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).

• Gene Expression Patterns Regulating Peanut Reproductive Phenology.

  PMID 42099581 · PMC13147162 · Plant direct · 2026 · 8 claims · 6 setups

  Full-text index only

  Overall gene expression was distinct between Tifrunner and GT-C20 in both leaf and shoot tip tissues

  leaf deseq2 shoot gene bulk differential principal

• Strawberry atlas: Fragaria vesca gene expression atlas for strawberry genomics.

  PMID 41664659 · PMC12883160 · PeerJ · 2026 · 8 claims · 8 setups

  Full-text index only

  A consolidated gene expression atlas of F. vesca built from 233 RNA-seq libraries across nine tissue categories, aligned to the v6 T2T reference genome, was constructed.

  vesca bulk rna-seq qpcr

• Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing.

  PMID 30476109 · PMC6320677 · Genome biology and evolution · 2019 · 8 claims · 8 setups

  Has reproduction · 87

  Subgenus Houzingenia likely originated via transoceanic dispersal from Africa about 6.6 Ma

  leaf trimmed species concatenated genome novo reference-assisted

• De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform.

  PMID 29451882 · PMC5815590 · PloS one · 2018 · 8 claims · 7 setups

  Has reproduction · 45

  This is the first de novo transcriptomic analysis of C. officinalis leaf and fruit tissue, performed using the Illumina HiSeq 4000 platform.

  cornus pooled assembled leaf rna-seq novo functional

• Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.

  PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  Nearly all (99.4%) ancient paralog pairs in Gossypium raimondii are differentially expressed in at least one of three tissues (petal, leaf, seed), indicating massive, near-complete expression-level divergence.

  gossypium transcripts uq-normalized differentially comparative coding bulk

• A phased, near-telomere-to-telomere chromosome-scale reference genome of the Moroccan argan tree.

  PMID 41673035 · PMC13002930 · Scientific data · 2026 · 8 claims · 7 setups

  Full-text index only

  Generated a chromosome-scale, phased reference genome of Argania spinosa using PacBio HiFi long reads combined with Hi-C scaffolding

  argania pacbio assembled pacbio hi-c rna-seq

• The genome sequence of the sweet violet, Viola odorata L. (Malpighiales: Violaceae).

  PMID 41960579 · PMC13058574 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  The Viola odorata genome assembly has a total length of 698.62 megabases, with 99.9% scaffolded into 10 chromosomal pseudomolecules.

  viola flow barcoding pacbio

• A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.

  PMID 37936069 · PMC10629022 · BMC genomics · 2023 · 8 claims · 4 setups

  Has reproduction

  Hypersensitive response (HR) accompanied by systemic acquired resistance is the primary contributor to resistance against purple curl leaf disease in agave

  agave bulk wgcna qpcr

• Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions.

  PMID 37085932 · PMC10120106 · Environmental microbiome · 2023 · 8 claims · 8 setups

  Has reproduction · 59

  Root and corm endosphere communities are significantly richer and compositionally distinct from leaf endosphere communities across Musa genotypes

  root musa assembled prokka-annotated shotgun culture-free metagenome

• Comparative transcriptome analysis of tomato (Solanum lycopersicum) in response to exogenous abscisic acid.

  PMID 24289302 · PMC4046761 · BMC genomics · 2013 · 8 claims · 7 setups

  Has reproduction · 63

  Exogenous ABA alters the expression of a majority (54.73%) of expressed tomato leaf transcripts, with 2,787 significantly differentially expressed genes, predominantly up-regulated.

  tomato assembled illumina read functional

• Serial Spatial Transcriptomes Reveal Regulatory Transitions in Maize Leaf Development.

  PMID 41493197 · PMC13110159 · Plant biotechnology journal · 2026 · 8 claims · 5 setups

  Full-text index only

  An optimised Visium spatial transcriptomics protocol (two-step OCT embedding combined with OCT-Immersion First cryopreservation) preserves high-integrity RNA from fragile plant tissues such as SAM

  maize integrated spatial integrity dimensional

• The genome sequence of the Roundleaf geranium, Geranium rotundifolium L. (Geraniales: Geraniaceae).

  PMID 42021764 · PMC13096780 · Wellcome open research · 2026 · 8 claims · 8 setups

  Full-text index only

  The genome assembly of Geranium rotundifolium has a total length of 497.00 megabases, with 97.57% scaffolded into 13 chromosomal pseudomolecules.

  leaf silica-dried pacbio alternate flow barcoding pacbio

• Stem rust resistance in wheat is suppressed by a subunit of the mediator complex.

  PMID 32111840 · PMC7048732 · Nature communications · 2020 · 8 claims · 8 setups

  Has reproduction · 95

  SuSr-D1 encodes Med15b.D, a subunit of the Mediator complex

  wheat flow-sorted uninoculated med15 seedling plant flow-sorted

• Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.

  PMID 35931984 · PMC9356423 · BMC genomics · 2022 · 8 claims · 8 setups

  Has reproduction

  114 CNGC genes were identified across the genomes of four cotton species (G. arboreum, G. raimondii, G. barbadense, G. hirsutum)

  arboreum cotton hirsutum ghcngc genome-wide phylogenetic gene

• Comprehensive Transcriptome Analysis Reveals Genome-Wide Changes Associated with Endoplasmic Reticulum (ER) Stress in Potato (Solanum tuberosum L.).

  PMID 36430273 · PMC9696714 · International journal of molecular sciences · 2022 · 8 claims · 3 setups

  Has reproduction · 62

  TM treatment of potato leaves produces widespread, time-dependent differential gene expression associated with ER stress and the UPR

  potato rna-seq gene alternative

• Chromosome-scale genome assembly for yellow wood sorrel, Oxalis stricta.

  PMID 41482730 · PMC12958822 · G3 (Bethesda, Md.) · 2026 · 8 claims · 8 setups

  Full-text index only

  O. stricta genome assembly is chromosome-scale, 436 Mb, spanning 12 chromosomes across 2 subgenomes

  stricta long-read short-read hi-c

• Chemically guided single-cell transcriptomics reveals sulfotransferase-mediated scaffold remodeling in securinine biosynthesis.

  PMID 41577683 · PMC12929733 · Nature communications · 2026 · 8 claims · 8 setups

  Full-text index only

  FsMS is a ketoreductase that reduces premenisdaurilide to menisdaurilide

  suffruticosa synthetic nicotiana pacbio single-cell d2o

• Unveiling the early defense response dynamics in grapevines against Plasmopara viticola by single-cell transcriptomics.

  PMID 41593733 · PMC12918531 · Genome biology · 2026 · 8 claims · 5 setups

  Full-text index only

  Generated the first single-cell transcriptome atlas (scRNA-seq + spRNA-seq) of grapevine leaves during P. viticola infection across four early time points (0, 3, 6, 12 hpi)

  vitis guard cabernet tissue-specific single-cell spatial pseudo-time

• Multiomics combined drugs to explore the potential mechanism and treatment of ankylosing spondylitis.

  PMID 41673882 · PMC13047816 · Journal of orthopaedic surgery and research · 2026 · 8 claims · 8 setups

  Full-text index only

  Effector CD8+ memory T (Tem) cells are significantly elevated in AS patients compared to healthy controls

  bone peripheral effector interspinous single-cell cibersortx cell-cell

• Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize.

  PMID 33705553 · PMC8195531 · Plant physiology · 2021 · 8 claims · 4 setups

  Has reproduction · 76

  Increasing maximum daily temperature (MDT) elevates the frequency of alternative splicing in maize leaves, particularly intron retention (IR) and exon skipping (ES).

  maize rna-seq gene differential