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 64

System / cell line: culture ✕ Assay: expressed ✕ Clear

Three-dimensional neuroblastoma cell culture: proteomic analysis between monolayer and multicellular tumor spheroids.

PMID 18797883 · PMC2804865 · Pediatric surgery international · 2008 · 7 claims · 3 setups

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18 protein spots were differentially over-expressed in neuroblastoma spheroids compared to monolayers

neuroblastoma excised monolayer 2-d lc-ms fractionation
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

Has reproduction · 53

Patient-derived colorectal cancer organoids (CRCOs) can be established from surgical CRC tissue with an 82% success rate (41/50)

crc colorectal crcos crco organoid drug bulk
Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

PMID 16079153 · PMC4729368 · Development (Cambridge, England) · 2005 · 7 claims · 7 setups

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Neocortical progenitor cells show rostrocaudal gradients of gene expression rather than discrete domains/compartments

neocortex dorsal cortex embryo oligonucleotide microarray non-isotopic
The role of proteomics in depression research.

PMID 19997739 · PMC2940035 · European archives of psychiatry and clinical neuroscience · 2010 · 8 claims · 8 setups

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Proteomics offers a complementary, functional-endpoint approach that can elucidate MDD pathophysiological mechanisms and biomarkers beyond transcriptomic/targeted studies

postmortem schizophrenia frontal hypothalamus gel shotgun proteome
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
Single-cell RNA-sequencing of dermal fibroblasts demonstrates culture-induced changes and variable persistence of keloid disease features.

PMID 42058918 · PMC13123497 · iScience · 2026 · 7 claims · 6 setups

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Fibroblast culture leads to subtype assimilation, with in vivo heterogeneity persisting only minimally by passage 4

dermal mesenchymal stromal patient-matched single-cell bulk qpcr
Olfactory epithelium organoid models identify Ddit3 as a potential therapeutic target against inflammation-related olfactory sensory neuronal loss and functional deficit.

PMID 42088417 · PMC13137857 · International journal of biological sciences · 2026 · 8 claims · 8 setups

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Three inflammatory OE organoid models (LPS instillation, TNFα treatment, doxycycline induction) were established and mimic impaired cell proliferation and neuronal genesis seen in olfactory inflammation

organoid organoids ddit3 olfactory organoid bulk aav-shrna
Bacillus velezensis EU07 suppresses Fusarium graminearum via transcriptomic reprogramming.

PMID 42103992 · PMC13234024 · Applied microbiology and biotechnology · 2026 · 8 claims · 7 setups

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EU07 exposure compromises fungal cellular integrity, causing severe hyphal distortion

graminearum five apolipophorin dual rna-seq gene
Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

PMID 27355630 · PMC4927094 · PloS one · 2016 · 8 claims · 8 setups

Has reproduction · 54

In Cstb-/- microglia, 184 genes were differentially expressed relative to control, of which 33 were identified by both microarray and RNA-seq.

analysis microarray rna-seq quantitative
SARS--beginning to understand a new virus.

PMID 15035025 · PMC7097337 · Nature reviews. Microbiology · 2003 · 8 claims · 8 setups

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A previously unknown coronavirus (SARS-CoV) was isolated from FRhK-4 and Vero E6 cells inoculated with clinical specimens from SARS patients and identified as the causative agent of SARS

frhk-4 macaques sars-cov coronavirus virus infection whole-genome
Multi-omics analysis of interspecies interactions in a soil Streptomyces community provides functional insights into siderophore ecology.

PMID 41942569 · PMC13061897 · Scientific reports · 2026 · 8 claims · 7 setups

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Strain A shows pronounced phenotypic growth stimulation (increased colony area, aerial hyphae) when co-cultured with strains B, C, and D, strongest with strain C

environmental agar streptomyces genomes pairwise untargeted rna-seq
Integrated multiomics reveals starvation-driven keratin degradation and persistence in Fervidobacterium islandicum AW-1.

PMID 42111188 · PMC13157175 · iScience · 2026 · 8 claims · 8 setups

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Keratinolytic proteases are constitutively expressed, but starvation induces a coordinated regulatory program that couples keratin degradation to stress adaptation.

fervidobacterium islandicum bulk quantitative untargeted
A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms.

