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 Deeper Insight into Evolutionary Patterns and Phylogenetic History of ASFV Epidemics in Sardinia (Italy) through Extensive Genomic Sequencing.

  PMID 34696424 · PMC8539718 · Viruses · 2021 · 7 claims · 8 setups

  Has reproduction · 76

  58 new whole genomes of Sardinian ASFV isolates were sequenced, the largest ASFV whole-genome sequencing effort to date

  asfv b602l porcine sardinian whole-genome sanger haemoadsorption

• Genome-wide siRNA-based functional genomics of pigmentation identifies novel genes and pathways that impact melanogenesis in human cells.

  PMID 19057677 · PMC2585813 · PLoS genetics · 2008 · 7 claims · 8 setups

  Full-text index only

  Genome-wide siRNA screening identified 92 novel genes that support melanin production in human melanocytes with a low false discovery rate.

  mnt-1 melanocyte melanocytes genome-wide secondary quantitative

• Biodefense versus bioterrorism.

  PMID 18771576 · PMC2575524 · Genome biology · 2008 · 5 claims · 4 setups

  Full-text index only

  Whole-genome sequencing and comparative genomics of the attack strain were used to trace the anthrax letters to a specific laboratory flask

  bacillus ancestral cultures anthrax whole-genome comparative colony

• Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.

  PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 5 setups

  Has reproduction

  Expression stability in CHO cell lines is controlled at three levels: choice of integration site, transgene integrity/concatemerization pattern, and stress-related cellular processes.

  horizon same cho genome rna-seq targeted

• Discovery of a novel filamentous prophage in the genome of the Mimosa pudica microsymbiont Cupriavidus taiwanensis STM 6018.

  PMID 36925474 · PMC10011098 · Frontiers in microbiology · 2023 · 8 claims · 8 setups

  Has reproduction · 74

  The STM 6018 genome contains two prophages: a complete Mu-like capsular phage and a filamentous phage that integrates into a putative dif site.

  cupriavidus stm taiwanensis genome 16s average

• High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.

  PMID 23222129 · PMC3553938 · Nucleic acids research · 2013 · 8 claims · 7 setups

  Has reproduction · 69

  NusA interacts with RNAP ubiquitously throughout the M. tuberculosis chromosome and its ChIP-seq profile mirrors RNAP distribution in both exponential and stationary phase, despite NusA not binding DNA directly.

  mycobacterium tuberculosis chip-seq input strand-specific

• Genome-wide analysis of KAP1 binding suggests autoregulation of KRAB-ZNFs.

  PMID 17542650 · PMC1885280 · PLoS genetics · 2007 · 8 claims · 7 setups

  Full-text index only

  H3me3K9 and H3me3K27 mark largely mutually exclusive, distinct classes of transcription factor genes: H3me3K9 at ZNF genes, H3me3K27 at homeobox genes

  ntera2 fibroblasts chip-chip chip-pcr expression

• Genome mapping and expression analyses of human intronic noncoding RNAs reveal tissue-specific patterns and enrichment in genes related to regulation of transcription.

  PMID 17386095 · PMC1868932 · Genome biology · 2007 · 8 claims · 4 setups

  Full-text index only

  More than 55,000 totally intronic noncoding (TIN) RNAs are transcribed from the introns of 74% of unique RefSeq genes.

  dbest liver cultures refseq est oligoarray polymerase

• Parasitic connections: a patescibacterial epibiont, its methylotrophic gammaproteobacterial host, and their phages.

  PMID 41805398 · PMC13059738 · mBio · 2026 · 8 claims · 7 setups

  Full-text index only

  Strigamonas methylophilicida sp. nov. is a new patescibacterial genus and species within the family Absconditicoccaceae

  freshwater fixed rsa individual phase transmission fluorescence-activated

• Systems biology of gene regulation fulfills its promise.

  PMID 16719937 · PMC1779525 · Genome biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Suz12, a Polycomb Group complex component, has DNA targets identifiable by ChIP-chip and can silence large genomic regions in a cell-type-specific manner.

  unspecified embryonic five yeast chip-chip chip-pet computational

• Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics.

  PMID 36854789 · PMC10119117 · The ISME journal · 2023 · 8 claims · 4 setups

  Has reproduction · 84

  Across all 16 replicate co-cultures of P. putida and P. lacustris, bacteria show a consistent succession of defense strategies over five weeks (~35 predator generations).

  pseudomonas filamentous axenically semi-continuous morphometric whole-genome

• The rates of adult neurogenesis and oligodendrogenesis are linked to cell cycle regulation through p27-dependent gene repression of SOX2.

  PMID 36627412 · PMC9832098 · Cellular and molecular life sciences : CMLS · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  p27 restricts residual CDK activity after mitogen withdrawal to antagonize cell cycling, but is not essential for cell cycle exit per se

  sez-derived computational nsc npc atac-seq bulk lisa

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse

• Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.

  PMID 32019831 · PMC7002113 · mSystems · 2020 · 7 claims · 8 setups

  Has reproduction · 57

  Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are expressed in the halite endolithic microbial community of the Atacama Desert

  halite same identified conserved strand-specific genome-resolved srna

• The dynamic distribution of genetic tandem amplifications in a heteroresistant Escherichia coli population revealed by ultra-deep long read sequencing.

  PMID 41760616 · PMC12953903 · Nature communications · 2026 · 8 claims · 6 setups

  Full-text index only

  Ultra-deep Nanopore sequencing of I-SceI-linearized plasmid DNA can detect and quantify full tandem amplification arrays at single-molecule resolution down to frequencies of 10^-5

  coli ultra-deep short-read digital

• Evolutionary repair: Changes in multiple functional modules allow meiotic cohesin to support mitosis.

  PMID 32155147 · PMC7138332 · PLoS biology · 2020 · 8 claims · 7 setups

  Has reproduction · 90

  Replacing Scc1 with Rec8 in mitosis impairs sister chromosome cohesion, advances the timing of genome replication, and reduces reproductive fitness by 45%

  saccharomyces cerevisiae competitive live-cell flow

• Systematic Assessment of Small RNA Profiling in Human Extracellular Vesicles.

  PMID 37444556 · PMC10340377 · Cancers · 2023 · 8 claims · 6 setups

  Has reproduction · 90

  EV extraction methods vary in reproducibility for isolating small RNAs, with effects on small RNA composition

  evs matched plasma cell-line small differential adapter

• Directing stem cell differentiation by chromatin state approximation.

  PMID 41734818 · PMC12956330 · Nucleic acids research · 2026 · 8 claims · 8 setups

  Full-text index only

  Greedy selection of culture conditions by chromatin (ATAC-seq) distance to target is a viable optimisation strategy for differentiation protocols

  cd34+ cd34+-derived erythroid bone atac-seq flow rt-qpcr

• The fungal pathogen Rhizoctonia solani AG-8 has 2 nuclear haplotypes that differ in abundance.

  PMID 41124349 · PMC12774589 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

  Full-text index only

  R. solani isolates AG8-1 and AG8-3 each possess 2 distinct nuclear haplotypes, each ~50 Mbp assembled into 16 chromosomes

  solani ag8-1 rhizoctonia annotated pacbio hi-c stranded

• Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.

  PMID 27092297 · PMC4820441 · Frontiers in cellular and infection microbiology · 2016 · 6 claims · 8 setups

  Has reproduction · 89

  STEC prevalence in surface water varies by watershed and by season in the Lower Mainland of British Columbia.

  surface sediment isolate presumptive hydrophobic stx monoplex