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).

• Chipping away at 'stemness'.

  PMID 15287966 · PMC507869 · Genome biology · 2004 · 8 claims · 6 setups

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  Global gene-expression analyses across five independent studies identify known and new candidate regulators of human ES-cell growth, self-renewal, and pluripotency.

  microarray sage custom

• Defining human diabetic nephropathy on the molecular level: integration of transcriptomic profiles with biological knowledge.

  PMID 18704688 · PMC2597685 · Reviews in endocrine & metabolic disorders · 2008 · 8 claims · 8 setups

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  Genetic predisposition determines susceptibility and rate of progression to ESRD in diabetic patients, in addition to environmental factors

  kidney proximal pbmcs macrophages gene qrt-pcr immunohistochemistry

• Integrative Transcriptomic Analysis and Co-Expression Network Characterization of Soybean Developmental Tissues.

  PMID 41977661 · PMC13075193 · Plants (Basel, Switzerland) · 2026 · 8 claims · 6 setups

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  Tissue identity (seed vs. non-seed) is the dominant driver of transcriptomic variation, as shown by clear separation on PC1

  glycine same seed-upregulated bulk principal differential

• PD-1 and TIGIT coexpression identifies a circulating CD8 T cell subset predictive of response to anti-PD-1 therapy.

  PMID 33188038 · PMC7668369 · Journal for immunotherapy of cancer · 2020 · 7 claims · 6 setups

  Has reproduction · 75

  The frequency of circulating PD-1+TIGIT+ (DPOS) CD8+ T cells after 1 month of anti-PD-1 therapy is associated with clinical response and overall survival

  pbmcs sorted expanded cancer multiparameter receptor targeted

• FLASH-MM: fast and scalable single-cell differential expression analysis using linear mixed-effects models.

  PMID 41644528 · PMC12982622 · Nature communications · 2026 · 8 claims · 6 setups

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  FLASH-MM produces LMM parameter estimates identical to lmer (lme4) up to the sixth decimal place while being 50- to 140-fold faster as sample size increases from 20,000 to 120,000 cells

  simulated same healthy female-biased simulated comparative single-cell

• Network Controllability Reveals Key Mitigation Points for Tumor-Promoting Signaling in Tumor-Educated Platelets.

  PMID 41226816 · PMC12609506 · International journal of molecular sciences · 2025 · 8 claims · 6 setups

  Has reproduction · 84

  TEPs from NSCLC patients show 111 upregulated and 108 downregulated genes compared to platelets from non-cancer donors

  platelets degs platelet-specific tep-specific transcriptome pathway k-means

• Identification and validation of hub genes involved in papillary thyroid carcinoma progression.

  PMID 41851690 · PMC13126906 · BMC cancer · 2026 · 8 claims · 8 setups

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  1550 overlapping DEGs (1149 upregulated, 401 downregulated) were identified in PTC compared to normal thyroid tissues

  thyroid upregulated degs ptc bulk protein-protein kegg

• D2H2: diabetes data and hypothesis hub.

  PMID 38107655 · PMC10723036 · Bioinformatics advances · 2023 · 6 claims · 6 setups

  Has reproduction

  D2H2 is a web-based portal integrating hundreds of curated diabetes-relevant transcriptomics datasets with bioinformatics tools for gene/gene set queries

  brain top curated d2h2 differential gene bulk

• Molecular Classification Models for Triple Negative Breast Cancer Subtype Using Machine Learning.

  PMID 34575658 · PMC8472680 · Journal of personalized medicine · 2021 · 7 claims · 4 setups

  Has reproduction · 86

  TNBC can be divided into four gene-expression-defined subtypes: BLIA, BLIS, MES, and LAR

  tnbc unique 719-gene gene term machine

• Machine learning-based identification of biomarkers and drugs in immunologically cold and hot pancreatic adenocarcinomas.

  PMID 39152432 · PMC11328457 · Journal of translational medicine · 2024 · 7 claims · 8 setups

  Has reproduction · 42

  PAAD tumors can be consensus-clustered into immunologically hot and cold subtypes based on CIBERSORT-derived immune cell fractions, with significantly different survival outcomes.

  paad degs bulk consensus tumor

• Identification of the shared hub gene signatures and molecular mechanisms between HIV-1 and pulmonary arterial hypertension.

