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).

• Chromatin spatial analysis by METALoci unveils sex-determining 3D regulatory hubs.

  PMID 41735611 · PMC13095655 · Nature structural & molecular biology · 2026 · 6 claims · 7 setups

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  TADs and large-scale chromatin structures remain largely unchanged during sex determination, suggesting a preformed configuration

  facs-sorted same integrated fgf9 hi-c chip-seq metaloci

• Comparative analysis of eccDNA and circRNA tools shows increased accuracy of tool combination.

  PMID 41738836 · PMC13154841 · GigaScience · 2026 · 8 claims · 6 setups

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  Detection accuracy of eccDNA/circRNA tools is highly influenced by sequencing depth, alignment algorithm, and experimental enrichment protocol

  genome transcriptome muscle dnase1l3 simulated circle-seq atac-seq

• Multi-modal skin atlas identifies a multicellular immune-stromal community associated with disrupted cornification and specific T cell expansion in atopic dermatitis.

  PMID 41741455 · PMC13057205 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated a multi-modal single-cell atlas of 280,518 cells from 27 samples/17 adults (healthy, AD non-lesional/lesional, scleroderma), integrated with 430,186 cells from four prior studies into a 710,704-cell human skin atlas with 86 annotated granular cell subsets.

  skin healthy keratinocytes re-annotated droplet-based scrna-seq bulk

• ASCL1 promotes nuclear shrinkage in transdifferentiation by suppressing NUP37.

  PMID 41759523 · PMC12985393 · Stem cell reports · 2026 · 7 claims · 8 setups

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  ASCL1-mediated transdifferentiation (AMp) of human fibroblasts to induced neurons causes marked nuclear shrinkage while cell size remains unchanged

  mrc5 ag22056 ipsc-derived embryonic immunofluorescence single-cell rt-qpcr

• Chromosome-level genome assembly of the deep-sea solemyid bivalve Acharax haimaensis.

  PMID 41760692 · PMC13066446 · Scientific data · 2026 · 7 claims · 9 setups

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  A. haimaensis genome was assembled to chromosome level (4.27 Gb, scaffold N50 195.52 Mb, anchored to 22 chromosomes) using PacBio HiFi, Illumina, and Hi-C sequencing

  acharax haimaensis illumina pacbio hi-c

• The chromosome-scale genome assembly, annotation of Bischofia polycarpa (H. Lév.) Airy Shaw, Phyllanthaceae.

  PMID 41765919 · PMC13066037 · Scientific data · 2026 · 8 claims · 8 setups

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  B. polycarpa genome was assembled de novo using PacBio HiFi reads and Hi-C data to a size of 585.68 Mb with contig N50 of 12.62 Mb

  polycarpa illumina pacbio hi-c

• IFN signaling is associated with radiotherapy response in malignant peripheral nerve sheath tumors.

  PMID 41766654 · PMC12948414 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

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  MPNST cells are more radioresistant than benign plexiform neurofibroma (pNF) cells in vitro

  mpnst st88-14 nf9511.b jh-2-002 flow fractionated bulk

• A chromosome-level reference genome of an endangered plant Craigia yunnanensis.

  PMID 41771874 · PMC13065974 · Scientific data · 2026 · 8 claims · 8 setups

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  A chromosome-level genome assembly of C. yunnanensis was generated using PacBio HiFi sequencing and Hi-C scaffolding

  yunnanensis pacbio hi-c illumina

• Acetylation of H3K115 is associated with fragile nucleosomes at CpG island promoters and active regulatory sites.

  PMID 41778583 · PMC12959880 · eLife · 2026 · 8 claims · 8 setups

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  H3K115ac is enriched at the TSS of active CpG island (CGI) promoters, far more than non-CGI promoters

  embryonic mescs synthetic mesc chip-seq atac-seq dot

• A high-quality chromosome-level genome assembly of a feather star Glyptometra sp. from a deep seamount.

