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).

• The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

  PMID 17299583 · PMC1797623 · PloS one · 2007 · 6 claims · 4 setups

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  5′-tagged PCR primers enable pooling of homologous PCR products from multiple sources into a single GS20 run with accurate post-hoc assignment of sequences to source

  extracts pooled same non-assigned pcr parallel conventional

• Integrated multi-level quality control for proteomic profiling studies using mass spectrometry.

  PMID 19055809 · PMC2657802 · BMC bioinformatics · 2008 · 7 claims · 5 setups

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  QC processes for identifying and removing low-quality spectra are often overlooked in proteomic profiling studies

  serum pooled duplicate full seldi-tof principal technical

• Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

  PMID 18989384 · PMC2579937 · Molecular vision · 2008 · 8 claims · 4 setups

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  Worn silicone hydrogel contact lenses deposit a wide array of proteins from the tear film and other sources.

  deposit excised pooled worn sds-page in-gel lc-ms-ms

• Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

  PMID 18984577 · PMC2649809 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 6 setups

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  Brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma

  csf brain normal 2d-dige label-free isotopic

• 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

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  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

• Potential biomarkers of human salivary function: a modified proteomic approach.

  PMID 18804197 · PMC2633945 · Archives of oral biology · 2009 · 6 claims · 6 setups

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  Two SDS-PAGE bands, identified by MS-MS as statherin and a truncated (N-terminal 8-aa-missing) cystatin S, are the strongest and most consistent predictors of HAA/LAA group membership and clinical/microbiological outcomes

  resting pooled saliva quantified preparative sds-page western

• Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

  PMID 18776137 · PMC2584123 · Diabetes · 2008 · 6 claims · 7 setups

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  Lymphocytes (but not monocytes) from type 1 diabetic patients show a distinct subset of genes with significantly increased H3K9me2 compared with healthy controls.

  blood pooled gene chip-chip conventional quantitative

• Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

  PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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  Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

  genomic commercial plco unrelated targeted long-range genotyping

• Current and future directions in genomics of amyotrophic lateral sclerosis.

  PMID 18625410 · PMC3524513 · Physical medicine and rehabilitation clinics of North America · 2008 · 8 claims · 8 setups

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  Familial ALS (FALS, 5-10% of cases) follows Mendelian autosomal dominant inheritance, with 20% caused by SOD1 mutations and 80% by unknown mutations

  american sals dutch irish genome laser expression

• Transcriptomics and adaptive genomics of the asymptomatic bacteriuria Escherichia coli strain 83972.

  PMID 18317809 · PMC2329726 · Molecular genetics and genomics : MGG · 2008 · 8 claims · 7 setups

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  Strain 83972 is best described as a 'deconstructed pathogen' rather than a true commensal that acquired fitness properties

  coli microarrays microarray comparative processing

• Next-generation sequencing.

  PMID 20030863 · PMC2797692 · Breast cancer research : BCR · 2009 · 8 claims · 7 setups

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  Massively parallel sequencing can simultaneously capture base-pair mutations, copy number aberrations and somatic rearrangements of a cancer genome in a single experiment

  individuals metastatic acute oestrogen whole-exome whole-genome large-scale

• Proteomic approaches to cancer biomarkers.

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

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  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

• Association of the MAPT locus with Parkinson's disease.

  PMID 19912324 · PMC3906622 · European journal of neurology · 2010 · 7 claims · 5 setups

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  H1/H2-tagging SNPs rs1052553 (MAPT) and rs62063857 (Saitohin/STH) are significantly associated with increased risk of PD

  patients caucasian snp haplotype linkage

• Serum S100A6 concentration predicts peritoneal tumor burden in mice with epithelial ovarian cancer and is associated with advanced stage in patients.

  PMID 19888321 · PMC2765613 · PloS one · 2009 · 8 claims · 8 setups

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  Serum S100A6 concentration correlates with peritoneal tumor burden in a mouse OVCA xenograft model, based on inverse regression calibration against bioluminescent imaging data.

  serum skov-3 pooled ovca lc-ms antigen whole-animal

• Evaluation of the bacterial diversity among and within individual venous leg ulcers using bacterial tag-encoded FLX and titanium amplicon pyrosequencing and metagenomic approaches.

  PMID 19860898 · PMC2773781 · BMC microbiology · 2009 · 7 claims · 5 setups

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  VLU infections are polymicrobial with no single bacterium colonizing the wounds

  individual pooled second btefap quantitative bulk

• Quantitative serum proteomics using dual stable isotope coding and nano LC-MS/MSMS.

  PMID 19817497 · PMC4684172 · Journal of proteome research · 2009 · 7 claims · 6 setups

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  DSIC labeling achieves high efficiency: 100% for Cysteine (acrylamide) and 98% for Lysine (succinic anhydride)

  standard dsic-labeled immunodepleted serum labeling quantitative in-solution

• Whither genomics?

  PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

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  Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

  mammalian budding yeast general expression genome-wide synthetic

• Association of MUTYH and colorectal cancer.

  PMID 16804517 · PMC2360610 · British journal of cancer · 2006 · 7 claims · 3 setups

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  Bi-allelic MUTYH mutations confer a very large increase in colorectal cancer risk (GRR=117), supporting a causal role in colorectal cancer

  blood pooled genotype genotyping meta-analysis chi-square

• MTHFR 677C>T and ACE D/I polymorphisms in migraine: a systematic review and meta-analysis.

  PMID 19925624 · PMC3071567 · Headache · 2010 · 6 claims · 3 setups

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  The MTHFR 677TT genotype is associated with increased risk of migraine with aura but not migraine without aura

  migraineurs pooled genotyping meta-analysis

• Peeling off the layers: skin taping and a novel proteomics approach to study atopic dermatitis.

  PMID 19748658 · PMC8648281 · The Journal of allergy and clinical immunology · 2009 · 8 claims · 3 setups

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  Noninvasive D-Squame tape stripping coupled with MS proteomics can profile the AD skin proteome

  skin extracted lesion skin lc-ms statistical