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).

• Comparative proteomics of clathrin-coated vesicles.

  PMID 17116749 · PMC2064594 · The Journal of cell biology · 2006 · 8 claims · 4 setups

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  A comparative proteomics strategy contrasting CCV fractions from control and clathrin-depleted (CHC siRNA knockdown) HeLa cells can distinguish genuine CCV proteins from copurifying contaminants

  hela western sds-page difference

• 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

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  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

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

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

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

  neuroblastoma excised monolayer 2-d lc-ms fractionation

• Discovery and functional interrogation of SARS-CoV-2 RNA-host protein interactions.

  PMID 33743211 · PMC7951565 · Cell · 2021 · 8 claims · 6 setups

  Has reproduction · 84

  ChIRP-MS identifies 309 host proteins that bind SARS-CoV-2 RNA during active infection across Huh7.5 and Vero E6 cells.

  huh7.5 host lung chirp-ms chirp-rna-seq sds-page

• Post-translational modifications of histones H3 and H4 associated with the histone methyltransferases Suv39h1 and G9a.

  PMID 18096052 · PMC2246272 · Genome biology · 2007 · 6 claims · 4 setups

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  Suv39h1 and G9a associate with previously reported methylation states (Suv39h1 with H3K9me3; G9a with H3K9me/me2)

  crude hela-suv39h1 suv39h1 normal propionylation-based double maldi-tof

• Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome.

  PMID 18490959 · PMC2386506 · Molecular vision · 2008 · 7 claims · 6 setups

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  A novel affinity-enrichment strategy using UV cross-linked protease inhibitor peptides on Protein A/G columns improves capture of the TM protease proteome compared to SDS-PAGE fractionation alone

  cytosolic affinity-eluted porcine affinity-enriched affinity western sds-page

• Identification of diagnostic markers for tuberculosis by proteomic fingerprinting of serum.

  PMID 16980117 · PMC7159276 · Lancet (London, England) · 2006 · 8 claims · 5 setups

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  An SVM classifier trained on serum proteomic profiles discriminated patients with active tuberculosis from controls with clinically overlapping conditions

  serum computational kda spin-column seldi-tof supervised peptide

• Methods for the proteomic identification of protease substrates.

  PMID 19729334 · PMC2787889 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Gel-based methods (2D-DiGE, diagonal electrophoresis, PROTOMAP) identify protease substrates by comparing proteolyzed versus control samples via electrophoretic migration differences followed by MS identification

  lysate jurkat apoptotic yeast 2d-dige protomap cofradic

• Coding and non-coding roles of MOCCI (C15ORF48) coordinate to regulate host inflammation and immunity.

  PMID 33837217 · PMC8035321 · Nature communications · 2021 · 8 claims · 8 setups

  Has reproduction · 68

  MOCCI (encoded by C15ORF48) is a mito-SEP upregulated during inflammation and infection that promotes host-protective resolution

  aortic failing colon hek293t ribo-seq wgcna-gsea gene