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 39

System / cell line: reference ✕ Assay: quantitative ✕ Clear

Allele quantification using molecular inversion probes (MIP).

PMID 16314297 · PMC1301601 · Nucleic acids research · 2005 · 8 claims · 5 setups

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MIP technology at high multiplex (>20,000 SNPs) can provide copy number measurements while simultaneously obtaining allele information

reference ffpe lines na18573 mip restriction quantitative
Imputation-based analysis of association studies: candidate regions and quantitative traits.

PMID 17676998 · PMC1934390 · PLoS genetics · 2007 · 8 claims · 2 setups

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Imputation-based Bayesian regression increases power to detect association compared with standard single-SNP tests, even when the causal variant is directly typed

study phenotyped genotype bayesian
A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

PMID 16351727 · PMC1327677 · BMC genomics · 2005 · 8 claims · 5 setups

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A qPCR method using unique-sequence primers can reproducibly detect chromosomal microdeletions and microduplications

genomic genome pcr real-time fluorescence sequence
Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

PMID 16512914 · PMC1413517 · BMC medical genetics · 2006 · 8 claims · 5 setups

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Patient carries a novel 2.3 Mb deletion in 22q11.2 with proximal breakpoint between RH48663/RH48348 and distal breakpoint between D22S1138/SHGC-145314

genomic maternal 22qtdr chromosome semi-quantitative pcr fish
3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

PMID 19917133 · PMC2781828 · BMC genomics · 2009 · 8 claims · 4 setups

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3' tag DGE transcript profiles are highly reproducible between technical and biological replicates, across libraries made at different labs, and across two generations of Illumina Genome Analyzers (GA I and GA II).

brain hbrr topo-cloned tag microarray quantitative
Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups

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Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation

gingivalis whole-cell comparative gene
ChIP-seq Data Processing and Relative and Quantitative Signal Normalization for Saccharomyces cerevisiae.

PMID 40364978 · PMC12067309 · Bio-protocol · 2025 · 8 claims · 6 setups

Has reproduction · 100

siQ-ChIP measures absolute protein–DNA interaction (IP efficiency) genome-wide without relying on exogenous spike-in chromatin, overcoming limitations of spike-in normalization.

cerevisiae pombe concatenated chip-seq chip-seq high-throughput fastq
Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

PMID 15502245 · PMC3839274 · Disease markers · 2004 · 7 claims · 3 setups

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Standardization of specimen collection, handling, storage, and choice of serum vs. plasma/anticoagulant is essential for comparable proteomic biomarker discovery.

plasma ppp reference identification quantitative specimen
A comparative study of techniques for differential expression analysis on RNA-Seq data.

PMID 25119138 · PMC4132098 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 58

edgeR performs slightly better than DESeq and Cuffdiff2 in terms of the ability to uncover true positives.

brain neurospheres lymphoblastoid simulation single-end paired-end rna-seq
A protein-based set of reference markers for liver tissues and hepatocellular carcinoma.

PMID 19725976 · PMC2742551 · BMC cancer · 2009 · 7 claims · 5 setups

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Three protein spots (beta-actin, HSP60, PDI) show low expression variability across tumourous, non-tumourous cirrhotic, and normal liver tissues by 2-DE (ANOVA p>0.99 ranking)

liver 2-de western immunohistochemistry
HUPO Highlights.

PMID 19862759 · PMC4594800 · Proteomics · 2009 · 8 claims · 8 setups

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Mass spectrometry analysis of human liver reference samples (French Reference liver + Huh7 hepatoma cells) achieves substantial human genome coverage via PeptideAtlas processing

liver subcellular models fetal mass antibody-based quantitative
Mutation in mitochondrial complex I ND6 subunit is associated with defective response to hypoxia in human glioma cells.

PMID 15248896 · PMC481082 · Molecular cancer · 2004 · 8 claims · 8 setups

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An unreported T14634C mutation in the mtDNA-encoded ND6 subunit of Complex I is present in the hypoxia-sensitive glioma cell line M010b but not in hypoxia-tolerant lines.

gbm m010b m006x mtdna quantitative mitochondrial
Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.

PMID 20016837 · PMC2790609 · PloS one · 2009 · 8 claims · 6 setups

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151 'geo-ancestral genes' were identified that are both differentially expressed between AA and CAU subjects and contain SNPs distinguishing YRI (African) from CEU (European) HapMap populations

leukocytes leukocyte-derived archived comparison whole-genome quantitative snp
A genome-wide screen for copy number alterations in Aicardi syndrome.

PMID 19760649 · PMC3640635 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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Aicardi syndrome is thought to result from heterozygous defects in an essential X-linked gene, or from a sex-limited autosomal gene defect, due to its occurrence almost exclusively in females and in 47,XXY males.

genomic subject array quantitative fluorescence
CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

PMID 16504045 · PMC1402331 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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CARAT is a novel algorithm that uses SNP probe intensity and genotype-based allelic dosage response in a regression framework to estimate allele-specific copy number genome-wide.

normal genomic sk-br-3 cancer snp quantitative allele-specific
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

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Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr
N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

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NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

random reference healthy long-term resequencing quantitative sequence
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

PMID 19919682 · PMC3091323 · Genome biology · 2009 · 8 claims · 4 setups

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BioGPS aggregates distributed, third-party gene annotation resources into a single customizable portal for human, mouse, and rat genes.

biogps diverse tissues specified web reference exon
Genome assembly comparison identifies structural variants in the human genome.

PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

genome ceph unrelated individuals whole-genome pcr quantitative
A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

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SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

teds diagnosed ceph snp individual transmission

Experiments

Allele quantification using molecular inversion probes (MIP).

Imputation-based analysis of association studies: candidate regions and quantitative traits.

A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer.

Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.

ChIP-seq Data Processing and Relative and Quantitative Signal Normalization for Saccharomyces cerevisiae.

Advancement of biomarker discovery and validation through the HUPO plasma proteome project.

A comparative study of techniques for differential expression analysis on RNA-Seq data.

A protein-based set of reference markers for liver tissues and hepatocellular carcinoma.

HUPO Highlights.

Mutation in mitochondrial complex I ND6 subunit is associated with defective response to hypoxia in human glioma cells.

Stable patterns of gene expression regulating carbohydrate metabolism determined by geographic ancestry.

A genome-wide screen for copy number alterations in Aicardi syndrome.

CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

Genome assembly comparison identifies structural variants in the human genome.

A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.