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).
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Has reproduction · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases
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Has reproduction · 27
Transcriptome profiling of radish (Raphanus sativus L.) root and identification of genes involved in response to Lead (Pb) stress with next generation sequencing.
PMID 23840502 · PMC3688795 · PloS one · 2013 · 8 claims · 5 setups
A de novo radish root transcriptome of 68,940 assembled transcripts including 33,337 unigenes was generated, providing the first comprehensive molecular characterization of the radish root response to Pb stress.
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Has reproduction · 87
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.
PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups
Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.
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Has reproduction · 59
Single-cell transcriptomics reveals maturation of transplanted stem cell-derived retinal pigment epithelial cells toward native state.
PMID 37339216 · PMC10293804 · Proceedings of the National Academy of Sciences of the United States of America · 2023 · 8 claims · 8 setups
Subretinally transplanted stem cell-derived RPE (ESC- and iPSC-derived) retain RPE identity and survive in vivo for at least 30 days in immunocompetent rabbit eyes
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Has reproduction · 100
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.
PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups
TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.
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Full-text index only
An integrative approach to reveal driver gene fusions from paired-end sequencing data in cancer.
PMID 19881495 · PMC3086882 · Nature biotechnology · 2009 · 8 claims · 8 setups
A 'concept signature' (ConSig) score algorithm ranks genes by association with molecular concepts characteristic of fusion or mutation cancer genes, nominating biologically important fusions from large candidate sets.
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Has reproduction · 93
A comparison of the large-scale gene expression patterns in summer and fall migratory Pantala flavescens (Fabricius) in northern China.
PMID 39108562 · PMC11301579 · Ecology and evolution · 2024 · 7 claims · 2 setups
624 DEGs were identified between summer (M7) and fall (M10) migratory P. flavescens, with 352 upregulated and 272 downregulated in M7 versus M10
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Has reproduction · 94
Transcriptomic and functional analyses of the piRNA pathway in the Chagas disease vector Rhodnius prolixus.
PMID 30303955 · PMC6179187 · PLoS neglected tropical diseases · 2018 · 7 claims · 6 setups
Rhodnius prolixus genome harbors four putative piwi orthologs (three piwi genes plus one ago3 ortholog), and core piRNA pathway components are expressed during previtellogenic oogenesis
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Has reproduction · 78
Transcriptomic and physiological analysis of atractylodes chinensis in response to drought stress reveals the putative genes related to sesquiterpenoid biosynthesis.
PMID 38317086 · PMC10845750 · BMC plant biology · 2024 · 8 claims · 6 setups
Drought stress significantly increases MDA, proline, soluble sugar, and crude protein content and antioxidative enzyme (SOD, POD, CAT) activity in A. chinensis seedlings
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Has reproduction · 75
Transcriptomic analysis unravels the molecular response of Lonicera japonica leaves to chilling stress.
PMID 36618608 · PMC9815118 · Frontiers in plant science · 2022 · 8 claims · 8 setups
Chilling stress significantly alters the ratio of anthocyanins, chlorophylls, and carotenoids, causing leaf color to change from green to purple
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Has reproduction · 91
Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.
PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 8 claims · 8 setups
175 conserved miRNAs (39 families) and 83 novel miRNAs were identified in C. sinensis one bud and two tender leaves using small RNA sequencing combined with genome survey scaffold data
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Has reproduction
Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.
PMID 35931984 · PMC9356423 · BMC genomics · 2022 · 7 claims · 8 setups
114 CNGC genes were identified across 4 cotton species (G. arboreum 20, G. raimondii 20, G. hirsutum 38, G. barbadense 36), clustering into 5 groups (I, II, III, IVa, IVb).
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Has reproduction · 71
Interpretable artificial intelligence based on immunoregulation-related genes predicts prognosis and immunotherapy response in lung adenocarcinoma.
PMID 41048340 · PMC12491262 · Frontiers in bioinformatics · 2025 · 8 claims · 8 setups
LUAD samples cluster into IRG-high and IRG-low groups, with the IRG-high group showing significantly better survival and greater immune cell infiltration.
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Has reproduction · 50
Microglial Fkbp5 Impairs Post-Stroke Vascular Integrity and Regeneration by Promoting Yap1-Mediated Glycolysis and Oxidative Phosphorylation.
PMID 41355597 · PMC13042415 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups
A post-stroke perivascular microglial niche (stroke-VAM) exists, characterized by low M2 marker expression and elevated glycolysis, OXPHOS, and phagocytic activity.
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Has reproduction · 78
Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.
PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups
73 IQD gene family members (TaIQD1-73) were identified in the wheat genome and phylogenetically divided into six major groups.