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).

• 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 · 7 setups

  Has reproduction · 95

  Mineralocorticoid (DOCA) 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 (DCT2) cells.

  kidney doca-salt serum heart single-nucleus bulk physiology

• 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 chromatin binding decreases linearly and proportionally with BRG1 protein dosage, independent of TFs or histone modifications (92.2% of binding peaks follow a linear model).

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

• 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

• Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets.

  PMID 35672799 · PMC9175345 · Genome biology · 2022 · 8 claims · 6 setups

  Has reproduction

  CD4 T cells and B cells independently mediate MS GWAS genetic signals through their open chromatin regions, beyond shared regulatory landscapes.

  flow-sorted cd4 gwas bulk ldsc

• 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 is a tool that uses the Density Peaks clustering algorithm plus a distribution test and fold-change filter to identify non-homologous inter-chromatin contacts (NHCCs) from Hi-C data

  olfactory mosn hesc type in-situ h3k27ac micro-c

• Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

  PMID 16822311 · PMC1553470 · Retrovirology · 2006 · 8 claims · 6 setups

  Full-text index only

  CTLL cells stably expressing wild-type Tax (CTLL/WT) show higher aneuploidy than a CREB-transactivation-deficient Tax clone (CTLL/703)

  ctll gene promoter metaphase microarray bioinformatics

• Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis.

  PMID 32155147 · PMC7138332 · PLoS biology · 2020 · 8 claims · 8 setups

  Has reproduction · 90

  Replacing the mitotic kleisin Scc1 with the meiotic kleisin Rec8 impairs sister chromosome cohesion, advances genome replication timing, and reduces reproductive fitness by 45%.

  cerevisiae parallel evolved rec8-expressing competitive experimental whole-genome

• Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation.

  PMID 37602956 · PMC10548174 · The EMBO journal · 2023 · 6 claims · 5 setups

  Has reproduction · 91

  E14.5 DFPs have a repressed transcriptional profile marked by high H3K27me3 and inaccessible chromatin at lineage-specific genes

  skin dermal single-cell chamber chip-seq

• Transcription dynamics.

  PMID 19782025 · PMC6326382 · Molecular cell · 2009 · 8 claims · 8 setups

  Full-text index only

  Transcription factors locate their sparse specific binding sites via a 3D scanning mechanism combining rapid nuclear diffusion with frequent, very transient (seconds-scale) nonspecific chromatin interactions.

  living linker lac glucocorticoid frap single-molecule nucleosome

• Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

  PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

  Full-text index only

  A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

  genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin

• Transgenerational inheritance of an acquired small RNA-based antiviral response in C. elegans.

  PMID 22119442 · PMC3250924 · Cell · 2011 · 8 claims · 8 setups

  Has reproduction · 68

  viRNA-mediated silencing of the FR1gfp Flock House virus is transmitted to RNAi-deficient (rde-1 or rde-4 homozygous) progeny and persists for many ensuing generations, i.e. an acquired antiviral trait is inherited.

  transgenic elegans four gfp genetic template-independence

• From linear genome sequence to three-dimensional organization of the cell nucleus.

  PMID 12620101 · PMC153456 · Genome biology · 2003 · 8 claims · 8 setups

  Full-text index only

  Chromosome conformation capture (3C) can quantify in vivo physical interaction frequencies between genomic loci by crosslinking, digestion, and intramolecular ligation followed by PCR

  saccharomyces mitotic nucleoplasm hela chromosome translocation stretched

• Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in DSRCTs.

  PMID 38781959 · PMC11228554 · Cell reports. Medicine · 2024 · 8 claims · 8 setups

  Has reproduction · 76

  DSRCT tumor cells cluster into consistent subpopulations with partially overlapping lineage- and metabolism-related transcriptional programs across patients and samples

  fresh matched archived dsrct scrna-seq single-nucleus bulk

• A statistical framework for consolidating "sibling" probe sets for Affymetrix GeneChip data.

  PMID 18435860 · PMC2397416 · BMC genomics · 2008 · 7 claims · 4 setups

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  A two-way ANOVA model with a treatment x probe-set interaction term can automatically determine whether sibling probe sets for a gene behave similarly (non-significant interaction, consolidate) or differently (significant interaction, treat as independent)

  retina thyroid spermatogonial differentially two-way paired anova-based

• The Cohesin Ring Uses Its Hinge to Organize DNA Using Non-topological as well as Topological Mechanisms.

  PMID 29754816 · PMC6371919 · Cell · 2018 · 8 claims · 8 setups

  Has reproduction · 80

  Sister chromatid cohesion is mediated by co-entrapment of both sister DNAs inside a single hetero-trimeric cohesin ring, perfectly correlating CD formation with cohesion

  cerevisiae smc1 minichromosome agarose western

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

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

  Has reproduction · 81

  Erg is essential for early B-cell development, with its loss causing developmental arrest at the pre–proB (Hardy fraction A-to-B) stage

  erg pre–prob b220+ prob lacz bulk flow

• Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation.

  PMID 18786246 · PMC2556353 · BMC genomics · 2008 · 6 claims · 6 setups

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  PLP, Sox10, SOD3, and Ptn are direct regulatory targets of Sox10, confirmed by chromatin immunoprecipitation binding to conserved cis-elements

  rt4d6 gst-sox10 microarray comparative real

• Differentiating Drosophila female germ cells initiate Polycomb silencing by regulating PRC2-interacting proteins.

  PMID 32773039 · PMC7438113 · eLife · 2020 · 7 claims · 3 setups

  Has reproduction · 87

  Drosophila female germline stem cells lack canonical Polycomb silencing and have a non-canonical H3K27me3 distribution resembling early embryos.

  drosophila facs-purified hsgfp germline-specific chipseq

• Toxoplasma: the next 100years.

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

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

  gondii mammalian cdna affymetrix sage