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).

• GAL08, an Uncultivated Group of Acidobacteria, Is a Dominant Bacterial Clade in a Neutral Hot Spring.

  PMID 35087491 · PMC8787282 · Frontiers in microbiology · 2021 · 8 claims · 8 setups

  Has reproduction · 50

  GAL08 is a dominant bacterial clade in a neutral hot spring, comprising up to 29.2% of the community by relative read abundance and up to 4.7 × 10^5 16S rRNA gene copies per gram sediment.

  dewar dchs_gal08 hoodoo gal08 16s qpcr single

• Organelle Genomes and Transcriptomes of Nymphaea Reveal the Interplay between Intron Splicing and RNA Editing.

  PMID 34576004 · PMC8466565 · International journal of molecular sciences · 2021 · 8 claims · 7 setups

  Has reproduction · 76

  Multiple partially or fully intron-spliced intermediates co-exist within an organelle, and both cis- and trans-splicing introns are spliced randomly (no fixed order), generating diverse intermediates.

  nymphaea liriodendron pacbio illumina strand-specific

• Mixed Cryptosporidium infections and HIV.

  PMID 16707069 · PMC3373040 · Emerging infectious diseases · 2006 · 7 claims · 5 setups

  Full-text index only

  Mixed Cryptosporidium infections were detected in 7 of 21 patients originally diagnosed with only C. canis or C. felis

  stool nested ssu sequencing

• Prevalence of A2143G mutation of H. pylori-23S rRNA in Chinese subjects with and without clarithromycin use history.

  PMID 18507832 · PMC2427034 · BMC microbiology · 2008 · 7 claims · 6 setups

  Full-text index only

  A2143G point mutation of the H. pylori 23S rRNA gene causes clarithromycin resistance

  fasting subjects serum pylori pcr 13c-urea elisa

• Deep transcriptomics reveals cell-specific isoforms of pan-neuronal genes.

  PMID 40379625 · PMC12084633 · Nature communications · 2025 · 8 claims · 5 setups

  Has reproduction · 84

  Pan-neuronal genes (expressed in many/all neurons) harbor highly cell-specific splice variants/isoforms restricted to single or few neuron types.

  elegans short-read whole-animal rt-pcr

• An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.

  PMID 19838300 · PMC2759515 · PloS one · 2009 · 8 claims · 7 setups

  Full-text index only

  An nc-rRNA is transcribed from the intergenic spacer upstream of the rRNA transcription start site in human lung epithelial and lung cancer cells, spanning roughly -1000 to at least +203/+300.

  lung hpl1d rrna external pcr rt-pcr quantitative

• Different Intestinal Microbiota with Growth Stages of Three-Breed Hybrid Pig.

  PMID 35978648 · PMC9377885 · BioMed research international · 2022 · 7 claims · 5 setups

  Has reproduction · 75

  The composition and relative abundance of intestinal microbiota in three-breed hybrid pigs differ significantly across growth stages (60, 120, 180 days)

  fecal same 16s otu alpha

• High-resolution metagenomic reconstruction of the freshwater spring bloom.

  PMID 36698172 · PMC9878933 · Microbiome · 2023 · 8 claims · 8 setups

  Has reproduction · 69

  High-frequency metagenomic sampling (57 samples, 3 filter sizes, 2 depths, 37 days) recovers thousands of prokaryotic, eukaryotic, and viral genomes tracking spring bloom succession in fine detail

  freshwater phytoplankton heterotrophic reservoir 16s 18s shotgun

• Comparison of RNA-Seq by poly (A) capture, ribosomal RNA depletion, and DNA microarray for expression profiling.

  PMID 24888378 · PMC4070569 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 77

  Ribo-Zero-Seq removes rRNA with efficiency comparable to poly(A)-based mRNA-Seq in both FF and FFPE RNA, whereas DSN-Seq leaves significantly more rRNA and shows greater variation.

  fresh-frozen ffpe breast unc microarray mrna-seq ribo-zero-seq

• R2DT is a framework for predicting and visualising RNA secondary structure using templates.

  PMID 34108470 · PMC8190129 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 87

  R2DT is a template-based computational framework/pipeline that predicts and visualises RNA 2D structure in standardised, community-accepted layouts

  rnacentral query input aligned covariance trna-specific structure-guided

• A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.

  PMID 36333777 · PMC9636832 · Microbiome · 2022 · 7 claims · 6 setups

  Has reproduction · 64

  Genome-resolved metagenomics of separated foregut and midgut reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut) and Deferribacteres (midgut).

  rimicaris foregut deferribacteres shotgun fluorescence yoyo-1

• Genotyping, Orientalis-like Yersinia pestis, and plague pandemics.

  PMID 15498160 · PMC3320270 · Emerging infectious diseases · 2004 · 6 claims · 6 setups

  Full-text index only

  Multiple spacer typing (MST), based on intergenic spacer sequencing, differentiates the three Y. pestis biovars

  pestis combined dental contemporary spacer phylogenetic pcr

• binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

  PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups

  Has reproduction · 67

  binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

  cami real-world metagenomic binned genome binning mag

• Headloop suppression PCR and its application to selective amplification of methylated DNA sequences.

  PMID 16091627 · PMC1184225 · Nucleic acids research · 2005 · 8 claims · 5 setups

  Full-text index only

  Headloop PCR: a 5' primer extension homologous to internal amplicon sequence causes hairpin formation after incorporation, suppressing further amplification of the matching sequence while unaffected sequences amplify normally

  plasmid genomic bacterial real-time methylation-specific

• Detection of genetic association and a functional polymorphism of dynamin 1 gene with nicotine dependence in European and African Americans.

  PMID 18987626 · PMC2656577 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 8 claims · 5 setups

  Full-text index only

  DNM1 SNP rs3003609 is significantly associated with Smoking Quantity (SQ) and Heaviness of Smoking Index (HSI) in the European-American (EA) sample, surviving correction for multiple testing.

  nuclear same sh-sy5y snp haplotype-based quantitative

• Epigenetics and phenotypic variation in mammals.

  PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

  Full-text index only

  Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

  mammalian mhc chromosomes embryonic methylation high-throughput chip

• Optimal scaling of digital transcriptomes.

  PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.

  tissues bodymap mapped 16-sample bulk read transcript