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).

• 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

• 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

• De novo identification of CD4(+) T cell epitopes.

  PMID 38658646 · PMC11093748 · Nature methods · 2024 · 7 claims · 8 setups

  Has reproduction · 83

  SABR-IIs (chimeric receptors linking a covalently attached peptide-MHC-II to CD28-CD3ζ signaling domains) present epitopes to CD4+ T cells and induce a readable NFAT-GFP/CD69 signal upon cognate TCR recognition

  nfat-gfp hla-dq8 5kc daudi nfat-gfp co-incubation species

• Genome-wide analysis of antisense transcription with Affymetrix exon array.

  PMID 18211689 · PMC2257944 · BMC genomics · 2008 · 8 claims · 4 setups

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  A modified cDNA synthesis protocol (ATE: Antisense Transcriptome analysis using Exon array), which skips the first-cycle cDNA synthesis and IVT amplification step, labels cDNA in reverse orientation, enabling Exon arrays to detect antisense transcripts

  jurkat exon orientation-specific

• 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