  PMID 38528047 · PMC10963360 · Scientific reports · 2024 · 6 claims · 8 setups

  Has reproduction · 71

  109 shared genes were identified between HIV-1- and PAH-associated WGCNA modules

  pbmc shared hub pbmcs weighted kegg differential

• Overview of microarray analysis of gene expression and its applications to cervical cancer investigation.

  PMID 18182341 · PMC7129792 · Taiwanese journal of obstetrics & gynecology · 2007 · 6 claims · 5 setups

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  Oligonucleotide microarray and cDNA microarray are the two main microarray platforms used to study gene expression genome-wide.

  cervical cdna microarray combinatorial

• Global and precise identification of functional miRNA targets in mESCs by integrative analysis.

  PMID 35899551 · PMC9442311 · EMBO reports · 2022 · 8 claims · 8 setups

  Has reproduction · 93

  Fewer than 10% of expressed genes are directly and functionally regulated by miRNAs in mESCs

  mirna_ko mescs drosha_ko escs bulk western ago2

• Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.

  PMID 18500686 · PMC2516917 · The Prostate · 2008 · 8 claims · 5 setups

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  Identified 32 genes (38 cDNAs) with an expression pattern of highest levels in seminal vesicle, lower in normal prostate, and lowest in prostate cancer

  normal prostate microarray cdna cross-tissue gene

• Single-cell gene expression and TCR profiling reveal age-related differences in recent thymic emigrants.

  PMID 42023153 · PMC13098507 · iScience · 2026 · 8 claims · 5 setups

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  Neonatal and adult CD8+ RTEs are phenotypically and functionally distinct despite equivalent post-thymic maturation time

  splenic neonatal sorted flow single-cell differential

• Creation of a Single Cell RNASeq Meta-Atlas to Define Human Liver Immune Homeostasis.

  PMID 34335581 · PMC8322955 · Frontiers in immunology · 2021 · 7 claims · 8 setups

  Has reproduction · 63

  Three independently generated human liver CD45+ scRNA-seq datasets (LACEe, Lnb, LCD45e) can be co-clustered and integrated despite differing sequencing platforms and processing protocols.

  liver pbmc integrated gene scrna-seq differential ingenuity

• Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

  PMID 18930150 · PMC2774125 · Methods (San Diego, Calif.) · 2008 · 8 claims · 8 setups

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  Data integration of multiple functional genomics datasets effectively predicts mitochondrial gene function and prioritizes candidate mitochondrial disease genes.

  saccharomyces higher yeast mitochondria genome-wide rnai gene

• Comprehensive data for studying serum exosome microRNA transcriptome in Parkinson's disease patients.

  PMID 39406833 · PMC11480472 · Scientific data · 2024 · 8 claims · 8 setups

  Has reproduction · 100

  The study presents comprehensive serum exosome miRNA transcriptome data from four independent Japanese cohorts of PD patients and controls.

  serum patients small mirna 123i-mibg

• Transcriptome-Proteome Profiling in Burkholderia thailandensis during the Transition from Exponential to Stationary Phase.

  PMID 40680064 · PMC12322963 · Journal of proteome research · 2025 · 8 claims · 7 setups

  Has reproduction · 80

  928 differentially accumulating mRNAs (564 up, 364 down) were identified between exponential and stationary phase

  burkholderia pseudomallei bulk tmt-based rt-qpcr

• Quemliclustat and chemotherapy with or without zimberelimab in metastatic pancreatic adenocarcinoma: a randomized phase 1 trial.

  PMID 41912809 · PMC13099643 · Nature medicine · 2026 · 7 claims · 8 setups

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  Quemliclustat combined with gemcitabine/nab-paclitaxel (G/nP) with or without zimberelimab has a safety profile consistent with G/nP alone across dose-escalation and dose-expansion phases

  mia hct-116 patients randomized rna-seq rt-pcr phase