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).

• Determination of point mutational spectra of benzo[a]pyrene-diol epoxide in human cells.

  PMID 1486852 · PMC1519600 · Environmental health perspectives · 1992 · 5 claims · 4 setups

  Full-text index only

  A new protocol combining en masse 6-thioguanine-resistant mutant selection, high-fidelity PCR amplification, and DGGE separation can determine point mutational spectra in human cells with high precision and reproducibility

  tk6 184-bp reconstruction point melting

• Calibration-free NGS quantitation of mutations below 0.01% VAF.

  PMID 34675197 · PMC8531361 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 96

  QBDA (Quantitative Blocker Displacement Amplification) integrates UMI molecular barcoding with BDA variant enrichment to enable calibration-free VAF quantitation

  h37rv repository healthy same single-plex 10-plex 22-plex

• Ultra-deep multi-oncopanel sequencing of benchmarking samples with a wide range of variant allele frequencies.

  PMID 35680918 · PMC9184574 · Scientific data · 2022 · 8 claims · 8 setups

  Has reproduction · 82

  Four reference samples (Sample A, Sample B, Sample C, Sample Spike-in/AC5) were developed with large numbers of high-confidence positive and negative small variant positions to serve as known content for oncopanel performance assessment.

  agilent burning integrated igenetech targeted

• Expression and Secretion of Circular RNAs in the Parasitic Nematode, Ascaris suum.

  PMID 35711944 · PMC9194832 · Frontiers in genetics · 2022 · 8 claims · 7 setups

  Has reproduction · 20

  A. suum expresses 1,997 distinct circRNAs identified via next-generation sequencing in adult female body wall and ovary-enriched tissue

  suum circrna qrt-pcr drug

• ChIP-seq Data Processing and Relative and Quantitative Signal Normalization for Saccharomyces cerevisiae.

  PMID 40364978 · PMC12067309 · Bio-protocol · 2025 · 8 claims · 6 setups

  Has reproduction · 100

  siQ-ChIP measures absolute protein–DNA interaction (IP efficiency) genome-wide without relying on exogenous spike-in chromatin, overcoming limitations of spike-in normalization.

  cerevisiae pombe concatenated chip-seq chip-seq high-throughput fastq

• Nimbus: a design-driven analyses suite for amplicon-based NGS data.

  PMID 29538618 · PMC6084620 · Bioinformatics (Oxford, England) · 2018 · 7 claims · 4 setups

  Has reproduction · 64

  Nimbus is an end-to-end software suite for amplicon-based NGS data that tracks source amplicons through alignment and variant calling, with tools for trimming, alignment, SNP/InDel calling, QC and visualization.

  blood twin na15510 haloplex snp whole-exome

• Whole genome amplification and de novo assembly of single bacterial cells.

  PMID 19724646 · PMC2731171 · PloS one · 2009 · 8 claims · 6 setups

  Full-text index only

  FACS-based single-cell isolation combined with strict handling procedures virtually eliminates contaminating DNA from single-cell MDA reactions

  prochlorococcus single-cell seven sag genome spike-in amplification

• DMN-seq enriches DNA hypomethylated regions for biomarker discovery using 5-methylcytosine glycosylase.

  PMID 41673887 · PMC13097799 · Genome biology · 2026 · 7 claims · 8 setups

  Has reproduction · 80

  DME-mediated nicking enables DMN-seq (DMN+) to detect 5mC at single-base resolution by ligating adaptors only to 5mC-containing fragments generated by DME excision

  synthetic partially embryonic mesc dmn+ ubs-seq dmn–

• Early noninvasive prenatal detection of a fetal CRB1 mutation causing Leber congenital amaurosis.

  PMID 18682814 · PMC2493031 · Molecular vision · 2008 · 8 claims · 6 setups

  Full-text index only

  dHPLC detected the paternally inherited fetal CRB1 mutation (p.Cys896ter) in maternal plasma collected at 12 weeks gestation

  maternal serial genomic chorion dhplc automated pcr

• Identification and recovery of minor HIV-1 variants using the heteroduplex tracking assay and biotinylated probes.

  PMID 18948297 · PMC2602764 · Nucleic acids research · 2008 · 6 claims · 8 setups

  Full-text index only

  Incorporating a biotin tag into the HTA probe enables purification of labeled heteroduplexes and direct sequencing of the separated query strand, allowing recovery of minor variant sequences

  hiv-1 biotin-hta-purified original recovered heteroduplex rt-pcr sanger

• Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

  PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

  Full-text index only

  aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

  pediatric tumor eight desmoplastic aprimes bisulfite quantitative