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 142

Assay: plasmid ✕ Clear

Use of modified U1 snRNAs to inhibit HIV-1 replication.

PMID 17158512 · PMC1802557 · Nucleic acids research · 2007 · 7 claims · 6 setups

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U1 snRNAs complementary to 5 of 15 targeted conserved regions in the HIV-1 terminal exon significantly suppress HIV-1 protein expression and viral replication, coincident with loss of viral RNA

hiv-1 293t hela bioinformatic western reporter
Detection of 100% of mutations in 124 individuals using a standard UV/Vis microplate reader: a novel concept for mutation scanning.

PMID 16554551 · PMC1409816 · Nucleic acids research · 2006 · 7 claims · 8 setups

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A cleavage-free mismatch oxidation assay using potassium permanganate and a standard UV/Vis microplate reader can detect DNA mismatches spectrophotometrically at 420 nm.

individual hybridized 38mer pbr322 colorimetric uv-vis mismatch
Microarray-based DNA methylation profiling: technology and applications.

PMID 16428248 · PMC1345696 · Nucleic acids research · 2006 · 7 claims · 6 setups

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A microarray-based method enriching unmethylated and methylated DNA fractions via methylation-sensitive restriction enzymes followed by hybridization enables high-throughput DNA methylation profiling of large genomic regions.

genomic postmortem ligated custom cpg tiling
Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

PMID 18047689 · PMC2106846 · Genome biology · 2007 · 8 claims · 6 setups

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Vector insertion site preferences differ substantially between viral vectors and transposons, affecting both oncogenic risk in gene therapy and utility for functional genomics

hela liver gene peripheral retroviral transposon hydrodynamic
A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm.

PMID 18034894 · PMC2241821 · BMC biotechnology · 2007 · 7 claims · 7 setups

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A human scFv library was built on the single scFv13R4 framework with CDR3 loops diversified to mimic natural human CDR3 amino-acid distributions.

coli hela filamentous scfv gfp sds-page fluorescence
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
Genetic variants of chemokine receptor CCR7 in patients with systemic lupus erythematosus, Sjogren's syndrome and systemic sclerosis.

PMID 17587445 · PMC1913537 · BMC genetics · 2007 · 6 claims · 4 setups

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CCR7 gene variants occur at extremely low frequency (allelic frequencies ≤5%) in the German population

genomic hut78 t-cells direct pcr dual
Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

PMID 17359525 · PMC1838427 · BMC molecular biology · 2007 · 8 claims · 8 setups

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OPTC is a candidate gene involved in POAG pathogenesis

genomic pcr optc retinal pcr-sscp dhplc sequencing
Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques.

PMID 17284462 · PMC1865043 · Nucleic acids research · 2007 · 6 claims · 6 setups

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Cryptic lox P sites occur frequently and are homogeneously distributed across the mouse genome (1.2 primary sites per megabase).

genome bac coli el350 genome-wide sequence bacterial
Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

PMID 19014550 · PMC2642827 · BMC genomics · 2008 · 6 claims · 6 setups

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The 2000 listeriosis outbreak was likely caused by an L. monocytogenes strain that persisted in the food processing facility for at least 12 years since 1988

monocytogenes additional food j774 whole-genome comparative pcr
Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

PMID 18990211 · PMC2585095 · BMC microbiology · 2008 · 8 claims · 7 setups

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The 55 clinical B. cereus isolates were phylogenetically diverse, comprising 38 sequence types (STs) distributed across two of three previously described clades.

clinical concatenated cereus isolates multilocus phylogenetic pcr
Bacteriophage Mu integration in yeast and mammalian genomes.

PMID 18953026 · PMC2602771 · Nucleic acids research · 2008 · 8 claims · 8 setups

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In vitro-assembled Mu transpososomes, delivered by electroporation, efficiently integrate marker genes into yeast, mouse ES, human HeLa, and human ES cell genomes

cerevisiae ab2.2 hela fes29 electroporation southern transposition
Molecular dynamics and mutational analysis of a channelopathy mutation in the IIS6 helix of Ca V 1.2.

PMID 18836301 · PMC3196984 · Channels (Austin, Tex.) · 2008 · 8 claims · 4 setups

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I781T in CaV1.2 shifts the voltage-dependence of activation and inactivation to hyperpolarized voltages, reproducing the channelopathy-like gating phenotype of CaV1.4 I745T

homology tsa-201 cav1.2 molecular whole-cell confocal
Functional analysis of the novel TBX5 c.1333delC mutation resulting in an extended TBX5 protein.

