims · 8 setups

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  MAAS integrates chromatin accessibility, CNVs, and SNVs from scATAC-seq data to identify functional tumor cell subpopulations

  tumor pediatric b-cell glioblastoma scatac-seq bulk gene

• YAP/TAZ-VGLL3 governs adipocyte fate via epigenetic reprogramming of PPARγ and its target enhancers.

  PMID 41533786 · PMC12802833 · Science advances · 2026 · 8 claims · 8 setups

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  TAZ represses PPARγ-bound target enhancers, evidenced by markedly reduced H3K27ac occupancy, leading to transcriptional repression of adipogenic genes including Pparg2

  c3h10t1 inguinal iwat adipose atac-seq rna-seq immunoblot

• PAF15-PCNA exhaustion governs the strand-specific control of DNA replication.

  PMID 41606318 · PMC12979207 · Nature · 2026 · 8 claims · 8 setups

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  Excessive origin firing saturates chromatin-bound PCNA, restricting further PCNA loading and lagging-strand synthesis when checkpoint control is lost.

  u2os embryonic qibc confocal western

• An integrated multi-omics and network analysis of neutrophil differentiation from initial- to late-stage.

  PMID 41618446 · PMC12934089 · Genome biology · 2026 · 8 claims · 6 setups

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  3D genome structure and chromatin accessibility change dramatically as early as 4 h after all-trans-retinoic acid (ATRA) treatment, preceding major transcriptional changes.

  hl-60 ocean-c atac-seq rna-seq

• Single-nucleus multiple-organ chromatin accessibility landscape in the adult rat.

  PMID 41632074 · PMC12954174 · GigaScience · 2026 · 8 claims · 5 setups

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  Generated a multi-organ snATAC-seq atlas of 9 adult rat organs comprising 25 libraries and over 110,000 cells

  organs publicly snatac-seq group-level snatac-seq scrna-seq gene