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).

• Hyb: a bioinformatics pipeline for the analysis of CLASH (crosslinking, ligation and sequencing of hybrids) data.

  PMID 24211736 · PMC3969109 · Methods (San Diego, Calif.) · 2014 · 8 claims · 6 setups

  Has reproduction · 71

  The 'hyb' pipeline detects, calls, folds and annotates chimeric reads from CLASH high-throughput sequencing data.

  ago1 test clash multiplexed clash benchmarking demultiplexing

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

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

  Full-text index only

  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

• Whole-Genome Sequence of Cervid atadenovirus A from the Initial Cases of an Adenovirus Hemorrhagic Disease Epizootic of Black-Tailed Deer in Canada.

  PMID 36129291 · PMC9584332 · Microbiology resource announcements · 2022 · 7 claims · 4 setups

  Has reproduction · 81

  A complete 30,616-nucleotide genome of Cervid atadenovirus A was determined from lung tissue of black-tailed deer that died of AHD in British Columbia in 2020

  lung sequencing assembled deer high-throughput metagenomic reference

• Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

  PMID 20011630 · PMC2790479 · Molecular vision · 2009 · 8 claims · 5 setups

  Full-text index only

  MDH1 is not the causative gene for RP28-linked autosomal recessive retinitis pigmentosa

  genomic lr-pcr uhts v-4 long-range ultra sanger

• Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

  PMID 24782521 · PMC4066758 · Nucleic acids research · 2014 · 8 claims · 5 setups

  Has reproduction · 79

  EDD is a new algorithm that detects broad (megabase-size) enrichment domains from ChIP-seq data of widely distributed chromatin proteins such as A- and B-type lamins.

  normal dermal analysis set chip-seq chip-qpcr rna-seq

• Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.

  PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 78

  In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.

  aeruginosa differentially paired rna-seq tn-seq computational

• High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro.

  PMID 35776646 · PMC9243297 · STAR protocols · 2022 · 8 claims · 8 setups

  Has reproduction · 65

  HT-SELEX enables unbiased, in vitro determination of preferred DNA target motifs for DNA-binding proteins by iterative selection and PCR amplification of bound oligonucleotides

  synthetic pcr-generated selex histidine-tagged pcr polyacrylamide spectrophotometry

• ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia.

  PMID 22955991 · PMC3431496 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 74

  ENCODE/modENCODE define a set of working standards and guidelines for ChIP-seq covering antibody validation, experimental replication, sequencing depth, data/metadata reporting, and data quality assessment.

  small-genome nuclear whole-cell encode chip-seq chip-chip immunoblot

• Massively parallel genomic perturbations with multi-target CRISPR interrogates Cas9 activity and DNA repair at endogenous sites.

  PMID 36064968 · PMC9481459 · Nature cell biology · 2022 · 8 claims · 6 setups

  Has reproduction · 98

  Multi-target gRNAs (mgRNAs) can direct Cas9 to over a hundred well-mapped endogenous genomic sites simultaneously, enabling massively parallel, high-throughput interrogation of Cas9 activity via short-read sequencing

  hg38 hela hek293t induced genome-wide high-throughput chip-seq

• 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

• GenBank.

  PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

  Full-text index only

  GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

  sapiens organisms genbank large-scale genome expressed blast