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).

• Identification of phenotype-specific networks from paired gene expression-cell shape imaging data.

  PMID 35197309 · PMC8997347 · Genome research · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  WGCNA-derived gene coexpression modules from breast cancer cell line RNA-seq data correlate significantly with specific cell-shape features

  breast same gene identified bulk high-content regulon

• CASK loss of function differentially regulates neuronal maturation and synaptic function in human induced cortical excitatory neurons.

  PMID 36262316 · PMC9574418 · iScience · 2022 · 7 claims · 8 setups

  Has reproduction · 62

  Immature (day 7) CASK KO induced neurons show increased dendritic complexity/neurite overgrowth and upregulated gene networks for cell adhesion, neurite outgrowth, and cytoskeletal organization.

  day mature bulk qrt-pcr gene

• mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations.

  PMID 31799603 · PMC6954439 · Nucleic acids research · 2020 · 5 claims · 5 setups

  Has reproduction · 89

  mitoXplorer integrates transcriptome, proteome, and mutation data with a manually curated mitochondrial interactome of ~1200 genes grouped into 38 mitochondrial processes across four model species.

  rpe-1 trisomic rpe yeast bulk proteomics mitotracker

• Inter- and Intraspecific Venom Variation in the Reclusive Rear-Fanged Black-Striped Snakes (Coniophanes).

  PMID 41745774 · PMC12945099 · Toxins · 2026 · 8 claims · 4 setups

  Has reproduction

  Coniophanes DVG transcriptomes contain 18 toxin families, with toxins comprising 38.8% to 66% of total transcriptome expression depending on species

  duvernoy's fissidens venom imperialis rna-seq dicect quantitative

• Transcriptomic Study on the Lungs of Broilers with Ascites Syndrome.

  PMID 36611783 · PMC9817706 · Animals : an open access journal from MDPI · 2023 · 8 claims · 6 setups

  Has reproduction · 71

  1442 genes were differentially expressed in AS broiler lung vs normal lung (614 up-regulated, 828 down-regulated)

  lung left blood heart sequencing functional quantitative

• Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

  PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

  erwinia intergenic candidate wounded small northern race

• Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes.

  PMID 34066626 · PMC8148590 · Toxins · 2021 · 8 claims · 5 setups

  Has reproduction · 97

  The T. nigriceps Duvernoy's gland transcriptome is dominated by three toxin families: three-finger toxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)

  duvernoy's nigriceps rna-seq differential extraction

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read

• Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity.

  PMID 36928603 · PMC10101853 · Nature genetics · 2023 · 8 claims · 6 setups

  Has reproduction · 80

  The WHO histopathological classification of MPM accounts for only up to ~10% of interpatient molecular differences

  mpm mesomics whole-genome bulk methylation

• Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice.

  PMID 27655631 · PMC5175363 · Nucleic acids research · 2016 · 8 claims · 8 setups

  Has reproduction · 10

  Embryonic ATZ exposure affects meiosis, spermiogenesis and reduces spermatozoa number in F3 generation male mice

  testis dissociated epididymis chip-seq strand-specific h&e

• GenomeRNAi: a database for cell-based RNAi phenotypes. 2009 update.

  PMID 19910367 · PMC2808900 · Nucleic acids research · 2010 · 7 claims · 7 setups

  Full-text index only

  GenomeRNAi is a database integrating RNAi phenotypes, reagents, and gene annotations from cell-based screens in Drosophila and human cells

  drosophila hela genome-scale image-based rna-seq

• Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.

  PMID 37652021 · PMC10588993 · Immunity · 2023 · 7 claims · 8 setups

  Has reproduction · 83

  Vascular macrophages form a spatiotemporal niche in direct contact with mural cells across microvascular and macrovascular beds

  cx3cr1-mφ rfp-rep coronary peritoneal intravital confocal single-cell

• Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-Grade Soluble Human ACE2.

  PMID 32333836 · PMC7181998 · Cell · 2020 · 8 claims · 7 setups

  Has reproduction · 87

  Clinical-grade hrsACE2 significantly inhibits SARS-CoV-2 infection of Vero-E6 cells in a dose-dependent manner

  nasopharyngeal vero-e6 ipsc-derived embryonic viral qrt-pcr organoid

• Cancer-cell-secreted miR-204-5p induces leptin signalling pathway in white adipose tissue to promote cancer-associated cachexia.

  PMID 37620316 · PMC10449837 · Nature communications · 2023 · 8 claims · 8 setups

  Has reproduction · 85

  Breast cancer cell-secreted exosomal miR-204-5p induces HIF1A in white adipose tissue by targeting the VHL gene.

  balb nsg ewat iwat orthotopic indirect sev

• An engineered tumor organoid model reveals cellular identity and signaling trajectories underlying SFPQ-TFE3 driven translocation RCC.

  PMID 40463960 · PMC12131257 · iScience · 2025 · 8 claims · 7 setups

  Has reproduction · 88

  SFPQ-TFE3 expression is sufficient to transform normal kidney epithelial tubuloids into tRCC

  kidney tubuloids immunodeficient tub rt-qpcr western histology

• Caecilians maintain a functional long-wavelength-sensitive cone opsin gene despite signatures of relaxed selection and more than 200 million years of fossoriality.

  PMID 40990923 · PMC12687342 · Evolution; international journal of organic evolution · 2025 · 8 claims · 5 setups

  Has reproduction · 64

  The LWS opsin gene was identified in 13 species of caecilians spanning 8 of 10 recognized families

  caecilian caecilia archival lws pcr eye histology

• Cell type differences in human cytomegalovirus transcription and epigenetic regulation with insights into major immediate-early enhancer-promoter control.

  PMID 40758707 · PMC12333995 · PLoS pathogens · 2025 · 8 claims · 7 setups

  Has reproduction · 90

  Six viral promoters (UL5, UL72, EP3, UL57-AS, US16-AS, US30-S) are ≥50-fold more active in D-NT2 than in HFF at 96 h post-infection and are classified as viral long promoters.

  d-nt2 hcmv-infected hcmv pro-seq dff-chip promoter

• Loss of mutual protection between human osteoclasts and chondrocytes in damaged joints initiates osteoclast-mediated cartilage degradation by MMPs.

  PMID 34811438 · PMC8608887 · Scientific reports · 2021 · 6 claims · 8 setups

  Has reproduction · 50

  Human osteoclasts can differentiate on acellular cartilage, express osteoclast markers, and degrade cartilage matrix in a contact-dependent manner without forming F-actin rings or resorption pits.

  knee cd14+ osteoclasts conditioned histology osteoclast gag

• A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms.

  PMID 35019679 · PMC8754136 · Microbiology spectrum · 2022 · 8 claims · 9 setups

  Has reproduction · 36

  Microbulbifer sp. YX04 shows high algicidal activity against P. globosa, peaking at 93.2% in the declining growth phase

  phaeocystis strain yx04 globosa algicidal 16s scanning

• Single-nucleus mRNA-sequencing reveals dynamics of lipogenic and thermogenic adipocyte populations in murine brown adipose tissue in response to cold exposure.

  PMID 40945691 · PMC12506565 · Molecular metabolism · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  snRNA-seq of murine BAT identifies seven distinct brown adipocyte subtypes with distinct metabolic profiles, part of a 21-cell-type atlas.

  interscapular ibat bat single-nucleus qpcr western