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 consensus approach to vertebrate de novo transcriptome assembly from RNA-seq data: assembly of the duck (Anas platyrhynchos) transcriptome.

  PMID 25009556 · PMC4070175 · Frontiers in genetics · 2014 · 8 claims · 8 setups

  Has reproduction · 67

  Multiple k-mer (MK) assemblies are more complete than single k-mer (SK) assemblies, showing higher reads-mapped-back-to-transcripts (RMBT) and higher CEGMA complete-gene percentages for all three tools.

  anas duck million random illumina read novo

• 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 haplotype-complete chromosome-level assembly of octoploid Urochloa humidicola cv. Tully reveals multiple genomic compositions and evolutionary histories in the species.

  PMID 41678351 · PMC13042314 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

  Full-text index only

  A haplotype-complete, chromosome-level genome assembly of octoploid U. humidicola cv. Tully was generated from PacBio HiFi reads alone

  humidicola chromosomes urochloa additional pacbio busco proteome

• A transcriptome sequence dataset characterizing eggs, nymphs and adults of Oxycarenus hyalinipennis, the cotton seed bug.

  PMID 41717652 · PMC12915258 · Data in brief · 2026 · 8 claims · 8 setups

  Full-text index only

  This dataset provides the first transcriptomic resources for the invasive pest Oxycarenus hyalinipennis

  whole-insect cross assembled global rna-seq differential sequence

• De Novo Assembly and Annotation of the Larval Transcriptome of Two Spadefoot Toads Widely Divergent in Developmental Rate.

  PMID 31217263 · PMC6686947 · G3 (Bethesda, Md.) · 2019 · 8 claims · 8 setups

  Has reproduction · 91

  De novo transcriptome assemblies were generated for larval P. cultripes and S. couchii, providing new genomic resources for spadefoot toads

  whole-body cultripes expression-filtered bulk novo transcriptome

• Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.

  PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups

  Has reproduction · 100

  Molecular techniques such as RT-PCR only allow detection of known viruses, with each test specific to one or a small number of related viruses, so unknown viruses can be missed

  garlic pepper pear grapevine rna-seq srna-seq

• Human endogenous retrovirus profiling reveals heterogenous expression in cutaneous melanoma.

  PMID 41971443 · PMC13061668 · Frontiers in oncology · 2026 · 7 claims · 8 setups

  Full-text index only

  HERV expression differs between primary and metastatic cutaneous melanoma

  tcga-skcm metastatic normal selected bulk consensus orf

• Integration of a neuronal RNAseq dataset with the draft Gryllus bimaculatus transcriptome refines gene predictions and highlights potential systematic response to injury.

  PMID 42054377 · PMC13127959 · PloS one · 2026 · 8 claims · 7 setups

  Full-text index only

  Integrating prothoracic ganglion RNAseq data with the draft genome refines gene predictions, adding 3,868 novel genes and 9,172 new transcript isoforms (including non-coding transcripts)

  bimaculatus prothoracic differentially gbig rna-seq genome differential

• Epigenetic profiling of hematopoietic stem cells from male mice identifies KDR and PU.1 as regulators of aging transcriptome and caloric restriction response.

  PMID 41720793 · PMC13035812 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  Lifelong CR reduces white blood cell production and shifts hematopoiesis toward myeloid and thrombo-erythroid lineages while suppressing lymphoid output

  peripheral sorted young aged complete flow bulk

• 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

• 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

• A comparative study of techniques for differential expression analysis on RNA-Seq data.

  PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 58

  edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

  brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq

• De novo assembly of a transcriptome for Calanus finmarchicus (Crustacea, Copepoda)--the dominant zooplankter of the North Atlantic Ocean.

  PMID 24586345 · PMC3929608 · PloS one · 2014 · 8 claims · 8 setups

  Has reproduction · 59

  A de novo transcriptome for Calanus finmarchicus was assembled from six developmental-stage libraries, yielding 206,041 contigs and a reference set of 96,090 unique comps, representing a new molecular resource for this species.

  calanus pooled raw combined bulk extraction read

• Data-driven projections of candidate enhancer-activating SNPs in immune regulation.

  PMID 40011812 · PMC11863423 · BMC genomics · 2025 · 7 claims · 7 setups

  Has reproduction · 57

  A data-driven computational protocol combining motif scanning, open-chromatin filtering, gene proximity, dbSNP validation, spacing, and cross-species conservation can prioritize SNPs likely to create functional GAS motifs.

  genome pbmc lung il4-stimulated motif chip-seq bulk

• Ordinal-level phylogenomics of the arthropod class Diplopoda (millipedes) based on an analysis of 221 nuclear protein-coding loci generated using next-generation sequence analyses.

  PMID 24236165 · PMC3827447 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 82

  An ordinal-level phylogeny of Diplopoda reconstructed from 221 nuclear protein-coding loci (61,641 aligned amino acid columns) differs from existing classifications in fundamental ways.

  exemplar paired-end cleaned assembled transcriptome read novo

• Eukan: a fully automated nuclear genome annotation pipeline for less studied and divergent eukaryotes.

  PMID 41567515 · PMC12817076 · NAR genomics and bioinformatics · 2026 · 8 claims · 7 setups

  Full-text index only

  Eukan automatically leverages RNA-Seq coverage to inform generalized Hidden Markov Model gene prediction and intron lengths to inform protein sequence alignments

  taxonomically paired-end rna-seq reference automated rna-seq novo

• Dynamics of the compartmentalized Streptomyces chromosome during metabolic differentiation.

  PMID 34471117 · PMC8410849 · Nature communications · 2021 · 8 claims · 5 setups

  Has reproduction · 97

  Chromosome structure correlates with genetic compartmentalization during exponential phase in S. ambofaciens

  ambofaciens comparative antismash rna-seq

• Analysis and comprehensive comparison of PacBio and nanopore-based RNA sequencing of the Arabidopsis transcriptome.

  PMID 32536962 · PMC7291481 · Plant methods · 2020 · 8 claims · 8 setups

  Has reproduction · 57

  ONT Pc produces higher raw data quality (higher alignment rate, lower error rate) than ONT Dc, while PacBio generates the longest reads

  arabidopsis pacbio randomly illumina pacbio nanopore

• Analysis of the genome of the New Zealand giant collembolan (Holacanthella duospinosa) sheds light on hexapod evolution.

  PMID 29041914 · PMC5644144 · BMC genomics · 2017 · 8 claims · 8 setups

  Has reproduction · 72

  Phylogenomic analysis (370,877 amino acids) placed H. duospinosa within the family Neanuridae

  holacanthella duospinosa genome transcriptome phylogenomics

• AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.

  PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures

  gene keratinocyte-derived ffpe spt6-depleted boolean rna-seq immunohistochemistry