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).

• A proteomic approach for plasma biomarker discovery with iTRAQ labelling and OFFGEL fractionation.

  PMID 19888438 · PMC2771280 · Journal of biomedicine & biotechnology · 2010 · 6 claims · 6 setups

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  iTRAQ labelling combined with OFFGEL fractionation improves proteome coverage of human plasma compared to iTRAQ alone or no iTRAQ

  pooled plasma prefractionated immunodepleted itraq 1-dimensional fluorescence-based

• Proteomics-derived cerebrospinal fluid markers of autopsy-confirmed Alzheimer's disease.

  PMID 19863188 · PMC2824250 · Biomarkers : biochemical indicators of exposure, response, and susceptibility to chemicals · 2009 · 8 claims · 8 setups

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  2D gel electrophoresis screening of pooled postmortem CSF identified ApoA1, hemopexin (HPX), transthyretin (TTR) and PEDF as differentially abundant among AD, ND and NADD groups

  pooled ventricular two-dimensional elisa

• Proteomic and functional characterisation of platelet microparticle size classes.

  PMID 19806257 · PMC2861410 · Thrombosis and haemostasis · 2009 · 8 claims · 8 setups

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  PMP separated by gel filtration into 4 size classes differ in protein content, phospholipid/protein ratio, and functional effects on platelets and endothelial cells

  pooled pmp citrated huvec gel dynamic lipid

• Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

  PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups

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  The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.

  pooled 16s sequenced topo 16s primer taxonomic

• Quantitative analysis of age specific variation in the abundance of human female parotid salivary proteins.

  PMID 19764810 · PMC2834885 · Journal of proteome research · 2009 · 7 claims · 5 setups

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  Protein expression in human female parotid saliva is age-dependent, with distinct protein sets differentially abundant between young and older healthy women

  pooled hcic trypsin-digested normalized hydrophobic sds-page mudpit

• Proteomics analysis reveals novel components in the detergent-insoluble subproteome in Alzheimer's disease.

  PMID 19746990 · PMC2784247 · Journal of proteome research · 2009 · 8 claims · 5 setups

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  A label-free XIC-based LC-MS/MS quantitation strategy, combined with an FTLD-U comparator cohort, can be used to identify AD-specific changes in the detergent-insoluble brain subproteome.

  pooled postmortem individual detergent-insoluble lc-ms sequential sds-page

• Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

  PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

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  159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

  pooled sequenced analysis predicted small bioinformatic qrt-pcr

• Measurement reproducibility in the early stages of biomarker development.

  PMID 15665389 · PMC3839328 · Disease markers · 2004 · 6 claims · 3 setups

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  Functional PCA can be used as the basis for gauge R&R (repeatability and reproducibility) assessment of mass spectra without prior identification of which spectral features are biomarkers

  pooled same registered seldi-tof univariate functional

• Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

  PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

  Has reproduction · 83

  MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

  pooled hc227 contig sets shotgun novo alignment-free

• The development of an integrated platform to identify breast cancer glycoproteome changes in human serum.

  PMID 19782370 · PMC4142217 · Journal of chromatography. A · 2010 · 8 claims · 6 setups

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  M-LAC (multi-lectin affinity chromatography combining Con A, WGA and Jacalin) provides comprehensive capture of glycoproteins from biological fluids based on differing glycan specificities

  pooled m-lac excised individual high-performance sds-page lectin

• Increased DNA microarray hybridization specificity using sscDNA targets.

  PMID 15847692 · PMC1090574 · BMC genomics · 2005 · 7 claims · 5 setups

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  A single round of ribo-SPIA amplification produces sufficient sscDNA for microarray hybridization from as little as 5 ng of starting total RNA

  cuhr k562 input sscdna microarray quantitative capillary

• PDA: Pooled DNA analyzer.

  PMID 16643673 · PMC1539032 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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  No software existed prior to PDA for complete pooled-DNA analysis including data standardization, allele frequency estimation, and single/multipoint association tests

  heterozygous pools ordered peak pooled single-point

• Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.

  PMID 33086062 · PMC7649750 · Cell reports · 2020 · 8 claims · 8 setups

  Has reproduction · 59

  KMT2D is a potent tumor suppressor in melanoma

  hmel-brafv600e tyr-creert2 tma kmt2d pooled xenograft genetically

• CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.

  PMID 31365872 · PMC6684324 · Cell reports · 2019 · 8 claims · 8 setups

  Has reproduction

  Genome-wide CRISPR/Cas9 screens in CD40L-stimulated Daudi B cells identify known CD40/NF-κB pathway components plus many novel positive and negative CD40 regulators.

  daudi celf1 genome-wide flow immunoblot

• Under the Shadow: Old-biased Genes Are Subject to Weak Purifying Selection at Both the Tissue- and Cell Type-Specific Levels.

  PMID 41092135 · PMC12569596 · Genome biology and evolution · 2025 · 7 claims · 6 setups

  Has reproduction · 93

  ADICT (age-related decrease in transcriptome conservation) is commonly found in ageing tissues of nonmammalian species, including chicken brain, killifish liver and skin, and fruit fly brain

  drosophila nothobranchius gallus heterocephalus bulk single-cell

• From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

  PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 6 setups

  Has reproduction · 59

  382 (over 383) genomic regions contain SNPs that are consistently zonated across all surveyed intertidal habitats spanning the North Atlantic.

  semibalanus individual rocky barnacles pool-seq sanger temperature

• Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

  PMID 16403238 · PMC1351203 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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  No NPC proteome database existed prior to this work despite availability of other cancer proteome databases

  nasopharyngeal excised subset monoisotopic 2-de maldi-tof q-tof

• Allelotyping of pooled DNA with 250 K SNP microarrays.

  PMID 17367522 · PMC1839100 · BMC genomics · 2007 · 8 claims · 5 setups

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  The polynomial based probe specific correction (PPC) algorithm is the most accurate method for estimating allele frequency from pooled DNA.

  pool nspi individual snp individual call

• Improved methods for the enrichment and analysis of glycated peptides.

  PMID 18989935 · PMC2752342 · Analytical chemistry · 2008 · 7 claims · 4 setups

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  Replacing off-line desalting with an online 50 mM NH4OAc wash (10 min) of boronate-bound glycated proteins improves the enrichment workflow while minimizing sample loss

  glucose-glycated tryptic glycated lc-ms boronate lc-etd-ms database

• Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

  PMID 18842124 · PMC2569949 · BMC genomics · 2008 · 7 claims · 7 setups

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  GS-FLX pyrosequencing of pooled amplicons detects sequence variants with high specificity (99.95%) and no false negatives at ≥30× coverage

  pools pcr genomic gs-flx massively sanger pcr