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 · 52
Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.
PMID 31980607 · PMC6981202 · Nature communications · 2020 · 8 claims · 8 setups
MetaMEx integrates transcriptomic data from 66 published human skeletal muscle studies (>1100 individuals) into an online meta-analysis resource (www.metamex.eu)
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Has reproduction · 75
Sequencing of human genomes with nanopore technology.
PMID 31015479 · PMC6478738 · Nature communications · 2019 · 8 claims · 7 setups
A novel reference panel-free, read-based phasing algorithm substantially improves SNV calling accuracy over standard filtering in ONT data.
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Has reproduction · 68
Microglia maintain structural integrity during fetal brain morphogenesis.
PMID 38309258 · PMC10869139 · Cell · 2024 · 8 claims · 8 setups
Embryonic ATM-like microglia accumulate at two fetal cortical boundaries, the cortico-striato-amygdalar boundary (CSA) and cortico-septal boundary (CSB), resembling post-natal axon-tract-associated microglia (ATM)
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Has reproduction · 68
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
Siphonophorae is the first diverging clade within Hydroidolina.
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Has reproduction · 79
Genome-wide prediction of DNase I hypersensitivity using gene expression.
PMID 29051481 · PMC5715040 · Nature communications · 2017 · 8 claims · 5 setups
Gene expression can, to a large extent, predict genome-wide DNase I hypersensitivity (chromatin accessibility)
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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 · 8 claims · 8 setups
C3 PLP2+ Tumor Epithelial Progenitor Cells are a noteworthy subpopulation exerting a pivotal influence on CC differentiation and progression
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Has reproduction
CRISPR/Cas9 Screens Reveal Multiple Layers of B cell CD40 Regulation.
PMID 31365872 · PMC6684324 · Cell reports · 2019 · 8 claims · 8 setups
Genome-wide CRISPR/Cas9 screening in Daudi B cells using CD40L-induced Fas upregulation as a readout identifies both positive and negative regulators of CD40
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Has reproduction · 55
Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies.
PMID 34107850 · PMC8806433 · Bioengineered · 2021 · 7 claims · 8 setups
131 robust DEGs (89 upregulated, 42 downregulated) were identified by RRA integration of three vitiligo datasets and are closely associated with melanogenesis and vitiligo development
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Has reproduction · 55
Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.
PMID 38566100 · PMC10985960 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups
Microglia, endothelial cells, and pericytes exhibit the highest IFN-I activity among PD midbrain cell types, with microglia and endothelial cells showing significantly elevated high-IFN-I-scoring proportions in PD versus controls
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Has reproduction · 96
In vivo induction of activin A-producing alveolar macrophages supports the progression of lung cell carcinoma.
PMID 36650150 · PMC9845242 · Nature communications · 2023 · 8 claims · 8 setups
AMs accumulate in human lung cancer tissue and support cancer cell proliferation, contributing to unfavourable outcome
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Has reproduction · 78
Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.
PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 6 claims · 8 setups
CIBERSORTx can combine scRNA-seq-derived signature matrices with bulk RNA-seq data to estimate proportions of 11 TIL subsets in HCC tumor and normal tissue
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Has reproduction · 68
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.
PMID 35012625 · PMC8743438 · Genome biology · 2022 · 8 claims · 9 setups
GENEVA (Gene Expression Variance Analysis) is a semi-automated framework that mines large-scale public RNA-seq datasets to identify conditions associated with a gene's expression variance
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Has reproduction · 85
Epigenome screening highlights that JMJD6 confers an epigenetic vulnerability and mediates sunitinib sensitivity in renal cell carcinoma.
PMID 33634984 · PMC7882098 · Clinical and translational medicine · 2021 · 8 claims · 8 setups
JMJD6 is identified as a potent epigenetic vulnerability/fitness gene in RCC by integrating GeCK CRISPR screening data with TCGA-KIRC epigenetic regulator survival analysis
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Has reproduction · 48
Indoleamine 2, 3-Dioxygenase 1 and CD8 Expression Profiling Revealed an Immunological Subtype of Colon Cancer With a Poor Prognosis.
PMID 33425745 · PMC7793995 · Frontiers in oncology · 2020 · 8 claims · 8 setups
A colon cancer subtype with CD8Ahigh IDO1high tumors shows the worst survival despite high CD8 T cell infiltrates
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Has reproduction · 44
Phased differentiation of γδ T and T CD8 tumor-infiltrating lymphocytes revealed by single-cell transcriptomics of human cancers.
PMID 34721945 · PMC8555559 · Oncoimmunology · 2021 · 7 claims · 6 setups
In tumors, TCRVγnon9 γδ T cells (the majority γδ TIL subset) are quantitatively correlated and aligned with T CD8 cells for differentiation, exhaustion, gene expression profile, and response to immune checkpoint therapy
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Has reproduction · 20
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.
PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups
AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats
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Has reproduction · 100
miR-4478 Accelerates Nucleus Pulposus Cells Apoptosis Induced by Oxidative Stress by Targeting MTH1.
PMID 36130054 · PMC9897280 · Spine · 2023 · 7 claims · 8 setups
miR-4478 is upregulated in NP tissues from IVDD patients compared to controls
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Has reproduction · 80
Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.
PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 8 claims · 8 setups
A neutrophil-related co-expression gene module (blue module) is significantly associated with aSAH occurrence
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Has reproduction · 84
TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.
PMID 37200521 · PMC10433534 · Chemical research in toxicology · 2023 · 8 claims · 5 setups
TransOrGAN can infer transcriptomic profiles between any 2 of 9 rat organs with an average cosine similarity of 0.984 versus real profiles
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Has reproduction · 50
Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing.
PMID 36401180 · PMC9673297 · Genetics, selection, evolution : GSE · 2022 · 8 claims · 8 setups
BaseVar + STITCH at 1.0X sequencing depth with a sample size >300 achieves the highest genotyping accuracy among tested imputation strategies (genotype concordance >98.8%, genotype accuracy >0.97).