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).

• Rapid preparation of nuclei-depleted detergent-resistant membrane fractions suitable for proteomics analysis.

  PMID 18534013 · PMC2440737 · BMC cell biology · 2008 · 6 claims · 4 setups

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  A modified differential detergent extraction method (pelleting nuclei/intact cells at low speed before detergent solubilization) yields DRM fractions with markedly reduced nuclear protein contamination compared to the conventional method.

  lncap fractions immunofluorescence differential concentration

• MIMIC: a flexible pipeline to register and summarize IMC-MSI experiments.

  PMID 41917425 · PMC13201759 · Communications biology · 2026 · 7 claims · 6 setups

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  MIMIC is a reproducible, semi-automated workflow that co-registers and jointly analyzes MALDI-MSI and IMC data using a chain of before/after microscopy images.

  liver regions artificial maldi-msi imaging multi-step

• Mitochondrial volume fraction and translation duration impact mitochondrial mRNA localization and protein synthesis.

  PMID 32762840 · PMC7413667 · eLife · 2020 · 7 claims · 8 setups

  Has reproduction · 81

  Mitochondrial mRNA localization is necessary and sufficient to increase protein production to levels required during respiratory growth

  cerevisiae live single-molecule single-cell

• 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

• siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake.

  PMID 17640392 · PMC2323231 · Genome biology · 2007 · 8 claims · 8 setups

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  The PtdIns(3,4,5)P3-mTOR signaling pathway is a primary positive regulator of transferrin uptake.

  hela sirna secondary synthetic

• A new paradigm for MAPK: structural interactions of hERK1 with mitochondria in HeLa cells.

  PMID 19847302 · PMC2760858 · PloS one · 2009 · 8 claims · 8 setups

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  hERK1 translocates to the mitochondria of HeLa cells upon a proliferative stimulus

  hela confocal immunofluorescence western

• TNF-⍺-mediated myeloid-instructed CD14(+)CD4(+) T cells are associated with poor survival in lung adenocarcinoma.

  PMID 41666923 · PMC12923953 · Cell reports. Medicine · 2026 · 8 claims · 5 setups

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  Tumors stratify into lymphoid-enriched, myeloid-enriched, and mixed immune-infiltrated subtypes independent of oncogenic driver status

  resected luad cd4+ multiplex spatial image

• Discovery and characterization of gene-by-environment and epistatic genetic effects in a vertebrate model.

  PMID 41672067 · PMC13174225 · Cell genomics · 2026 · 7 claims · 7 setups

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  A segregation analysis in an F2 medaka cross identified 16 QTLs linked to embryonic heart rate variation across temperatures

  mikk medaka discovered informed high-throughput heart shallow

• A novel approach to tag and identify geranylgeranylated proteins.

  PMID 19784953 · PMC2855049 · Electrophoresis · 2009 · 7 claims · 7 setups

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  Metabolic incorporation of azido-GG alcohol followed by Cu(I)-catalyzed click reaction with TAMRA-alkyne selectively labels geranylgeranylated proteins for fluorescence detection

  jurkat cos-7 mcf-7 embryonic metabolic comparative fractionation

• Proteomics technologies and challenges.

  PMID 17893073 · PMC5054093 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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  The proteome reflects the dynamic state of a cell, tissue, or organism more accurately than the genome, so proteomics is expected to yield better disease markers for diagnosis and therapy monitoring.

  serum myeloid formalin-fixed general maldi-tof phage maldi

• Spatial transcriptomics maps host-gut microbiome biogeography at high resolution.

  PMID 41792309 · PMC13171632 · Nature microbiology · 2026 · 7 claims · 6 setups

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  Enzymatic in situ polyadenylation increases bacterial RNA recovery in oligo(dT)-based spatial transcriptomics arrays by up to ~100-fold while preserving host gene capture

  apc-deficient heart ileum fresh-frozen spatial high-resolution bulk

• Dictionary of human intestinal organoid responses to secreted niche factors at single cell resolution.

  PMID 41513700 · PMC12891662 · Nature communications · 2026 · 8 claims · 8 setups

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  Cytomix (TNFɑ+IFNɣ+IL1β) treatment of human colon organoids best recapitulates molecular features of human IBD compared to DSS or irradiation injury models.

  colon cytomix-treated scrna-seq immunofluorescence activated

• 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

• Deciphering the RNA landscapes on mammalian cell surfaces.

  PMID 40973153 · PMC12959771 · Protein & cell · 2026 · 7 claims · 8 setups

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  AMOUR, a T7 RNA polymerase-based in-situ linear amplification method, enables high-throughput profiling of outer membrane surface RNAs while preserving plasma membrane integrity, including in rare primary cell populations.

  live hucb-mncs hela amour-treated transmission-through-dye intact-surface-fish amour

• 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

• Identification of androgen-coregulated protein networks from the microsomes of human prostate cancer cells.

  PMID 14709176 · PMC395736 · Genome biology · 2003 · 8 claims · 5 setups

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  Distinct cellular processes are coregulated by androgen while others are essentially unaffected in LNCaP cells

  lncap computational icat western hypergeometric

• Physiology engages with functional genomics - at last.

  PMID 16086845 · PMC1273626 · Genome biology · 2005 · 8 claims · 8 setups

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  Large-scale QTL phenotyping in rat strains reveals that most hypertension-related traits are sexually dimorphic

  wild-type caenorhabditis kidney pcr qtl enu copas

• Genomic instability and mono-parental expression mitigate genomic shock in a cross-subgenus Leishmania hybrid.

  PMID 41918820 · PMC13034039 · NAR molecular medicine · 2026 · 7 claims · 8 setups

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  An in vitro cross between L. infantum and L. tarentolae produced a viable inter-subgenus hybrid, demonstrating genomic compatibility between highly divergent Leishmania species.

  infantum linf-gfp bone bmdms genetic flow morphological

• Neuropixels Opto: combining high-resolution electrophysiology and optogenetics.

  PMID 42225964 · PMC13259958 · Nature methods · 2026 · 8 claims · 7 setups

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  Neuropixels Opto probes integrate 960 recording sites and two sets of 14 light emitters (blue and red) on a 70-μm-wide, 1-cm-long shank via monolithic CMOS+photonics integration

  neuropixels test visual hippocampus electrode optical light

• 93rd Annual Meeting of the American Association for Cancer Research, San Francisco, CA, USA, 6-10 April 2002.

  PMID 12100742 · PMC138737 · Breast cancer research : BCR · 2002 · 8 claims · 8 setups

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  Serial analysis of gene expression identifies genes preferentially expressed in ductal carcinoma in situ

  breast laser serum bladder cdna western seldi-tof