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).

• A search for structurally similar cellular internal ribosome entry sites.

  PMID 17591613 · PMC1950536 · Nucleic acids research · 2007 · 8 claims · 7 setups

  Full-text index only

  Cellular IRES are not defined by an overall conserved structure (unlike viral IRES) but instead depend on short RNA motifs and shared trans-acting factors (ITAFs)

  transcribed hek 293t enzymatic chemical structural

• Disease-specific proteins from rheumatoid arthritis patients.

  PMID 16778393 · PMC2729955 · Journal of Korean medical science · 2006 · 8 claims · 6 setups

  Full-text index only

  Fibronectin, semaphorin 7A precursor, growth factor receptor-bound protein 7 (GRB7), and immunoglobulin µ chain specifically associate with antibodies purified from RA synovial fluid

  synovium synovial synoviocytes western affinity antibody-affinity

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• Nitrosothiol reactivity profiling identifies S-nitrosylated proteins with unexpected stability.

  PMID 19101475 · PMC2628636 · Chemistry & biology · 2008 · 8 claims · 7 setups

  Full-text index only

  Most protein nitrosothiols are rapidly denitrosylated by physiological GSH, but a small subset show markedly reduced GSH reactivity and remain stably S-nitrosylated

  brain hemoglobin crystal send.1 biotin chemical snocap

• Targeted intracellular protein degradation induced by a small molecule: En route to chemical proteomics.

  PMID 18752944 · PMC3175619 · Bioorganic & medicinal chemistry letters · 2008 · 7 claims · 2 setups

  Full-text index only

  An all-small-molecule SARM-nutlin PROTAC induces degradation of the androgen receptor in cells

  hela western

• Proteomic identification of nitrated brain proteins in amnestic mild cognitive impairment: a regional study.

  PMID 17760844 · PMC3823261 · Journal of cellular and molecular medicine · 2007 · 8 claims · 5 setups

  Full-text index only

  Total protein nitration (3-NT immunoreactivity) is significantly increased in MCI hippocampus and IPL compared to age-matched control brain

  postmortem excised mci 2d-page sypro in-gel

• A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

  PMID 18301748 · PMC2244703 · PloS one · 2008 · 8 claims · 7 setups

  Full-text index only

  FOXO1a mRNA and protein expression are elevated in human liver compared to chimpanzee liver

  chimpanzee hepg2 promoters liver quantitative western sirna

• A novel approach to tag and identify geranylgeranylated proteins.

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

  Full-text index only

  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

• NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution.

  PMID 31156037 · PMC6693550 · RNA biology · 2019 · 8 claims · 7 setups

  Has reproduction · 67

  NET-prism, an adapted NET-seq protocol using immunoprecipitation of Pol II-associated factors, enables strand-specific, nucleotide-resolution interrogation of transcription dynamics for any Pol II-interacting protein.

  e14 mass western net-prism

• Breast cancer proteomics reveals correlation between estrogen receptor status and differential phosphorylation of PGRMC1.

  PMID 18922159 · PMC2614521 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

  Full-text index only

  PGRMC1 protein spots are differentially abundant between ER-negative and ER-positive breast tumors, with two of three spots more abundant in ER-negative tumors

  sections pooled mcf7 paraffin-embedded 2d-page shrimp viability

• Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

  PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

  heart degs dgat2 mitodegs microarray kegg protein-protein

• Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length.

  PMID 34871442 · PMC8682771 · Nucleic acids research · 2021 · 8 claims · 8 setups

  Has reproduction · 58

  RPS6 becomes progressively dephosphorylated on ribosomes as they translate along an mRNA CDS

  hela mef phospho-rps6-selective 80s immunoblotting

• The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.

  PMID 21857667 · PMC3173870 · Nature cell biology · 2011 · 8 claims · 8 setups

  Has reproduction · 90

  Brain tumors in l(3)mbt mutants originate from overproliferation of neuroepithelial cells of the optic lobes, not from defects in asymmetric cell division.

  drosophila chip-seq chip immunostaining

• Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.

  PMID 17704778 · PMC2872770 · Nature genetics · 2007 · 8 claims · 6 setups

  Full-text index only

  Mutations in UPF3B cause syndromic (Lujan-Fryns syndrome, FG syndrome) and nonsyndromic X-linked mental retardation

  probands lymphoblastoid lcls tissues gene quantitative cycloheximide

• Proteomic approaches to cancer biomarkers.

  PMID 19931265 · PMC2873613 · Gastroenterology · 2010 · 8 claims · 8 setups

  Full-text index only

  Combining abundant-protein depletion, offline fractionation, and subproteome (e.g., glycoproteome) enrichment with 2D LC-MS/MS increases the dynamic range and depth of blood proteome analysis for biomarker discovery.

  plasma serum capan-2 apcδ580 lectin silac elisa

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

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

  Full-text index only

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

  hela confocal immunofluorescence western

• CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.

  PMID 31365872 · PMC6684324 · Cell reports · 2019 · 8 claims · 8 setups

  Has reproduction

  Genome-wide CRISPR/Cas9 screens in CD40L-stimulated Daudi B cells identify known CD40/NF-κB pathway components plus many novel positive and negative CD40 regulators.

  daudi celf1 genome-wide flow immunoblot

• A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

  PMID 17186946 · PMC1860054 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 8 setups

  Full-text index only

  Three complementary membrane-enrichment proteomic methods (lectin affinity, biotin/NeutrAvidin affinity, free flow electrophoresis) combined with LC-MS/MS identify 136 transmembrane proteins in human platelets, including many novel ones.

  washed platelets tryptic hek293t lc-ms free longsage

• Proteomic analysis of RCL2 paraffin-embedded tissues.

  PMID 19012729 · PMC4506168 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups

  Full-text index only

  RCL2-fixed paraffin-embedded (RCL2P) tissue consistently gives the highest protein yield compared to FFPE and frozen tissue across extraction protocols

  normal rcl2p ffpe frozen yield 1-dimensional 2-dimensional

• Proteomic analyses associate cystatin B with restricted HIV-1 replication in placental macrophages.

  PMID 18951626 · PMC3867668 · Placenta · 2008 · 6 claims · 6 setups

  Full-text index only

  Placental macrophages support significantly lower HIV-1 replication than monocyte-derived macrophages

  placental mdm hiv-1 seldi-tof sds-page