PMID 35019679 · PMC8754136 · Microbiology spectrum · 2022 · 8 claims · 9 setups

Has reproduction · 36

Microbulbifer sp. YX04 shows high algicidal activity against P. globosa, peaking at 93.2% in the declining growth phase

phaeocystis strain yx04 globosa algicidal 16s scanning
Defining the signature of deformable and infectious Plasmodium falciparum gametocytes.

PMID 42064353 · PMC13126010 · Wellcome open research · 2026 · 7 claims · 7 setups

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Deformable gametocytes are immediately infectious upon release from the bone marrow into circulation.

synchronized falciparum blood microsphere bulk exflagellation
Development and validation of a potency assay matrix for optimized and consistent manufacture of clinical mesenchymal stem/stromal cells.

PMID 41798920 · PMC12960169 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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MSCs consistently suppress T cell proliferation

pbmcs cd4+ monocytes msc-conditioned suppression regulatory macrophage
Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.

PMID 32019831 · PMC7002113 · mSystems · 2020 · 7 claims · 8 setups

Has reproduction · 57

Hundreds of intergenic (itsRNAs) and antisense (asRNAs) sRNAs are expressed in the halite endolithic microbial community of the Atacama Desert

halite same identified conserved strand-specific genome-resolved srna
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
CAF-enriched COL4A6 promotes gastric cancer progression and stromal remodeling despite an inverse association in bulk transcriptomes.

PMID 41735371 · PMC13031391 · Scientific reports · 2026 · 7 claims · 7 setups

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COL4A6 carries an inverse association (OR<1) in bulk transcriptome-based risk models despite being markedly upregulated and predominantly localized to the CAF compartment in clinical specimens

tcga-stad gse66229 gse183904 paired bulk microarray scrna-seq
GRAMD1B is a regulator of lipid homeostasis, autophagic flux and phosphorylated tau.

PMID 40204713 · PMC11982250 · Nature communications · 2025 · 8 claims · 7 setups

Has reproduction · 91

GRAMD1B is increased in excitatory neurons of human neural organoids (HNOs) carrying the MAPT R406W mutation

neural hno single-cell immunofluorescence western
Enterotoxins A and B produced by Staphylococcus aureus increase cell proliferation, invasion and cytarabine resistance in acute myeloid leukemia cell lines.

PMID 37810000 · PMC10559070 · Heliyon · 2023 · 8 claims · 8 setups

Has reproduction · 88

SEA and SEB treatment increases cell proliferation in AML cell lines

aml cgp differentially proliferation culture transwell

Experiments

Three-dimensional neuroblastoma cell culture: proteomic analysis between monolayer and multicellular tumor spheroids.

Molecular Biomarker of Drug Resistance Developed From Patient-Derived Organoids Predicts Survival of Colorectal Cancer Patients.

Genomic characterisation of a Fgf-regulated gradient-based neocortical protomap.

The role of proteomics in depression research.

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

Single-cell RNA-sequencing of dermal fibroblasts demonstrates culture-induced changes and variable persistence of keloid disease features.

Olfactory epithelium organoid models identify Ddit3 as a potential therapeutic target against inflammation-related olfactory sensory neuronal loss and functional deficit.

Bacillus velezensis EU07 suppresses Fusarium graminearum via transcriptomic reprogramming.

Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

SARS--beginning to understand a new virus.

Multi-omics analysis of interspecies interactions in a soil Streptomyces community provides functional insights into siderophore ecology.

Integrated multiomics reveals starvation-driven keratin degradation and persistence in Fervidobacterium islandicum AW-1.

A Novel Algicidal Bacterium, Microbulbifer sp. YX04, Triggered Oxidative Damage and Autophagic Cell Death in Phaeocystis globosa, Which Causes Harmful Algal Blooms.

Defining the signature of deformable and infectious Plasmodium falciparum gametocytes.

Development and validation of a potency assay matrix for optimized and consistent manufacture of clinical mesenchymal stem/stromal cells.

Regulatory Noncoding Small RNAs Are Diverse and Abundant in an Extremophilic Microbial Community.

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

CAF-enriched COL4A6 promotes gastric cancer progression and stromal remodeling despite an inverse association in bulk transcriptomes.

GRAMD1B is a regulator of lipid homeostasis, autophagic flux and phosphorylated tau.

Enterotoxins A and B produced by Staphylococcus aureus increase cell proliferation, invasion and cytarabine resistance in acute myeloid leukemia cell lines.