PMID 18828908 · PMC2567295 · BMC medical genetics · 2008 · 8 claims · 6 setups

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c.1333delC is a novel de novo frameshift mutation in TBX5 exon 9 predicted to produce an elongated 580-amino-acid protein (74 miscoding + 62 supernumerary C-terminal residues) instead of a truncated one

peripheral cos-7 direct confocal co-localization
Ankyrin-linked hereditary spherocytosis in an African-American kindred.

PMID 18704959 · PMC11304496 · American journal of hematology · 2008 · 6 claims · 7 setups

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A novel heterozygous initiator methionine mutation (ATG→ATA, Met1Ile), termed ankyrin New Haven, was identified in exon 1 of the ankyrin-1 gene as the cause of HS in this kindred.

genomic erythrocyte rabbit dhplc sscp nucleotide
Rise of the machines.

PMID 18670625 · PMC2467494 · PLoS genetics · 2008 · 8 claims · 4 setups

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New short-read sequencing platforms (Illumina Genome Analyzer, 454 FLX, ABI SOLiD) enable rapid, scalable whole-genome resequencing that was previously restricted to dedicated sequencing centers using Sanger methods.

bacillus independent subtilis whole-genome read
Strict sun protection results in minimal skin changes in a patient with xeroderma pigmentosum and a novel c.2009delG mutation in XPD (ERCC2).

PMID 18637129 · PMC2605190 · Experimental dermatology · 2009 · 8 claims · 5 setups

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Strict, rigorous sun protection starting at age 2 resulted in minimal skin disease (only mild lip freckling, no skin cancer) in XP2GO despite an XP diagnosis

fibroblasts xp2go post-uv host real-time
Development of functional genomic tools in trematodes: RNA interference and luciferase reporter gene activity in Fasciola hepatica.

PMID 18612418 · PMC2440534 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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Developed a firefly luciferase (fLUC) reporter gene assay to test for the presence of a viable RNAi pathway in helminth parasites

fasciola schistosoma electroporation-mediated rnai whole-mount
Primase-based whole genome amplification.

PMID 18559358 · PMC2490742 · Nucleic acids research · 2008 · 8 claims · 6 setups

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A primase-based Whole Genome Amplification (pWGA) method was developed using T7 gp4 primase to synthesize primers on-template, removing the requirement for synthetic primers

genomic plasmids circular agarose picogreen dye-terminator
Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.

PMID 18477650 · PMC2443277 · Carcinogenesis · 2008 · 8 claims · 7 setups

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HBx C-terminal deletion mutants (HBx3'-30 and HBx3'-40) produce differentially expressed gene and protein profiles in transfected Huh7 HCC cells, mostly involving transcriptional regulation, oncogenes/tumor suppressors, cell junctions, signal transduction, metabolism and immune response

huh7 frozen hcc genomic cdna two-dimensional western

Experiments

Use of modified U1 snRNAs to inhibit HIV-1 replication.

Detection of 100% of mutations in 124 individuals using a standard UV/Vis microplate reader: a novel concept for mutation scanning.

Microarray-based DNA methylation profiling: technology and applications.

Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm.

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

Genetic variants of chemokine receptor CCR7 in patients with systemic lupus erythematosus, Sjogren's syndrome and systemic sclerosis.

Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

Cryptic loxP sites in mammalian genomes: genome-wide distribution and relevance for the efficiency of BAC/PAC recombineering techniques.

Short-term genome evolution of Listeria monocytogenes in a non-controlled environment.

Genetic diversity of clinical isolates of Bacillus cereus using multilocus sequence typing.

Bacteriophage Mu integration in yeast and mammalian genomes.

Molecular dynamics and mutational analysis of a channelopathy mutation in the IIS6 helix of Ca V 1.2.

Functional analysis of the novel TBX5 c.1333delC mutation resulting in an extended TBX5 protein.

Ankyrin-linked hereditary spherocytosis in an African-American kindred.

Rise of the machines.

Strict sun protection results in minimal skin changes in a patient with xeroderma pigmentosum and a novel c.2009delG mutation in XPD (ERCC2).

Development of functional genomic tools in trematodes: RNA interference and luciferase reporter gene activity in Fasciola hepatica.

Primase-based whole genome amplification.

Mutations in the C-terminus of the X protein of hepatitis B virus regulate Wnt-5a expression in hepatoma Huh7 cells: cDNA microarray and proteomic analyses.