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).

• Elevated serum levels of interferon-regulated chemokines are biomarkers for active human systemic lupus erythematosus.

  PMID 17177599 · PMC1702557 · PLoS medicine · 2006 · 8 claims · 4 setups

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  30 of 160 measured serum analytes (cytokines, chemokines, growth factors, soluble receptors) are dysregulated in SLE serum

  serum blood peripheral custom luminex blood

• 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

• Antibody protein array analysis of the tear film cytokines.

  PMID 18677223 · PMC3786218 · Optometry and vision science : official publication of the American Academy of Optometry · 2008 · 7 claims · 4 setups

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  Tear fluid contains factors with affinity for plastic, capture antibodies, and IgG that create matrix effects profoundly impacting dot ELISA/array reliability

  tear normalized antibody 12-plex two-step

• A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm.

  PMID 18034894 · PMC2241821 · BMC biotechnology · 2007 · 7 claims · 7 setups

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  A human scFv library was built on the single scFv13R4 framework with CDR3 loops diversified to mimic natural human CDR3 amino-acid distributions.

  coli hela filamentous scfv gfp sds-page fluorescence

• Immuno-detection by sequencing enables large-scale high-dimensional phenotyping in cells.

  PMID 29921844 · PMC6008431 · Nature communications · 2018 · 8 claims · 8 setups

  Has reproduction · 96

  ID-seq combines antibody-based protein detection with DNA-sequencing of DNA-tagged antibodies to measure large numbers of (phospho-)proteins in many samples in parallel

  epidermal fixed skin differentiating id-seq immuno-pcr in-cell-western

• p53 expression and its relationship to DNA alterations in bone and soft tissue sarcomas.

  PMID 8260365 · PMC1968651 · British journal of cancer · 1993 · 8 claims · 6 setups

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  25.7% (29/113) of bone and soft tissue sarcomas show positive p53 immunostaining

  frozen subset saos-2 immunohistochemistry southern pcr-single

• Brain progranulin expression in GRN-associated frontotemporal lobar degeneration.

  PMID 19649643 · PMC3104467 · Acta neuropathologica · 2010 · 8 claims · 8 setups

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  GRN transcript haploinsufficiency, previously shown in blood-derived cells, does not hold in most brain regions of GRN mutation carriers

  peripheral postmortem hek293 qrt-pcr microarray rt-pcr

• Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

  PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups

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  A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity

  serum hplc-purified trypsin-digested crude seldi-tof-ms solid-phase maldi-tof-ms

• Genomics--from Neanderthals to high-throughput sequencing.

  PMID 16934106 · PMC1779599 · Genome biology · 2006 · 8 claims · 8 setups

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  Next-generation sequencing platforms (GS20/454 and Solexa) can deliver the throughput and cost reductions needed for population-scale and medical resequencing.

  bacterial ion-channel drosophila arrays next-generation pooled multiplex

• Identification of HLA-DRPhebeta47 as the susceptibility marker of hypersensitivity to beryllium in individuals lacking the berylliosis-associated supratypic marker HLA-DPGlubeta69.

  PMID 16098233 · PMC1198259 · Respiratory research · 2005 · 7 claims · 4 setups

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  HLA-DPGlu69 is the primary marker of Be-hypersensitivity, present at higher frequency in berylliosis patients than in Be-sensitized subjects and Be-exposed controls

  pbmc peripheral population high beryllium lymphocyte

• Comprehensive phenotyping in multiple sclerosis: discovery based proteomics and the current understanding of putative biomarkers.

  PMID 17124343 · PMC3851054 · Disease markers · 2006 · 8 claims · 8 setups

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  No single diagnostic test exists for MS; diagnosis relies on clinical evaluation, MRI abnormalities, and CSF chemistry

  csf cns igg brain comprehensive immunohistochemical solid-phase

• Evaluation of the genetic polymorphism of Plasmodium falciparum P126 protein (SERA or SERP) and its influence on naturally acquired specific antibody responses in malaria-infected individuals living in the Brazilian Amazon.

  PMID 18667071 · PMC2515332 · Malaria journal · 2008 · 8 claims · 4 setups

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  Only two OR fragment types were identified in P. falciparum isolates from the Brazilian Amazon: OR-I (175 bp) and OR-II (199 bp)

  falciparum pcr-amplified p126 sera nested agarose sequencing

• Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

  PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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  Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

  families genes individuals kidney genome-wide sanger resequencing

• Sample preparation for serum/plasma profiling and biomarker identification by mass spectrometry.

  PMID 17166507 · PMC7094463 · Journal of chromatography. A · 2007 · 8 claims · 8 setups

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  Standardizing sample preparation procedures for serum/plasma profiling is critical for obtaining reliable biomarkers, since slight procedural changes can produce very different protein profiles.

  serum aqueous maldi-tof seldi-tof peak

• Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

  PMID 17359525 · PMC1838427 · BMC molecular biology · 2007 · 8 claims · 8 setups

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  OPTC is a candidate gene involved in POAG pathogenesis

  genomic pcr optc retinal pcr-sscp dhplc sequencing

• A novel recessive Nefl mutation causes a severe, early-onset axonal neuropathy.

  PMID 20039262 · PMC4439312 · Annals of neurology · 2009 · 8 claims · 8 setups

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  A homozygous NEFL nonsense mutation (E210X) causes a severe, early-onset recessive axonal neuropathy in four siblings of a consanguineous family

  family sural nefl-null sw-13 clinical genetic immunohistochemistry

• Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

  PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 6 setups

  Has reproduction

  Expression stability in CHO cell lines is controlled at three levels: choice of integration site, integrity/concatemerization pattern of the transgene, and stress-related cellular processes.

  horizon six cho-k1 cho genome rna-seq targeted

• Characterization of the 3a protein of SARS-associated coronavirus in infected vero E6 cells and SARS patients.

  PMID 15312778 · PMC7127270 · Journal of molecular biology · 2004 · 8 claims · 7 setups

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  ORF3a of SARS-CoV encodes an actual 31 kDa, 274-residue protein detected in infected cells and virions

  vero crude sera sars-cov 2d-lc-ms sds-page western

• The use of proteomics in biomarker discovery in neurodegenerative diseases.

  PMID 15920295 · PMC3850612 · Disease markers · 2005 · 8 claims · 8 setups

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  A combination of low CSF-β-amyloid(1-42) with high CSF-tau and high CSF-phospho-tau is associated with an AD diagnosis

  csf serum two-dimensional seldi liquid-phase

• Proteomic surveillance of retinal autoantigens in endogenous uveitis: implication of esterase D and brain-type creatine kinase as novel autoantigens.

  PMID 18552983 · PMC2426731 · Molecular vision · 2008 · 7 claims · 6 setups

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  Six novel candidate retinal autoantigens (β-actin, esterase D, tubulin β-2, brain-type creatine kinase, VDAC, aspartate aminotransferase) were identified by 2D-WB and mass spectrometry in EAU mice

  c57bl retinal recombinant eau two-dimensional maldi-tof one-dimensional