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).

• 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

• Integrative Transcriptomic and Evolutionary Analysis of Drought and Heat Stress Responses in Solanum tuberosum and Solanum lycopersicum.

  PMID 41470732 · PMC12736803 · Plants (Basel, Switzerland) · 2025 · 7 claims · 8 setups

  Has reproduction · 84

  Drought and heat stress induce coordinated transcriptional reprogramming in potato and tomato: induction of molecular chaperone activity, oxidative stress responses, and immune signaling, with repression of photosynthetic and primary metabolic pathways reflecting energy reallocation.

  solanum bulk term novo

• Conservation and losses of non-coding RNAs in avian genomes.

  PMID 25822729 · PMC4378963 · PloS one · 2015 · 8 claims · 6 setups

  Has reproduction · 100

  Homology-based covariance model (Rfam CM) annotation, combined with tRNAscan-SE and miRBase-derived models, identifies ncRNA loci across 48 avian genomes

  avian bird chicken covariance trna microrna

• Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.

  PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 8 claims · 7 setups

  Has reproduction

  Increasing salinity to ≥43 ppt inhibits Trichodesmium growth while stimulating growth of the associated Alteromonas

  alteromonas trichodesmium differential classical smrt

• Cell type- and species-specific regulation of hepatic lncRNAs by TCDD-activated aryl hydrocarbon receptor.

  PMID 41136526 · PMC12552753 · Scientific reports · 2025 · 8 claims · 6 setups

  Has reproduction · 71

  AHR-mediated lncRNA dysregulation may be a contributing mechanism in TCDD-elicited progression of steatosis to steatohepatitis with fibrosis

  liver mm39 bulk single-nuclei ahr

• Interplay between Non-Coding RNA Transcription, Stringent/Relaxed Phenotype and Antibiotic Production in Streptomyces ambofaciens.

  PMID 34438997 · PMC8388888 · Antibiotics (Basel, Switzerland) · 2021 · 8 claims · 5 setups

  Has reproduction · 49

  The S. ambofaciens ATCC 23877 transcriptome was redefined from RNAseq data into 5587 transcriptional units (4433 monocistronic, 1154 polycistronic) covering 90.8% of the linear chromosome

  streptomyces ambofaciens bulk rna-seq target

• RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

  PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 38

  A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

  gossypium uppermost root reads bulk leaf rt-qpcr

• Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

  PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

  erwinia intergenic candidate wounded small northern race

• OptiType: precision HLA typing from next-generation sequencing data.

  PMID 25143287 · PMC4441069 · Bioinformatics (Oxford, England) · 2014 · 8 claims · 8 setups

  Has reproduction · 95

  OptiType, an ILP-based HLA genotyping algorithm, produces accurate four-digit HLA-I predictions from NGS data not enriched for the HLA cluster.

  colorectal lymphoblastic hapmap genomes rna-seq low-coverage exome

• Phylogenetic analysis of higher-level relationships within Hydroidolina (Cnidaria: Hydrozoa) using mitochondrial genome data and insight into their mitochondrial transcription.

  PMID 26618080 · PMC4655093 · PeerJ · 2015 · 8 claims · 8 setups

  Has reproduction · 68

  Siphonophorae is the first diverging clade within Hydroidolina.

  hydroidolinan nanomia liriope assembled long-range rna-seq dna-seq

• A Meta-Analysis of Wolbachia Transcriptomics Reveals a Stage-Specific Wolbachia Transcriptional Response Shared Across Different Hosts.

  PMID 32718933 · PMC7467002 · G3 (Bethesda, Md.) · 2020 · 7 claims · 8 setups

  Has reproduction · 89

  Across datasets re-analyzed with a unified workflow, there is a general lack of global Wolbachia gene regulation.

  wolbachia wbm differentially rna-seq comparative co-expression

• 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

• Horizontal transmission enables flexible associations with locally adapted symbiont strains in deep-sea hydrothermal vent symbioses.

  PMID 35349333 · PMC9168483 · Proceedings of the National Academy of Sciences of the United States of America · 2022 · 8 claims · 6 setups

  Has reproduction · 66

  Host populations of Alviniconcha and Ifremeria are not genetically differentiated across an ~800-km geographic gradient

  gill chemosynthetic host epsilon rna-seq-based metagenomic phylogenomic

• Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

  PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups

  Has reproduction · 100

  Hsp90-dependent gene expression varies among different yeast strains

  diverse same yeast genomes rna-seq v-src growth

• Polyploidy and the petal transcriptome of Gossypium.

  PMID 24393201 · PMC3890615 · BMC plant biology · 2014 · 8 claims · 8 setups

  Has reproduction · 51

  Most homoeologous gene pairs in polyploid cotton petals are expressed at equal levels, indicating a surprising level of expression homeostasis; only ~20% of expressed genes show significant genome bias.

  petal rna-seq commonly polyploid rna-seq read universal

• Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

  PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

  brassica r500 rapa genomic bulk reference-based snp

• HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.

  PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups

  Has reproduction · 66

  HTSstation is a web application suite coupling simple web forms to modular analysis pipelines for ChIP-seq, RNA-seq, 4C-seq and re-sequencing HTS applications, accessible at http://htsstation.epfl.ch.

  embryonic mycobacterium forebrain rna-seq re-sequencing 4c-seq

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

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

  Has reproduction · 57

  Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are diverse and abundant in the halite endolithic microbial community, with 1,538 total ncRNAs discovered across Archaea and Bacteria.

  halite discovered conserved itsrnas strand-specific genome-resolved srna

• 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

• Sequencing mRNA from cryo-sliced Drosophila embryos to determine genome-wide spatial patterns of gene expression.

  PMID 23951250 · PMC3741199 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 67

  Cryosectioning single blastoderm-stage D. melanogaster embryos along the A–P axis and sequencing mRNA from each slice yields reliable genome-wide spatial expression patterns.

  single methanol-fixed reads slice mrna-seq light-microscopy read