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 · 69
Clinical and molecular correlation defines activity of physiological pathways in life-sustaining kidney xenotransplantation.
PMID 37311769 · PMC10264453 · Nature communications · 2023 · 7 claims · 8 setups
Porcine kidney xenografts transplanted into NHPs show only modest growth over time.
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Has reproduction · 89
In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.
PMID 32898168 · PMC7478592 · PLoS biology · 2020 · 8 claims · 6 setups
SARS-CoV-2 infection induces a strong interferon-mediated antiviral response in the nasopharynx, up-regulating antiviral factors (OAS1-3, IFIT1-3, MX2, RSAD2, HERC5) and Th1 chemokines CXCL9/10/11, while down-regulating ribosomal protein transcripts.
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Has reproduction · 30
Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes.
PMID 30503143 · PMC6327112 · Cell stem cell · 2019 · 8 claims · 6 setups
A core set of 60 genes captures a continuous pseudotemporal disease axis from control to PD GBA-N370S iPSC-derived dopamine neurons (52 downregulated, 8 upregulated).
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Has reproduction · 95
Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.
PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups
Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity
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Has reproduction · 60
Core transcriptional signatures of phase change in the migratory locust.
PMID 31292921 · PMC6881432 · Protein & cell · 2019 · 8 claims · 7 setups
PhaseCore genes defined by AC-PCA contribution to phase differentiation predict phase status with >87.5% accuracy
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Has reproduction · 75
Integrative analysis reveals chemokines CCL2 and CXCL5 mediated shear stress-induced aortic dissection formation.
PMID 38163105 · PMC10757018 · Heliyon · 2024 · 7 claims · 8 setups
Chemokines CCL2 and CXCL5 mediate a shear stress-induced 'Endothelial-Monocyte-Neutrophil' axis that contributes to aortic dissection development.
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Has reproduction · 56
Identification of key genes in chickpea transcriptomics and the development of ChickpeaOmicsR as a comprehensive resource to advance breeding and genomic studies.
PMID 41909810 · PMC13022592 · Frontiers in bioinformatics · 2026 · 8 claims · 4 setups
ChickpeaOmicsR is the first comprehensive/specialized R package integrating transcriptomic, genomic, and proteomic (RNA-seq, GWAS, PPI) data within a unified, reproducible framework and standardizing fragmented chickpea gene nomenclature.
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Has reproduction · 57
Diapause vs. reproductive programs: transcriptional phenotypes in a keystone copepod.
PMID 33782539 · PMC8007741 · Communications biology · 2021 · 8 claims · 7 setups
t-SNE clustering of all-gene expression data groups field-collected (diapause program) samples into one cluster while early and late culture (reproductive program) samples separate into two distinct phenotypes
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Has reproduction · 67
Leveraging RNA-seq deconvolution to improve complex in vitro model characterization.
PMID 40701251 · PMC12391696 · The Journal of biological chemistry · 2025 · 8 claims · 6 setups
RNA-seq deconvolution can predict cell type proportions from bulk RNA-seq using scRNA-seq references, offering a useful characterization tool for CIVMs where single-cell methods are impractical
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Has reproduction · 67
Optimal scaling of digital transcriptomes.
PMID 24223126 · PMC3819321 · PloS one · 2013 · 8 claims · 8 setups
Fifteen existing and novel transcript-count normalization algorithms can be compared with two novel, mutually independent metrics: the number of "uniform" genes (sufficiently low coefficient of variation after normalization) and low average Spearman correlation between normalized expression profiles of gene pairs.
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Has reproduction · 88
From bud formation to flowering: transcriptomic state defines the cherry developmental phases of sweet cherry bud dormancy.
PMID 31830909 · PMC6909552 · BMC genomics · 2019 · 8 claims · 7 setups
Flower buds in organogenesis, paradormancy, endodormancy and ecodormancy stages are each defined by expression of genes in specific pathways, and the transcriptional state accurately captures the dormancy state.
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Has reproduction
A newly identified glycosyltransferase AsRCOM provides resistance to purple curl leaf disease in agave.
PMID 37936069 · PMC10629022 · BMC genomics · 2023 · 6 claims · 5 setups
The glycosyltransferase gene AsRCOM is the most critical disease-resistance gene against agave purple curl leaf disease, and its overexpression significantly enhances resistance.
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Has reproduction · 50
Transcriptome profiling of osteoclast subsets associated with arthritis: A pathogenic role of CCR2(hi) osteoclast progenitors.
PMID 36591261 · PMC9797520 · Frontiers in immunology · 2022 · 8 claims · 6 setups
CCR2hi and CCR2lo periarticular bone marrow OCP subsets show a disparate transcriptome (863 differentially expressed genes)
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Has reproduction · 50
Ancient gene duplicates in Gossypium (cotton) exhibit near-complete expression divergence.
PMID 24558256 · PMC3971588 · Genome biology and evolution · 2014 · 8 claims · 8 setups
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.
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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 · 80
Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.
PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 7 claims · 8 setups
C3 PLP2+ Tumor Epithelial Progenitor Cells are a key subpopulation that drives differentiation and progression of cervical carcinoma
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Has reproduction · 10
Gli1-expressing stromal cells are highly reparative precursors of long-lived chondroprogenitors in the fetal murine limb.
PMID 41253754 · PMC12627582 · Nature communications · 2025 · 7 claims · 8 setups
Fetal Gli1+ cells (including cells outside the cartilage) are the precursors of postnatal long-lived chondroprogenitors and give rise to most growth-plate chondrocytes juvenile/adult.
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Has reproduction
Predicting favorable landing pads for targeted integrations in Chinese hamster ovary cell lines by learning stability characteristics from random transgene integrations.
PMID 33304461 · PMC7710658 · Computational and structural biotechnology journal · 2020 · 7 claims · 6 setups
Expression stability in CHO cell lines is controlled at three levels: choice of integration site, integrity/concatemerization pattern of the transgene, and stress-related cellular processes.
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Has reproduction · 78
Tumor methionine metabolism drives T-cell exhaustion in hepatocellular carcinoma.
PMID 33674593 · PMC7935900 · Nature communications · 2021 · 8 claims · 8 setups
A transcriptome-derived T-cell exhaustion score (ES) is prognostic for HCC patient survival independent of known clinical/molecular factors
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Has reproduction · 86
RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.
PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups
RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.