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 63

System / cell line: same ✕ Assay: specific ✕ Clear

Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

Has reproduction · 74

Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

intestinalis same rna-seq strand-specific technical reverse
Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

PMID 38230570 · PMC10795782 · Cancer biology & therapy · 2024 · 8 claims · 6 setups

Has reproduction · 87

NOR-specific and MES-specific gene expression patterns are largely mutually exclusive, exhibiting a teams-like behavior across multiple bulk NB transcriptomic datasets

lines bulk single-cell housekeeping bulk pca single-sample
Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

PMID 41064594 · PMC12501775 · NAR genomics and bioinformatics · 2025 · 8 claims · 8 setups

Has reproduction · 51

Single-cell eQTL analysis across eight immune cell types identified 2593 genes whose expression is significantly associated with common genetic polymorphisms, with most genes showing cell type-specific effects

pbmcs eight pbmc monocytes scrna-seq genetic cis-eqtl
ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

Full-text index only

Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

ductal same sporadic paired cdna quantitative genotyping
A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

PMID 36694043 · PMC9873918 · Communications biology · 2023 · 8 claims · 7 setups

Has reproduction · 83

The DSS phenotype-by-time interaction defines parsimonious temporal (dynamic) expression and splicing signatures of acute and chronic colitis distinct from time-specific differential expression.

intestine colon dss distal bulk phenotypic h&e
A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population.

PMID 16904005 · PMC1779589 · Genome biology · 2006 · 8 claims · 7 setups

Full-text index only

Eight SNPs with extreme European-branch locus-specific branch length (LSBL) were selected from a genome-wide FST dataset as candidates for selection in Europe.

snp irish french fst-based microsatellite genome-wide
The FAS gene, brain volume, and disease progression in Alzheimer's disease.

PMID 19766542 · PMC3100774 · Alzheimer's & dementia : the journal of the Alzheimer's Association · 2010 · 8 claims · 4 setups

Full-text index only

The minor (T) allele of rs1468063 in FAS is significantly associated with faster AD progression after permutation-based multiple-testing correction

peripheral longitudinally same subset snp survival permutation
A novel, non-functional, COL1A1 polymorphism is not associated with lumbar disk disease in young male Greek subjects unlike that of the Sp1 site.

PMID 18694864 · PMC3124709 · Hormones (Athens, Greece) · 2008 · 5 claims · 3 setups

Full-text index only

The COL1A1 3'UTR 4bp insertion polymorphism (A1/A2 alleles) is not associated with LDD in young male Greek subjects

genomic subset genotype pcr-based sequencing chi-square
Association of CFH, LOC387715, and HTRA1 polymorphisms with exudative age-related macular degeneration in a northern Chinese population.

PMID 18682812 · PMC2493029 · Molecular vision · 2008 · 7 claims · 3 setups

Full-text index only

CFH Y402H (rs1061170) variant is not associated with exudative AMD in this northern Chinese cohort

peripheral subset same pcr direct statistical
Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

Has reproduction · 95

Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

breast-cancer-specific tcga ccle four single-sample survival genome-wide
Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

PMID 37138775 · PMC10149407 · iScience · 2023 · 8 claims · 7 setups

Has reproduction · 100

Hsp90-dependent gene expression varies among different yeast strains

diverse same yeast genomes rna-seq v-src growth
TP73 allelic expression in human brain and allele frequencies in Alzheimer's disease.

PMID 15175114 · PMC420466 · BMC medical genetics · 2004 · 8 claims · 6 setups

Full-text index only

A -386G/A SNP in the TP73 P3 promoter is weakly but significantly associated with AD risk in a tri-ethnic elderly population.

brain peripheral sk-nsh-n genomic rt-pcr direct snp
Future possibilities in the prevention of breast cancer: intervention strategies in BRCA1 and BRCA2 mutation carriers.

PMID 11250722 · PMC138789 · Breast cancer research : BCR · 2000 · 8 claims · 8 setups

Full-text index only

BRCA1 and BRCA2 mutations confer an 80-85% lifetime risk (by age 80) of female breast cancer

normal affected women brca1 clonogenic germline mammographic
IgVH genes from different anatomical regions, with different histopathological patterns, of a rheumatoid arthritis patient suggest cyclic re-entry of mature synovial B-cells in the hypermutation process.

PMID 11056671 · PMC17813 · Arthritis research · 2000 · 8 claims · 5 setups

Full-text index only

Somatically mutated IgVH genes with amino acid deletions and mixed IgV molecules were found in all three anatomical regions, suggesting a novel pathway for generating (auto)antibody specificities

synovial same cryosections formalin-fixed cdna seminested double
Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

PMID 18606010 · PMC2464579 · BMC medical genetics · 2008 · 6 claims · 4 setups

Full-text index only

Methylation of the MHC2TA promoter pIV is not associated with MS susceptibility; no methylation was detected in any twin sample regardless of disease status

peripheral mhc2ta pcr sanger bisulfite cpg
An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups

Has reproduction · 85

Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines

oral ffpe scrna-seq integrated scrna-seq spatial ligand-receptor
Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.

PMID 11161385 · PMC2363700 · British journal of cancer · 2001 · 8 claims · 6 setups

Full-text index only

PDC shows frequent alterations of K-ras, p53, p16 and DPC4, confirming these as the core molecular fingerprint of ductal cancer

pancreatic same tumor pet sscp methylation-specific microsatellite
A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

PMID 18940863 · PMC2602776 · Nucleic acids research · 2008 · 7 claims · 4 setups

Full-text index only

A novel Invader assay-based procedure can accurately determine SNP genotypes in trisomic genomic DNA samples in a simple, cost-effective manner

genomic same synthetic invader pyrosequencing hplc
Adaptive history of single copy genes highly expressed in the term human placenta.

PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

Full-text index only

222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

term single same lists microarray comparative site
CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.

PMID 12556968 · PMC2376780 · British journal of cancer · 2003 · 8 claims · 4 setups

Full-text index only

RB1 CpG island hypermethylation is a common epigenetic event associated with development of malignant nervous system tumours

nervous bisulphite-modified same pcr-sscp methylation-specific bisulphite

Experiments

Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

Mutually exclusive teams-like patterns of gene regulation characterize phenotypic heterogeneity along the noradrenergic-mesenchymal axis in neuroblastoma.

Cell type-specific eQTL analysis of COVID-19 based on single-cell transcriptomic data.

ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients.

A genome-wide approach to identify genetic loci with a signature of natural selection in the Irish population.

The FAS gene, brain volume, and disease progression in Alzheimer's disease.

A novel, non-functional, COL1A1 polymorphism is not associated with lumbar disk disease in young male Greek subjects unlike that of the Sp1 site.

Association of CFH, LOC387715, and HTRA1 polymorphisms with exudative age-related macular degeneration in a northern Chinese population.

Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

TP73 allelic expression in human brain and allele frequencies in Alzheimer's disease.

Future possibilities in the prevention of breast cancer: intervention strategies in BRCA1 and BRCA2 mutation carriers.

IgVH genes from different anatomical regions, with different histopathological patterns, of a rheumatoid arthritis patient suggest cyclic re-entry of mature synovial B-cells in the hypermutation process.

Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.

A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

Adaptive history of single copy genes highly expressed in the term human placenta.

CpG island methylation status and mutation analysis of the RB1 gene essential promoter region and protein-binding pocket domain in nervous system tumours.