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 28

System / cell line: extract ✕ Assay: analysis ✕ Clear

Methods for proteomic analysis of transcription factors.

PMID 19726046 · PMC2778203 · Journal of chromatography. A · 2009 · 8 claims · 8 setups

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Systematic oligonucleotide 'trapping' at nM DNA concentrations allows purification of TF-RE complexes in a highly purified state, exploiting the high specific affinity vs. low non-specific affinity of TFs for DNA

nuclear crude intact partially emsa southwestern systematic
Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

PMID 18989384 · PMC2579937 · Molecular vision · 2008 · 8 claims · 4 setups

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Worn silicone hydrogel contact lenses deposit a wide array of proteins from the tear film and other sources.

deposit excised pooled worn sds-page in-gel lc-ms-ms
Gene Ontology annotations: what they mean and where they come from.

PMID 18460184 · PMC2367625 · BMC bioinformatics · 2008 · 7 claims · 3 setups

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A GO annotation is a formal statement linking a gene product type to a molecular function, biological process, or cellular component type, based on experimental observations or inferences.

extract embryo preimplantation enzymatic mutational immunofluorescence
Genomics: applications in mechanism elucidation.

PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

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Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

extract panel saccharomyces inbred affinity cytotoxicity genome-wide
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
Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.

PMID 39227168 · PMC11412076 · FEMS microbiology ecology · 2024 · 5 claims · 8 setups

Has reproduction · 83

A near-complete metagenome-assembled genome (MAG) of Dolichospermum lemmermannii (FEM_B0920) was recovered from a Lake Garda bloom and clarified the species' taxonomic position within the genus Dolichospermum and the ADA group.

dolichospermum filter fem_b0920 lake shotgun cyanotoxin phylogenomic
Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.

PMID 16209721 · PMC1262696 · BMC biology · 2005 · 8 claims · 9 setups

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hLsg1 is the human orthologue of yeast Lsg1p and defines a family of circularly permuted GTPases named YRG (YlqF Related GTPases)

multi-species recombinant immunoprecipitated hela phylogenetic gtp gtpase
Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

PMID 17927842 · PMC2174947 · BMC molecular biology · 2007 · 7 claims · 8 setups

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A 34-nt sequence motif (-81 to -48) is present in all primate edn promoters and in macaque ecp promoter but is deleted in other primate ecp promoters

primate hepg2 32p-labeled sequence rt-pcr luciferase
Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

PMID 18348714 · PMC2311278 · Journal of translational medicine · 2008 · 8 claims · 8 setups

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Crude LASH extract and its purified components (withanone, withaferin A) act through distinct but partially overlapping molecular gene-regulatory networks

tumor-derived tumor lash gene cytotoxicity sirna ribozyme
'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.

PMID 20001958 · PMC3022307 · The Biochemical journal · 2009 · 8 claims · 8 setups

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Comparative genomics is the single most effective strategy for predicting functions of unknown proteins and finding genes for orphan enzymes

lactococcus lactis arabidopsis coli gene recombinant enzyme
MSH6 missense mutations are often associated with no or low cancer susceptibility.

PMID 15354210 · PMC2409912 · British journal of cancer · 2004 · 7 claims · 8 setups

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Most MSH6 missense changes found in MSI-positive tumours are likely clinically innocent or of low cancer-susceptibility significance

microdissected blood individuals paraffin-embedded microsatellite exon sscp
Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome.

PMID 18490959 · PMC2386506 · Molecular vision · 2008 · 7 claims · 6 setups

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A novel affinity-enrichment strategy using UV cross-linked protease inhibitor peptides on Protein A/G columns improves capture of the TM protease proteome compared to SDS-PAGE fractionation alone

cytosolic affinity-eluted porcine affinity-enriched affinity western sds-page
Mucospheres produced by a mixotrophic protist impact ocean carbon cycling.

PMID 35288549 · PMC8921327 · Nature communications · 2022 · 8 claims · 8 setups

Has reproduction · 58

P. cf. balticum constructs carbon-rich mucospheres that attract, capture and immobilise microbial prey to facilitate phago-heterotrophic consumption

tara four xenic balticum 18s its toxin
A conserved glycan motif induces broadly reactive functional antibodies against the zoonotic pathogen Streptococcus suis.

