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 14

System / cell line: conventional ✕ Assay: pcr ✕ Clear

TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

PMID 17526832 · PMC2884950 · Microbiology (Reading, England) · 2007 · 7 claims · 8 setups

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tccP2 is present in 26 of 27 (96.2%) EPEC 2 lineage strains and absent from all 34 EPEC 1 strains tested

clinical pcr-negative representative whole-cell conventional colony locus-specific
Somatic deletion of the NF1 gene in a neurofibromatosis type 1-associated malignant melanoma demonstrated by digital PCR.

PMID 16961930 · PMC1570477 · Molecular cancer · 2006 · 8 claims · 6 setups

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Somatic deletion of the maternal NF1 allele occurred in the melanoma of an NF1 patient, demonstrating biallelic NF1 inactivation.

peripheral microdissected formalin-fixed microsatellite conventional digital
Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

PMID 19133980 · PMC4303606 · British journal of haematology · 2009 · 7 claims · 6 setups

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Downregulation of GR mRNA in the resistant myeloma cell line is caused by a block to transcriptional elongation within intron B of the GR gene

mm.1s pcr demethylating quantitative
Metagenomic analysis of human diarrhea: viral detection and discovery.

PMID 18398449 · PMC2290972 · PLoS pathogens · 2008 · 8 claims · 7 setups

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Micro-mass sequencing (minimal stool input, minimal purification, ~384 reads/sample) can detect known enteric viruses in diarrhea specimens

stool divergent extract preparations sequence-independent maximum enzyme
Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

PMID 16141191 · PMC1197137 · Nucleic acids research · 2005 · 8 claims · 6 setups

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A novel 'bioluminometric assay coupled with terminator (ddNTP) incorporation' (BATI) platform was developed for multiplex SNP typing in a single reaction chamber.

pcr-amplified same sequence luciferase bioluminometric bati comparison
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

PMID 17299583 · PMC1797623 · PloS one · 2007 · 6 claims · 4 setups

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5′-tagged PCR primers enable pooling of homologous PCR products from multiple sources into a single GS20 run with accurate post-hoc assignment of sequences to source

extracts pooled same non-assigned pcr parallel conventional
Competitive enzymatic reaction to control allele-specific extensions.

PMID 15767273 · PMC1065263 · Nucleic acids research · 2005 · 6 claims · 7 setups

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Protease-mediated allele-specific extension (PrASE) uses competition between polymerase activity and Proteinase K-mediated polymerase degradation to allow extension of perfectly matched primers while eliminating slower mismatched primer extension.

genomic immobilized four individuals multiplex protease-mediated effect
A comprehensive catalogue of somatic mutations from a human cancer genome.

PMID 20016485 · PMC3145108 · Nature · 2010 · 8 claims · 7 setups

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Whole-genome sequencing of COLO-829 melanoma cells and matched COLO-829BL normal cells produced the first comprehensive catalogue of somatic mutations from an individual cancer genome

colo-829 additional whole-genome conventional pcr
DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.

PMID 17576693 · PMC1934997 · Nucleic acids research · 2007 · 6 claims · 7 setups

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DNA bar coding combined with pyrosequencing allows parallel, deep characterization of drug resistance mutations across many HIV populations in a single experiment

hiv pooled plasma pyrosequencing conventional rt-pcr
Rare mutations predisposing to familial adenomatous polyposis in Greek FAP patients.

PMID 15833136 · PMC1097718 · BMC cancer · 2005 · 8 claims · 6 setups

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A 250 Kbp deletion spanning intron 5 to beyond exon 15 of APC was identified in one FAP patient using MLPA, karyotyping, and FISH.

genomic peripheral metaphase dhplc sequencing rt-pcr
Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

PMID 18003658 · PMC2248751 · Nucleic acids research · 2008 · 8 claims · 8 setups

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p110 CUX1 is recruited to promoters of cell cycle-related target genes preferentially during S phase

hela hs578t nih3t3 genomic chap-chip conventional scanning
The use of multiple displacement amplification to amplify complex DNA libraries.

PMID 18285362 · PMC2275127 · Nucleic acids research · 2008 · 7 claims · 8 setups

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MDA alone cannot select against/remove plasmid ligation multimers, unlike bacterial propagation

hes3 hes3-derived coli plasmids isolation flcdna gis-pet
Genome profiling of chronic myelomonocytic leukemia: frequent alterations of RAS and RUNX1 genes.

PMID 18925961 · PMC2588460 · BMC cancer · 2008 · 8 claims · 4 setups

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aCGH profiling of CMML samples reveals three profile types: normal-like (two-thirds of cases), large chromosomal abnormalities, and focal single/few-gene gains or losses

bone array-cgh sanger nested
Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

PMID 18776137 · PMC2584123 · Diabetes · 2008 · 6 claims · 7 setups

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Lymphocytes (but not monocytes) from type 1 diabetic patients show a distinct subset of genes with significantly increased H3K9me2 compared with healthy controls.

blood pooled gene chip-chip conventional quantitative

Experiments

TccP2-mediated subversion of actin dynamics by EPEC 2 - a distinct evolutionary lineage of enteropathogenic Escherichia coli.

Somatic deletion of the NF1 gene in a neurofibromatosis type 1-associated malignant melanoma demonstrated by digital PCR.

Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

Metagenomic analysis of human diarrhea: viral detection and discovery.

Multiplex SNP typing by bioluminometric assay coupled with terminator incorporation (BATI).

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

Competitive enzymatic reaction to control allele-specific extensions.

A comprehensive catalogue of somatic mutations from a human cancer genome.

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.

Rare mutations predisposing to familial adenomatous polyposis in Greek FAP patients.

Genome-wide location analysis and expression studies reveal a role for p110 CUX1 in the activation of DNA replication genes.

The use of multiple displacement amplification to amplify complex DNA libraries.

Genome profiling of chronic myelomonocytic leukemia: frequent alterations of RAS and RUNX1 genes.

Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.