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).

• Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.

  PMID 40849297 · PMC12375038 · Nature communications · 2025 · 8 claims · 6 setups

  Has reproduction · 90

  A single-nucleus transcriptomic atlas of 37 human sural nerves (365,708 nuclei) defines 24 cell clusters and reveals unexpected heterogeneity of perineurial cells (periC1-3).

  sural rodent single-nucleus subcellular immunofluorescence

• Genome-wide kinetic properties of transcriptional bursting in mouse embryonic stem cells.

  PMID 32596448 · PMC7299619 · Science advances · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  Genome-wide transcriptional bursting kinetics (intrinsic noise, burst size, frequency) can be estimated from allele-specific scRNA-seq of hybrid mESCs

  cast inbred gfp mescs single-cell smfish flow

• MitoP2: the mitochondrial proteome database--now including mouse data.

  PMID 16381964 · PMC1347489 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  MitoP2 is a database integrating manually annotated mitochondrial reference proteins, functions, and disease associations for yeast, human, and mouse, with cross-species orthologue mapping

  saccharomyces yeast heart liver genome-wide single transcriptome

• Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.

  PMID 36253367 · PMC9576764 · Nature communications · 2022 · 8 claims · 4 setups

  Has reproduction · 100

  The P. magna mitoribosome contains rRNA split into 13 fragments (LSU1-8, SSU1-4, mt-5S)

  mitoribosome polytomella cross-species single-particle novo comparative

• Single-cell transcriptomics reveals maturation of transplanted stem cell-derived retinal pigment epithelial cells toward native state.

  PMID 37339216 · PMC10293804 · Proceedings of the National Academy of Sciences of the United States of America · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Subretinally transplanted stem cell-derived RPE (ESC- and iPSC-derived) retain RPE identity and survive in vivo for at least 30 days in immunocompetent rabbit eyes

  hpsc-derived day esc dutch qrt-pcr immunofluorescence transepithelial

• Spatial organization shapes the turnover of a bacterial transcriptome.

  PMID 27198188 · PMC4874777 · eLife · 2016 · 7 claims · 6 setups

  Has reproduction · 71

  The E. coli transcriptome is spatially organized genome-wide: mRNAs encoding inner-membrane proteins are enriched at the membrane, while mRNAs encoding cytoplasmic, periplasmic and outer-membrane proteins are distributed throughout the cytoplasm.

  coli single-molecule fish time-resolved

• H-DBAS: human-transcriptome database for alternative splicing: update 2010.

  PMID 19969536 · PMC2808982 · Nucleic acids research · 2010 · 8 claims · 4 setups

  Full-text index only

  RNA-Seq tags from the polysome fraction identify AS exons that are very likely used for protein synthesis

  dld-1 rna-seq western real-time

• Large-scale and high-confidence proteomic analysis of human seminal plasma.

  PMID 16709260 · PMC1779515 · Genome biology · 2006 · 8 claims · 6 setups

  Full-text index only

  923 proteins were identified with high confidence in seminal plasma from a single individual, combining results from three ejaculate samples

  seminal same list combined sds-page database decoy

• MAPU: Max-Planck Unified database of organellar, cellular, tissue and body fluid proteomes.

  PMID 17090601 · PMC1781136 · Nucleic acids research · 2007 · 8 claims · 8 setups

  Full-text index only

  MAPU is a unified, freely accessible database integrating organellar, cellular, tissue and body fluid proteomes generated by high-resolution mass spectrometry.

  urine tear seminal breast gel lc-ms3 in-depth

• Free circular introns with an unusual branchpoint in neuronal projections.

  PMID 31697236 · PMC6879206 · eLife · 2019 · 8 claims · 7 setups

  Has reproduction · 99

  A set of free circular introns with a non-canonical (C) branchpoint is enriched in distal neuronal projections; these appear to be tailless lariats that escape debranching.

  hippocampal cytoplasmic rrna-depleted polya-site ribosome

• A global database for modeling tumor-immune cell communication.

  PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups

  Has reproduction · 66

  TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures

  pubmed scrna-seq tcga basal manual scrna-seq bulk

• Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles.

  PMID 29907695 · PMC6068466 · The EMBO journal · 2018 · 8 claims · 8 setups

  Has reproduction · 46

  B16F1 and B16F10 melanoma subclones functionally exchange EVs in vivo, transferring Cre mRNA cargo detectable via a Cre-LoxP color-switch reporter system

  co-injected b16f1 locally 16.5k intravital cre-loxp rt-pcr

• Whither genomics?

  PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

  Full-text index only

  Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

  mammalian budding yeast general expression genome-wide synthetic

• A haplotype variation affecting the mitochondrial transportation of hMYH protein could be a risk factor for colorectal cancer in Chinese.

  PMID 18811933 · PMC2565682 · BMC cancer · 2008 · 7 claims · 2 setups

  Full-text index only

  The hMYH haplotype T/A variant allele is present at significantly higher frequency in CRC patients than in healthy controls

  peripheral cos-7 dhplc immunofluorescence

• Identification of a dominant epitope of glutamic acid decarboxylase (GAD-65) recognized by autoantibodies in stiff-man syndrome.

  PMID 8245784 · PMC2191306 · The Journal of experimental medicine · 1993 · 8 claims · 6 setups

  Full-text index only

  All 30 SMS patient sera selectively recognize GAD-65, but not GAD-67, when tested by Western blotting on denatured GAD.

  brain bacterial triton cho western immunoprecipitation immunocytochemistry

• The secrets of a functional synapse--from a computational and experimental viewpoint.

  PMID 16723009 · PMC1810317 · BMC bioinformatics · 2006 · 8 claims · 8 setups

  Full-text index only

  Kinesin motor proteins move cargo along axonal microtubules to the synapse, with cargo specificity determined by adaptor/linker proteins rather than lipid recognition

  mammalian kinesin cholinergic dendrites kinesin sequence-based comparative

• Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.

  PMID 41796334 · PMC12969887 · Genome biology · 2026 · 8 claims · 8 setups

  Has reproduction · 68

  Retrovirus-derived LTR8B acts as a trophoblast-specific cis-regulatory element within the PSG array, with LTR8B at PSG9 influencing other PSG family members as a master regulator

  sghpl-4 trophoblast placenta bewo chip-exonuclease crispr-cas9 chromatin