  PMID 41786724 · PMC13079724 · Scientific data · 2026 · 8 claims · 8 setups

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  This is the first chromosome-level genome assembly of a feather star (Glyptometra sp. CNS01629) from a deep seamount

  genomic arm middle assembled k-mer whole-genome pacbio

• APC coordinates GSK3 phosphorylation of SETD8 to suppress colorectal cancer.

  PMID 41790555 · PMC13123626 · Cell reports · 2026 · 8 claims · 8 setups

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  SETD8 Thr138 (mouse)/Thr140 (human) is a bona fide GSK3 phosphorylation site whose phosphorylation is dependent on APC in vivo and in vitro

  intestinal recombinant apk setd8 phosphoproteomic radioactive western

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

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

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  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 Improved Chromosome-Level Genome Assembly and Comprehensive Annotation of the Model Ascidian Ciona savignyi.

  PMID 41792167 · PMC13087180 · Scientific data · 2026 · 8 claims · 8 setups

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  An improved chromosome-level genome assembly of C. savignyi was generated using Illumina short reads, ONT long reads, and Hi-C data.

  savignyi illumina oxford hi-c

• A new chromosome-level genome assembly for western painted turtle Chrysemys picta bellii, a model for extreme physiological adaptations.

  PMID 41792601 · PMC13077969 · BMC genomics · 2026 · 6 claims · 8 setups

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  A new haplotype-resolved, chromosome-level reference genome assembly (SLU_Cpb5.0) was generated for C. picta bellii using combined PacBio HiFi, 10x Genomics Chromium, Hi-C, and Bionano optical mapping data from a single individual.

  genomic ultra-high tissues heart 10x pacbio hi-c

• Ectopic CD11c Drives SMAD3-Mediated Aberrant Antigen Presentation and Epithelial-Mesenchymal Transition in Esophageal Squamous Cell Carcinoma.

  PMID 41799568 · PMC12963642 · Cancer communications (London, England) · 2026 · 8 claims · 13 setups

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  An ESCC epithelial cell subcluster with ectopic CD11c (ITGAX) expression, found in both mice and humans, exhibits concurrent impaired antigen presentation and EMT phenotypes

  4-nqo-induced escc esophageal lung multiplex flow whole-genome

• Evolutionary genomic basis of mimicry diversity of Epicopeiidae moths.

  PMID 41802886 · PMC13014123 · Molecular biology and evolution · 2026 · 8 claims · 8 setups

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  Genomic structural variations and gene family expansions contributed little to morphological (mimicry) evolution in Epicopeiidae

  epicopeiidae mencia ancestral chromosome-level whole-genome hi-c comparative

• Human neuronal differentiation under Aβ exposure: a single-cell transcriptomic and epigenomic dataset.

  PMID 41807428 · PMC13103403 · Scientific data · 2026 · 8 claims · 4 setups

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  A paired scRNA-seq and scATAC-seq dataset was generated from NPCs differentiated over Days 0, 7, 13, and 20 under baseline and Aβ 1-42 exposure conditions

  hipsc-derived hippocampal scrna-seq scatac-seq flow

• SMARCA4/2 loss reduces BCL-xL expression and confers a druggable MCL1 dependency in cancer.

  PMID 41807550 · PMC13249849 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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  MCL1 inhibition is synthetic lethal with SMARCA4/2 loss in SCCOHT and NSCLC cells

  nsclc lung smarca4 bin-67 genome-wide drug colony

• HIF3A-mediated aberrant activation of TXNIP promotes Alzheimer's disease progression.

  PMID 41807716 · PMC13096512 · Scientific reports · 2026 · 8 claims · 8 setups

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  OS activity is significantly elevated in AD and shows pronounced heterogeneity across brain cell types

  entorhinal brain middle c57bl scrna-seq bulk animal

• Protease-mediated PRC1 dissociation promotes H2AK119ub remodeling during stress responses.

  PMID 41813846 · PMC13083880 · The EMBO journal · 2026 · 8 claims · 8 setups

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  CAPN3 promotes rapid dissociation of PRC1 complexes from chromatin in response to stress

  hepatocytes liver doxycycline-inducible capn3 chip-seq cut&tag western