PMID 41880495 · PMC13015895 · Science advances · 2026 · 8 claims · 8 setups

Has reproduction · 77

Pathogenic S. suis lineages express two structural RPS variants that differ by presence/absence of glucose but share a conserved glycan core

publicly suis rps δsrpp comparative plant glycosyl
Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

PMID 19082872 · PMC3693453 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups

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GroEL/osmolyte mixtures can be used to refold difficult-to-fold chimeric affinity-tagged proteins by exploiting intrinsic chaperonin binding.

coli sds-page glutathione pepck-gst sds-page maldi-tof native
Slowly progressive encephalopathy with hearing loss due to a mutation in the mtDNA tRNA(Leu(CUN)) gene.

PMID 20022607 · PMC3891822 · Journal of the neurological sciences · 2010 · 8 claims · 7 setups

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The heteroplasmic m.12276G>A mtDNA tRNA Leu(CUN) mutation causes a childhood-onset, slowly progressive encephalopathy with ataxia, cognitive impairment, dyspraxia, and sensorineural hearing loss

skeletal muscle genomic individual histochemistry biochemical direct
Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

PMID 35784648 · PMC9243631 · Cell reports methods · 2022 · 8 claims · 7 setups

Has reproduction · 66

A purification-free hyperTRIBE adaptation using FMR1-ADARcd-V5 identifies stress granule RNAs via condition-specific A-to-G editing read out by VASA-seq.

drosophila predicted vasa-seq single-cell single-molecule
Neuroacanthocytosis associated with a defect of the 4.1R membrane protein.

PMID 17298666 · PMC1805452 · BMC neurology · 2007 · 8 claims · 8 setups

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Four unrelated NA patients show a novel erythrocyte membrane defect: 4.1R protein deficiency

erythrocyte genomic peripheral erythrocytes sds-page non-denaturing direct
Asthma investigators begin to reap the fruits of genomics.

PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups

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Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.

monkey models lung inbred cdna oligonucleotide northern
Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.

PMID 15230980 · PMC459218 · BMC molecular biology · 2004 · 8 claims · 8 setups

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P. falciparum produces full-length PfCnA/PfCnB (calcineurin) and PP7 as well as proteolytically processed catalytic cores in vivo, likely as intermediates of a degradation pathway

falciparum coli native falciparum-infected rt-pcr recombinant peptide

Experiments

Methods for proteomic analysis of transcription factors.

Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

Gene Ontology annotations: what they mean and where they come from.

Genomics: applications in mechanism elucidation.

Metagenomic analysis of human diarrhea: viral detection and discovery.

Taxonomic and functional metagenomic assessment of a Dolichospermum bloom in a large and deep lake south of the Alps.

Human Lsg1 defines a family of essential GTPases that correlates with the evolution of compartmentalization.

Transcriptional regulation of human eosinophil RNases by an evolutionary- conserved sequence motif in primate genome.

Merger of ayurveda and tissue culture-based functional genomics: inspirations from systems biology.

'Unknown' proteins and 'orphan' enzymes: the missing half of the engineering parts list--and how to find it.

MSH6 missense mutations are often associated with no or low cancer susceptibility.

Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome.

Mucospheres produced by a mixotrophic protist impact ocean carbon cycling.

A conserved glycan motif induces broadly reactive functional antibodies against the zoonotic pathogen Streptococcus suis.

Strategies for folding of affinity tagged proteins using GroEL and osmolytes.

Slowly progressive encephalopathy with hearing loss due to a mutation in the mtDNA tRNA(Leu(CUN)) gene.

Identification of the stress granule transcriptome via RNA-editing in single cells and in vivo.

Neuroacanthocytosis associated with a defect of the 4.1R membrane protein.

Asthma investigators begin to reap the fruits of genomics.

Post-translational generation of constitutively active cores from larger phosphatases in the malaria parasite, Plasmodium falciparum: implications for proteomics.