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).

Publications 1.3k Datasets 392.5k Experiments 43

System / cell line: qpcr ✕ Assay: kegg ✕ Clear

Warming Causes a Decline in Baltic Sea Coastal Sediment Microbial Abundance.

PMID 41712959 · PMC12920023 · Environmental microbiology · 2026 · 6 claims · 5 setups

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Contrary to the expected increase in productivity, long-term warming decreased sediment microbial (bacterial and archaeal) cell abundance in the heated bay compared to the control bay

baltic sediment 16s qpcr propidium 16s
PUM2 knockdown regulates the expression and alternative splicing of genes associated with myocardial fibrosis in H9C2 cells.

PMID 41694110 · PMC12902810 · Experimental and therapeutic medicine · 2026 · 7 claims · 7 setups

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PUM2 knockdown regulates the expression and alternative splicing of genes associated with myocardial fibrosis in H9C2 cells

h9c2 rt-qpcr western counting
TBL1X/TBL1XR1 govern β-cell identity through a PAX6-containing gene regulatory network.

PMID 42020373 · PMC13102947 · Nature communications · 2026 · 8 claims · 8 setups

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TBL/R1 are crucial regulators of β-cell identity and determinants of diabetes development and progression

pancreatic fed paraffin-embedded pancreas qpcr blood oral
TGFβ-activated PDHB promotes mitochondrial pyruvate metabolism and contributes to human endoderm differentiation via ATP-dependent BRG1.

PMID 41702907 · PMC13022444 · Nature communications · 2026 · 8 claims · 8 setups

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DE differentiation requires a TGFβ-driven metabolic switch characterized by reduced lactate production and enhanced TCA cycle activity/oxidative phosphorylation, mediated by PDHB

escs crispr flow qrt-pcr
Transcriptomic Responses of the Marine Diatom Phaeodactylum tricornutum to High Carbon and Low Nitrogen Stress.

PMID 41522215 · PMC12789813 · Ecology and evolution · 2026 · 8 claims · 6 setups

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Low nitrogen elicits a broader transcriptomic response than high CO2 (4267 vs. 2424 DEGs)

phaeodactylum bulk qpcr enrichment
Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

PMID 32714363 · PMC7344232 · Frontiers in genetics · 2020 · 6 claims · 6 setups

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The midnight blue module and the yellow module play vital roles in the pathogenesis of CAD in non-diabetic patients

pbmcs blood apoe genes microarray rt-qpcr elisa
Integrative miRNA-mRNA Network and Molecular Dynamics-Based Identification of Therapeutic Candidates for Paroxysmal Nocturnal Hemoglobinuria.

PMID 41599741 · PMC12845513 · Pharmaceuticals (Basel, Switzerland) · 2026 · 8 claims · 8 setups

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A PIGA-knockout (PIGA-KO) THP-1 cell model was successfully established using CRISPR/Cas9 RNP technology as a PNH model

thp-1 literature-validated pnh cxcl8 crispr rt-qpcr bulk
Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

PMID 40520228 · PMC12162626 · Frontiers in genetics · 2025 · 8 claims · 8 setups

Has reproduction · 49

ENTPD1, SERPINA1, and TACSTD2 are potential transcriptomic biomarkers for PTC

ptc degs key bulk kegg weighted
Integrated multi-omics analysis combined with clinical validation reveals that HLA-DRB5 and ODAPH are causal risk genes for keratoconus.

PMID 41803193 · PMC13179358 · Scientific reports · 2026 · 8 claims · 8 setups

Has reproduction · 64

2,884 differentially expressed genes (DEGs) were identified as the union of upregulated genes from two independent KC transcriptome datasets (GSE151631, GSE77938), enriched in cell adhesion, immune response, and TNF/IL-17 signaling pathways.

corneal deg gwas eqtl bulk kegg summary-data
Uncovering the transcriptional landscape of estrogen-induced gonadal feminization in the Chinese giant salamander.

PMID 41808025 · PMC13085422 · BMC genomics · 2026 · 8 claims · 7 setups

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E2 exposure induces male-to-female gonadal sex reversal in CGS, confirmed by histological evidence across developmental stages.

gonadal tail-tip deg candidate rna-seq histology rt-qpcr
Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

PMID 26248502 · PMC4528194 · Scientific reports · 2015 · 8 claims · 8 setups

Has reproduction · 70

AS events, including differentially-expressed-transcript-containing genes (DETs), are ubiquitous in head-kidney and spleen transcriptomes of C. idella

head-kidney idella assembled il-12p40α rna-seq rt-qpcr pcr
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
Microglia-containing cerebral organoids derived from induced pluripotent stem cells for the study of neurological diseases.

