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).

• Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics.

  PMID 36854789 · PMC10119117 · The ISME journal · 2023 · 8 claims · 4 setups

  Has reproduction · 84

  Across all 16 replicate co-cultures of P. putida and P. lacustris, bacteria show a consistent succession of defense strategies over five weeks (~35 predator generations).

  pseudomonas filamentous axenically semi-continuous morphometric whole-genome

• Directing stem cell differentiation by chromatin state approximation.

  PMID 41734818 · PMC12956330 · Nucleic acids research · 2026 · 8 claims · 8 setups

  Full-text index only

  Greedy selection of culture conditions by chromatin (ATAC-seq) distance to target is a viable optimisation strategy for differentiation protocols

  cd34+ cd34+-derived erythroid bone atac-seq flow rt-qpcr

• Three-dimensional neuroblastoma cell culture: proteomic analysis between monolayer and multicellular tumor spheroids.

  PMID 18797883 · PMC2804865 · Pediatric surgery international · 2008 · 7 claims · 3 setups

  Full-text index only

  18 protein spots were differentially over-expressed in neuroblastoma spheroids compared to monolayers

  neuroblastoma excised monolayer 2-d lc-ms fractionation

• Aerobic nonylphenol degradation and nitro-nonylphenol formation by microbial cultures from sediments.

  PMID 20043151 · PMC2825322 · Applied microbiology and biotechnology · 2010 · 8 claims · 8 setups

  Full-text index only

  Aerobic biodegradation of branched NP in polluted river sediment occurs within 8 days after a 2-day lag phase at 30°C

  np-polluted sediment-derived fourth-generation extracted biodegradation serial metabolite

• Microglia-containing cerebral organoids derived from induced pluripotent stem cells for the study of neurological diseases.

  PMID 36936782 · PMC10014280 · iScience · 2023 · 8 claims · 8 setups

  Has reproduction · 74

  A novel protocol using FGF/EGF/heparin growth factor supplementation and 10% CO2 culture generates cerebral organoids containing neurons, astrocytes, and microglia from iPSCs/hESCs

  hesc-derived hesc als-pdc-affected cerebral microarray immunostaining bulk

• Alzheimer's disease biomarker discovery in symptomatic and asymptomatic patients: experimental approaches and future clinical applications.

  PMID 19796674 · PMC2840994 · Experimental gerontology · 2010 · 8 claims · 4 setups

  Full-text index only

  cDNA microarray screening of 6794 genes identified 32 genes aberrantly expressed (>1.8-fold) in the superior temporal gyrus of moderate dementia cases versus cognitively normal controls

  post-mortem cortico-hippocampal cdna western culture

• Influenza A (H3N2) outbreak, Nepal.

  PMID 16102305 · PMC3320503 · Emerging infectious diseases · 2005 · 7 claims · 6 setups

  Full-text index only

  Nepal H3N2 outbreak isolates show antigenic drift, with ~40% antigenically distinct from the A/Wyoming/3/03 vaccine strain by hemagglutination inhibition

  influenza throat ha1 amino hemagglutination rt-pcr rapid

• Biodefense versus bioterrorism.

  PMID 18771576 · PMC2575524 · Genome biology · 2008 · 5 claims · 4 setups

  Full-text index only

  Whole-genome sequencing and comparative genomics of the attack strain were used to trace the anthrax letters to a specific laboratory flask

  bacillus ancestral cultures anthrax whole-genome comparative colony

• Pre-operative urinary cathepsin D is associated with survival in patients with renal cell carcinoma.

  PMID 19789534 · PMC2768081 · British journal of cancer · 2009 · 8 claims · 7 setups

  Full-text index only

  Cathepsin D, identified via comparative 2D PAGE of conditioned media from RCC cell lines vs normal renal cultures, is a candidate secreted biomarker of RCC

  htb49 excised conditioned urine page maldi western

• Mucospheres produced by a mixotrophic protist impact ocean carbon cycling.

  PMID 35288549 · PMC8921327 · Nature communications · 2022 · 8 claims · 8 setups

  Has reproduction · 58

  P. cf. balticum produces carbon-rich 'mucospheres' that attract, capture and immobilise a wide range of prokaryotic and eukaryotic prey

  balticum xenic tara prokaryotic its lc-ms 18s

• A need for a 'whole-istic functional genomics' approach in complex human diseases: arthritis.

  PMID 12718747 · PMC165036 · Arthritis research & therapy · 2003 · 8 claims · 6 setups

  Full-text index only

  A systems ('whole-istic') functional genomics approach integrating multiple technologies and biological levels (cell, tissue, organ, organism) is necessary to understand complex diseases like arthritis.

  oa-affected cartilage type zebrafish gene differential genetic

• Ratiocinative screen of eukaryotic integral membrane protein expression and solubilization for structure determination.

  PMID 19031011 · PMC2756966 · Journal of structural and functional genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  A discovery-oriented pipeline using standardized single-condition methods (one expression system, one detergent, one SEC buffer) can efficiently triage large numbers of eukaryotic IMP targets to identify well-behaved candidates for crystallization

  cerevisiae ddm-solubilized sec-included tmhmm ligase-independent small-scale

• Stemming cancer: functional genomics of cancer stem cells in solid tumors.

  PMID 18561035 · PMC2758383 · Stem cell reviews · 2008 · 8 claims · 8 setups

  Full-text index only

  Cancer stem cells are a minority tumor subpopulation that alone can maintain indefinite tumor growth, as shown by serial transplantation experiments

  solid fetal cd133+ breast facs neurosphere genome-wide

• Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.

  PMID 32019831 · PMC7002113 · mSystems · 2020 · 7 claims · 8 setups

  Has reproduction · 57

  Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are expressed in the halite endolithic microbial community of the Atacama Desert

  halite same identified conserved strand-specific genome-resolved srna