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).

• Global mapping of the topography and magnitude of proteolytic events in apoptosis.

  PMID 18724940 · PMC2597167 · Cell · 2008 · 7 claims · 6 setups

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  PROTOMAP, a method combining 1D SDS-PAGE fractionation with LC-MS/MS-derived sequence coverage and spectral counting visualized as 'peptographs', enables global mapping of proteolytic topography and magnitude

  jurkat sds-page fragmentation caspase-3

• Control of gene expression during T cell activation: alternate regulation of mRNA transcription and mRNA stability.

  PMID 15907206 · PMC1156890 · BMC genomics · 2005 · 8 claims · 5 setups

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  Regulation of mRNA stability accounts for as much as 50% of all measured changes in polyA mRNA levels, inferred from absence of corresponding nuclear transcription changes.

  jurkat nuclear polya single

• Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

  PMID 18722006 · PMC2566540 · Cell · 2008 · 7 claims · 8 setups

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  A subtiligase-based N-terminal biotinylation and enrichment method enables global identification and sequencing of protease cleavage sites in complex mixtures

  jurkat computational immunoblotting structural protein-protein

• Molecular analysis of tumor suppressor genes, Rb, p53, p16INK4A, p15INK4B and p14ARF in natural killer cell neoplasms.

  PMID 11676855 · PMC5926606 · Japanese journal of cancer research : Gann · 2001 · 8 claims · 5 setups

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  Gene amplification of p53 was detected in one nasal NK cell lymphoma

  same shifted neoplasm cases southern pcr-sscp direct

• The impact of peptide abundance and dynamic range on stable-isotope-based quantitative proteomic analyses.

  PMID 18798661 · PMC2746028 · Journal of proteome research · 2008 · 8 claims · 7 setups

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  Over half of confidently identified peptides in complex mixtures have S/N ratios below 10 on both FT-ICR and Orbitrap instruments

  jurkat silac-based sds-page database

• iceDP: identifying inter-chromatin engagement via density peaks clustering algorithm.

  PMID 41499218 · PMC12777978 · Briefings in bioinformatics · 2026 · 7 claims · 8 setups

  Has reproduction · 53

  iceDP is a tool that uses the Density Peaks clustering algorithm plus a distribution test and fold-change filter to identify non-homologous inter-chromatin contacts (NHCCs) from Hi-C data

  olfactory mosn hesc type in-situ h3k27ac micro-c

• HIT: a versatile proteomics platform for multianalyte phenotyping of cytokines, intracellular proteins and surface molecules.

  PMID 18849997 · PMC3334282 · Nature medicine · 2008 · 8 claims · 8 setups

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  HIT uses oligonucleotide-tagged (Fab- or mSA-conjugated) antibodies, T7 polymerase amplification, and DNA microarray hybridization to indirectly measure multiple analytes in a fluid-phase multiplex format

  hsp70-coated hsp70 secreted jurkat fluid-phase multiplex hit

• Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

  PMID 18684996 · PMC2532738 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  SISSRs identifies binding sites from ChIP-Seq short reads with much higher resolution than the standard region-clustering approach

  cd4+ jurkat hela computational chip-seq novo motif

• Downregulation of death-associated protein kinase 1 (DAPK1) in chronic lymphocytic leukemia.

  PMID 17540169 · PMC4647864 · Cell · 2007 · 8 claims · 13 setups

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  DAPK1 promoter is epigenetically silenced by DNA methylation in almost all sporadic CLL cases

  cd19+ leukemia raji jurkat quantitative cobra chromatin

• A global proteomics approach identifies novel phosphorylated signaling proteins in GPVI-activated platelets: involvement of G6f, a novel platelet Grb2-binding membrane adapter.

  PMID 16941570 · PMC1869047 · Proteomics · 2006 · 8 claims · 7 setups

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  96 proteins undergo post-translational modification (phosphorylation) in response to CRP stimulation of human platelets, including 11 proteins not previously identified in platelets

  washed 293t g6f-transfected hek phosphotyrosine 2-de western

• CTCF binding site classes exhibit distinct evolutionary, genomic, epigenomic and transcriptomic features.

  PMID 19922652 · PMC3091324 · Genome biology · 2009 · 8 claims · 8 setups

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  CTCF binding sites can be classified into three occupancy-based classes (LowOc, MedOc, HighOc) based on similarity to the CTCF PWM motif

  cd4+ hela imr90 embryonic chip-seq computational gene

• Are gene expression microarray analyses reliable? A review of studies of retinoic acid responsive genes.

  PMID 15626329 · PMC5171945 · Genomics, proteomics & bioinformatics · 2003 · 6 claims · 8 setups

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  Published microarray studies aiming to identify RA-responsive genes show substantial, often contradictory, differences in results across research groups.

  nb4 tf1 tracheobronchial moser affymetrix cdna microarray

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc