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).

• Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.

  PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups

  Has reproduction · 63

  The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.

  balb cl-sl donovani experimental transgenic genome

• The transcription factor HHEX maintains glucocorticoid levels and protects adrenals from androgen-induced lipid depletion.

  PMID 41519914 · PMC12891536 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  HHEX is the most enriched transcription factor in glucocorticoid-producing zona fasciculata (zF) cells, conserved across mouse, rat, and human adrenal

  sf1-cre-high adrenocortical scrna-seq rnascope immunohistochemistry

• The transcription factor EHF promotes the maturation and immunosuppression of conventional dendritic cells.

  PMID 41730908 · PMC13039115 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  EHF orchestrates an immunosuppressive maturation program in cDC1s and cDC2s downstream of TLR7/8/9 sensing of self-nucleic acids

  ehf facs-sorted dss-induced lethal cd4+

• Microbial genomics: from sequence to function.

  PMID 10998380 · PMC2627950 · Emerging infectious diseases · 2000 · 8 claims · 4 setups

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  Whole-genome shotgun sequencing (sequencing and assembly of random genome fragments), first demonstrated with Haemophilus influenzae in 1995, is now the method of choice for sequencing most genomes, including the human genome.

  yeast bacteria microbial high-throughput microarray ribosomal

• Congenital bovine spinal dysmyelination is caused by a missense mutation in the SPAST gene.

  PMID 19714378 · PMC2854348 · Neurogenetics · 2010 · 8 claims · 5 setups

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  A missense mutation (R560Q) in the SPAST gene's ATPase domain causes bovine spinal dysmyelination

  cattle bovine coli affinity-purified snp reverse cdna

• The chromatin remodeller CHD4 regulates transcription factor binding to both prevent activation of silent enhancers and maintain active regulatory elements.

  PMID 41632506 · PMC12867480 · eLife · 2026 · 8 claims · 8 setups

  Full-text index only

  CHD4 acts via a second mechanism beyond nucleosome sliding: actively restricting the residence time of transcription factors on chromatin

  chd4-maid sall1 western flow calibrated

• Alexander Meissner: learning the reprogramming code.

  PMID 19704017 · PMC2733751 · The Journal of cell biology · 2009 · 8 claims · 6 setups

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  A defined set of factors present in oocytes and embryonic stem (ES) cells can reprogram a somatic cell to pluripotency, as shown by nuclear transfer and ES cell/somatic cell fusion experiments

  blastocysts somatic fused genomic nuclear inducible fusion

• A novel mutation causing mild, atypical fumarylacetoacetase deficiency (Tyrosinemia type I): a case report.

  PMID 20003495 · PMC2802351 · Orphanet journal of rare diseases · 2009 · 8 claims · 7 setups

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  A novel FAH gene mutation, c.103G>A (Ala35Thr), causes a mild, atypical form of tyrosinemia type I

  fibroblasts liver genomic tnt northern western liver

• Single-Cell RNA-Seq Profiling of Transposable Element Expression in Human Peripheral Blood Cells During Viral Infections.

  PMID 41683713 · PMC12898442 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

  Full-text index only

  TE expression is significantly higher in PBMCs from viral infection cohorts (and recovered individuals) compared to healthy controls

  pbmcs pbmc cd8+ single-cell cell-type expression

• Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

  PMID 34297416 · PMC8766893 · Neuropathology and applied neurobiology · 2022 · 8 claims · 5 setups

  Has reproduction · 92

  Systematic review of 306 eligible articles identified 196 distinct proteins constituting the ADRA (AD reactive astrocyte) protein set

  post-mortem adra immunohistochemistry protein-protein pathway

• Ovarian cancer biomarkers: current options and future promise.

  PMID 18926090 · PMC3381792 · Journal of the National Comprehensive Cancer Network : JNCCN · 2008 · 8 claims · 8 setups

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  CA125 lacks the sensitivity and specificity needed for reliable early-stage ovarian cancer detection, since only ~50% of stage I/II cases show elevated levels

  serum plasma preoperative advanced serum plasma elisa

• Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

  PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 8 claims · 8 setups

  Has reproduction · 91

  175 conserved miRNAs (39 families) and 83 novel miRNAs were identified in C. sinensis one bud and two tender leaves using small RNA sequencing combined with genome survey scaffold data

  one sinensis small-molecular-weight leaves small genome mirna

• A cross-species approach to identify transcriptional regulators exemplified for Dnajc22 and Hnf4a.

  PMID 28642491 · PMC5481429 · Scientific reports · 2017 · 8 claims · 8 setups

  Has reproduction · 76

  Hnf4a is a major transcriptional regulator of Dnajc22

  atlas roadmap liver-specific kidney co-expression transcription reanalysis

• Phylogenetic reconstruction of ancestral character states for gene expression and mRNA splicing data.

  PMID 15921519 · PMC1166541 · BMC bioinformatics · 2005 · 6 claims · 4 setups

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  A minimum evolution algorithm (implemented in software 'phyrex') can reconstruct ancestral states of continuous characters like gene expression or splicing levels along a phylogeny

  gene upstream chimpanzee reconstructed minimum sequence ancestral

• Vector algebra in the analysis of genome-wide expression data.

  PMID 11897023 · PMC88809 · Genome biology · 2002 · 8 claims · 6 setups

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  The angle θ between expression (experiment) vectors is the geometric counterpart of the Pearson correlation coefficient r, providing a rigorous measure of similarity between profiles.

  saccharomyces microarray

• PromoterPlot: a graphical display of promoter similarities by pattern recognition.

  PMID 15980503 · PMC1160174 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  PromoterPlot is a web-based tool that displays and processes TransFac transcription factor search results as an interactive SVG page

  under set transcription microarray proteomics

• Genome-wide analysis of antisense transcription with Affymetrix exon array.

  PMID 18211689 · PMC2257944 · BMC genomics · 2008 · 8 claims · 4 setups

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  A modified cDNA synthesis protocol (ATE: Antisense Transcriptome analysis using Exon array), which skips the first-cycle cDNA synthesis and IVT amplification step, labels cDNA in reverse orientation, enabling Exon arrays to detect antisense transcripts

  jurkat exon orientation-specific

• Gata-3 and mammary cell fate.

  PMID 17381824 · PMC1868924 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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  Gata-3 is required for formation of mammary placodes during embryonic development

  mammary gata-3 k14-cre mmtv-cre microarray lacz cre

• Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor.

  PMID 30576656 · PMC6310685 · Molecular cell · 2018 · 8 claims · 7 setups

  Has reproduction

  Rap1 represses divergent noncoding transcription at highly expressed RP gene promoters (e.g., IRT2 at RPL43B, iMLP1 at RPL40B)

  cerevisiae northern western sequencing

• Expression spectrum of TE-driven transcripts in human adult tissues.

  PMID 41593763 · PMC12924553 · Genome biology · 2026 · 8 claims · 8 setups

  Full-text index only

  TE-driven transcripts are broadly expressed across human adult tissues and contribute to both housekeeping and tissue-specific gene regulation

  tissues paired sequences genome bulk differential chip-seq