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 · 94
Eye in a Disk: eyeIntegration Human Pan-Eye and Body Transcriptome Database Version 1.0.
PMID 31343654 · PMC6660187 · Investigative ophthalmology & visual science · 2019 · 8 claims · 6 setups
EiaD is a reproducible, versioned pan-eye and body RNA-seq transcriptome dataset built from 916 eye and 1375 GTEx samples via a Snakemake pipeline output as a single SQLite database.
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Has reproduction · 53
Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients.
PMID 35425715 · PMC9004628 · Frontiers in oncology · 2022 · 8 claims · 7 setups
Patient-derived colorectal cancer organoids (CRCOs) can be established from surgical CRC tissue with an 82% success rate (41/50)
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Has reproduction · 50
Patient-Derived Meningioma Organoids: A Reliable Model for Studying Human Tumor Pathophysiology.
PMID 39941893 · PMC11817449 · Cancers · 2025 · 8 claims · 7 setups
A standardized, reproducible protocol can establish meningioma organoids (MEN-Os) from patient-resected tumor tissue without mechanical/enzymatic dissociation, using serum-free medium lacking growth factors or exogenous ECM.
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Has reproduction · 84
Genetically engineered stem cell-derived retinal grafts for improved retinal reconstruction after transplantation.
PMID 34409267 · PMC8361135 · iScience · 2021 · 8 claims · 7 setups
Bhlhb4−/− and Islet1−/− grafts have markedly reduced bipolar cell populations after transplantation while retaining intact photoreceptor cell layers
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Has reproduction · 78
Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.
PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 7 claims · 7 setups
An integrative consensus WGCNA analysis across matched tumor, matched organoid, and an independent organoid drug-response dataset identifies significant gene modules and hub genes associated with CRC chemotherapy response.
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Has reproduction · 65
comBO: A combined human bone and lympho-myeloid bone marrow organoid for preclinical modeling of hematopoietic disorders.
PMID 41734765 · PMC7618947 · Cell stem cell · 2026 · 8 claims · 8 setups
comBO is a single iPSC differentiation generating lymphoid, myeloid, vascular, mesenchymal stromal, and functional osteo/adipogenic lineages within one organoid
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Has reproduction · 50
CHD7 regulates otic lineage specification and hair cell differentiation in human inner ear organoids.
PMID 36396635 · PMC9672366 · Nature communications · 2022 · 8 claims · 7 setups
Loss of CHD7 or its chromatin remodeling (ATPase) activity causes complete absence of hair cells and supporting cells in inner ear organoids.
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Has reproduction · 72
Neoadjuvant sintilimab plus chemotherapy in EGFR-mutant NSCLC: Phase 2 trial interim results (NEOTIDE/CTONG2104).
PMID 38897205 · PMC11293361 · Cell reports. Medicine · 2024 · 6 claims · 8 setups
Neoadjuvant sintilimab plus carboplatin/nab-paclitaxel is clinically feasible, well tolerated, and yields comparable surgical outcomes in early-stage EGFR-mutant NSCLC, with 44% MPR and no pCR.
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Has reproduction · 70
The manganese transporter SLC39A8 links alkaline ceramidase 1 to inflammatory bowel disease.
PMID 38839750 · PMC11153611 · Nature communications · 2024 · 8 claims · 8 setups
Intestinal epithelial cell-specific deletion of Slc39a8 causes systemic manganese (Mn) deficiency in blood and multiple organs.
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Has reproduction · 84
AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.
PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups
An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures
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Has reproduction · 87
Inhibition of SARS-CoV-2 Infections in Engineered Human Tissues Using Clinical-Grade Soluble Human ACE2.
PMID 32333836 · PMC7181998 · Cell · 2020 · 8 claims · 7 setups
Clinical-grade hrsACE2 significantly inhibits SARS-CoV-2 infection of Vero-E6 cells in a dose-dependent manner
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Has reproduction · 85
COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.
PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups
COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).
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Has reproduction · 65
Cancer-predicting transcriptomic and epigenetic signatures revealed for ulcerative colitis in patient-derived epithelial organoids.
PMID 29983891 · PMC6033374 · Oncotarget · 2018 · 8 claims · 6 setups
UC patient-derived epithelial organoids histologically phenocopy primary UC tissue, while non-IBD organoids resemble healthy colonic epithelium.
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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 an epigenetic vulnerability/fitness gene in RCC, identified by integrating GeCK CRISPR screening data with TCGA/ICGC RCC cohorts.
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Has reproduction · 63
Stromal androgen signaling acts as tumor niches to drive prostatic basal epithelial progenitor-initiated oncogenesis.
PMID 36323713 · PMC9630272 · Nature communications · 2022 · 7 claims · 7 setups
Loss of AR in stromal Gli1-lineage cells diminishes prostate epithelial oncogenesis and tumor development.
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Has reproduction · 54
Single-Cell Transcriptome Analysis Revealed Heterogeneity and Identified Novel Therapeutic Targets for Breast Cancer Subtypes.
PMID 37190091 · PMC10137100 · Cells · 2023 · 8 claims · 8 setups
Single-cell transcriptomic analysis of EPCAM+Lin- epithelial cells identified unique gene signatures/markers that distinguish ER+, HER2+, ER+HER2+, and TNBC molecular subtypes
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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 · 64
Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.
PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups
Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.
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Has reproduction · 71
Utilizing the codon adaptation index to evaluate the susceptibility to HIV-1 and SARS-CoV-2 related coronaviruses in possible target cells in humans.
PMID 36760235 · PMC9905242 · Frontiers in cellular and infection microbiology · 2022 · 7 claims · 8 setups
CAI is positively correlated with translational efficiency, supporting its use as a proxy for viral mRNA translation in cell types.