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 · 30
SMRT and Illumina RNA sequencing reveal novel insights into the heat stress response and crosstalk with leaf senescence in tall fescue.
PMID 32746857 · PMC7397585 · BMC plant biology · 2020 · 7 claims · 5 setups
Short-term heat stress strongly and specifically activates Hsps, Hsfs, FKBPs, calcium signaling, glutathione S-transferase, photosynthesis, and phytohormone signaling genes.
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Has reproduction · 72
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
A high-quality ~375 Mbp draft genome and transcriptome of Holacanthella duospinosa was assembled and annotated, providing a genomic resource for hexapod evolution.
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Has reproduction · 97
Duvernoy's Gland Transcriptomics of the Plains Black-Headed Snake, Tantilla nigriceps (Squamata, Colubridae): Unearthing the Venom of Small Rear-Fanged Snakes.
PMID 34066626 · PMC8148590 · Toxins · 2021 · 8 claims · 5 setups
The T. nigriceps Duvernoy's gland transcriptome is dominated by three toxin families: three-finger toxins (3FTxs), cysteine-rich secretory proteins (CRISPs), and snake venom metalloproteinases (SVMPIIIs)
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Has reproduction · 68
LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq.
PMID 24709818 · PMC4079972 · Genome research · 2014 · 8 claims · 8 setups
LaSSO (Lariat Sequence Site Origin) identifies intronic lariat reads and pinpoints branch points genome-wide from RNA-seq data by considering every intronic base as a potential branch point and including all possible exon-skipping lariats.
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Has reproduction · 61
Comprehensive transcriptome study to develop molecular resources of the copepod Calanus sinicus for their potential ecological applications.
PMID 24982883 · PMC4055022 · BioMed research international · 2014 · 8 claims · 8 setups
Illumina RNA-Seq with Trinity de novo assembly produced a C. sinicus transcriptome of 69,751 contigs (average 928.8 bp, N50 1,127 bp) from 58.9 million reads.
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Has reproduction · 43
Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice.
PMID 34089405 · PMC8179884 · Rice (New York, N.Y.) · 2021 · 8 claims · 7 setups
N22 performs better under dual (low N + low water) stress owing to better root architecture, chlorophyll/porphyrin synthesis and oxidative stress management
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Has reproduction · 73
Integrated multiomic analysis reveals disulfidptosis subtypes in glioblastoma: implications for immunotherapy, targeted therapy, and chemotherapy.
PMID 38504986 · PMC10950096 · Frontiers in immunology · 2024 · 8 claims · 8 setups
Consensus clustering on 32 disulfidptosis-associated genes stratifies GBM patients into two subtypes, DRGcluster A and B, with distinct survival outcomes.
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Has reproduction · 78
Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.
PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups
KCTD16, CD3D and GSDMB are succinylation-related prognostic genes in BLCA
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Has reproduction · 73
Design of a targeted blood transcriptional panel for monitoring immunological changes accompanying pregnancy.
PMID 38352867 · PMC10861739 · Frontiers in immunology · 2024 · 6 claims · 3 setups
A targeted panel of 176 transcripts plus 8 housekeeping genes was identified for monitoring immunological changes during pregnancy
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Has reproduction · 78
Disrupted PGR-B and ESR1 signaling underlies defective decidualization linked to severe preeclampsia.
PMID 34709177 · PMC8553341 · eLife · 2021 · 8 claims · 5 setups
A 120-gene endometrial transcriptomic fingerprint encodes defective decidualization associated with severe preeclampsia.
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Has reproduction · 95
Identification and Characterization of Small Noncoding RNAs in Genome Sequences of the Edible Fungus Pleurotus ostreatus.
PMID 27703969 · PMC5040776 · BioMed research international · 2016 · 8 claims · 7 setups
254 small noncoding RNAs (snRNAs, snoRNAs, tRNAs, miRNAs) were detected in the P. ostreatus CCEF00389 genome assembly, the first genome-scale identification of sncRNAs for a basidiomycete.
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Has reproduction · 23
Accelerated Evolution of Tissue-Specific Genes Mediates Divergence Amidst Gene Flow in European Green Lizards.
PMID 33988711 · PMC8382678 · Genome biology and evolution · 2021 · 8 claims · 8 setups
The Adriatic lineage is a sister taxon to L. bilineata based on mitogenome and autosomal phylogenies
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Has reproduction · 85
Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain).
PMID 37137526 · PMC10214862 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2023 · 8 claims · 8 setups
First high-quality chromosome-level genome assembly and annotation of P. lilfordi, generated via a mixed sequencing strategy (10X linked reads, ONT long reads, Hi-C) plus RNAseq/Iso-Seq
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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 · 89
Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.
PMID 41738778 · PMC12962854 · Genome biology and evolution · 2026 · 8 claims · 8 setups
Eight sericin genes were identified in the Actias luna genome, including two clusters of closely related paralogs.
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Has reproduction · 100
Viral Diagnostics in Plants Using Next Generation Sequencing: Computational Analysis in Practice.
PMID 29123534 · PMC5662881 · Frontiers in plant science · 2017 · 8 claims · 8 setups
NGS/RNA-seq enables unbiased, hypothesis-free detection of multiple known and emergent plant viruses, unlike RT-PCR which only detects one or a few known viruses per test.
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Has reproduction · 66
HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.
PMID 24475057 · PMC3903476 · PloS one · 2014 · 8 claims · 5 setups
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.
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Has reproduction · 50
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
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.
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Has reproduction · 78
Requirements for Pseudomonas aeruginosa acute burn and chronic surgical wound infection.
PMID 25057820 · PMC4109851 · PLoS genetics · 2014 · 8 claims · 8 setups
In vivo gene expression is generally not correlated with a gene's importance for fitness, with the exception of metabolic genes, for which differential expression is more predictive of fitness.
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Has reproduction · 81
Chromosome-scale Elaeis guineensis and E. oleifera assemblies: comparative genomics of oil palm and other Arecaceae.
PMID 38918881 · PMC11373658 · G3 (Bethesda, Md.) · 2024 · 8 claims · 8 setups
Improved E. guineensis genome assembly achieved with substantially increased continuity and completeness compared to prior assemblies