PMID 36936782 · PMC10014280 · iScience · 2023 · 8 claims · 8 setups

Has reproduction · 74

A novel protocol using FGF/EGF/heparin growth factor supplementation and 10% CO2 culture generates cerebral organoids containing neurons, astrocytes, and microglia from iPSCs/hESCs

hesc-derived hesc als-pdc-affected cerebral microarray immunostaining bulk
Hypoxia-Induced Osteopontin-Positive Glioma-Associated Macrophages Facilitate Glioma Mesenchymal Transition via NF-κB Pathway Activation.

PMID 41625475 · PMC12857759 · Cancer communications (London, England) · 2026 · 6 claims · 8 setups

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A subset of GAMs with elevated OPN expression accumulates in response to hypoxic stimulation

thp-1 glioma orthotopic gbm bulk single-cell spatial
Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

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Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

luad demtdmrgs gse131907 wgcna kegg univariate
Decoding the circRNA-miRNA-mRNA regulatory network in hepatitis B virus-driven hepatocellular carcinoma.

PMID 41845440 · PMC13107627 · Cell communication and signaling : CCS · 2026 · 8 claims · 8 setups

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A bioinformatic pipeline combining RNA-seq, circRNA calling, ECDF analysis, PPI, and survival analysis identifies a circRNA-miRNA-mRNA ceRNA network in HBV-integrated HCC cells

hep3b qpcr dysregulated target bulk circrna rt-qpcr
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
Integrated Analysis of Transcriptome and Metabolome Reveals Metabolite Biosynthesis in Pigmented Potatoes.

PMID 41898740 · PMC13026113 · International journal of molecular sciences · 2026 · 7 claims · 7 setups

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Pigmented potato cultivars (DG26, DJ247) accumulate higher levels of flavonoids and linoleic acid derivatives than the white-fleshed cultivar (AG594)

potato bioinformatic untargeted rna-seq rt-qpcr
Patient-derived kidney organoids recapitulate ADPKD and facilitate the identification of Rho pathway inhibitors as candidate therapeutics.

PMID 41946363 · PMC13130689 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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Multi-lineage adult renal organoids (MAROs) can be established directly from adult human kidney tissue and expanded long-term while retaining proximal tubule and collecting duct lineages

maros patient-derived pkd_orgs bulk single-cell immunofluorescence
CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.

PMID 36072582 · PMC9441746 · Frontiers in immunology · 2022 · 8 claims · 8 setups

Has reproduction · 81

Higher stromal and ESTIMATE scores are associated with favorable prognosis in DLBCL

dlbcl ici-related degs ffpe estimate consensus differential

Experiments

Warming Causes a Decline in Baltic Sea Coastal Sediment Microbial Abundance.

PUM2 knockdown regulates the expression and alternative splicing of genes associated with myocardial fibrosis in H9C2 cells.

TBL1X/TBL1XR1 govern β-cell identity through a PAX6-containing gene regulatory network.

TGFβ-activated PDHB promotes mitochondrial pyruvate metabolism and contributes to human endoderm differentiation via ATP-dependent BRG1.

Transcriptomic Responses of the Marine Diatom Phaeodactylum tricornutum to High Carbon and Low Nitrogen Stress.

Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

Integrative miRNA-mRNA Network and Molecular Dynamics-Based Identification of Therapeutic Candidates for Paroxysmal Nocturnal Hemoglobinuria.

Integrative transcriptomics and single-cell transcriptomics analyses reveal potential biomarkers and mechanisms of action in papillary thyroid carcinoma.

Integrated multi-omics analysis combined with clinical validation reveals that HLA-DRB5 and ODAPH are causal risk genes for keratoconus.

Uncovering the transcriptional landscape of estrogen-induced gonadal feminization in the Chinese giant salamander.

Transcriptome analysis provides insights into the regulatory function of alternative splicing in antiviral immunity in grass carp (Ctenopharyngodon idella).

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

Microglia-containing cerebral organoids derived from induced pluripotent stem cells for the study of neurological diseases.

Hypoxia-Induced Osteopontin-Positive Glioma-Associated Macrophages Facilitate Glioma Mesenchymal Transition via NF-κB Pathway Activation.

Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

Decoding the circRNA-miRNA-mRNA regulatory network in hepatitis B virus-driven hepatocellular carcinoma.

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

Integrated Analysis of Transcriptome and Metabolome Reveals Metabolite Biosynthesis in Pigmented Potatoes.

Patient-derived kidney organoids recapitulate ADPKD and facilitate the identification of Rho pathway inhibitors as candidate therapeutics.

CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.