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 502

Assay: blot ✕ Clear

Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection.

PMID 17052347 · PMC1622754 · BMC infectious diseases · 2006 · 8 claims · 4 setups

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TMA/IHC staining patterns of GroEL, GroES, GspD, Ndk and Pyk in cell pellets generally corresponded to differential regulation patterns previously found by 2D gel proteomic analysis of IFN-γ-induced persistence

hep-2 archival pneumoniae immunohistochemistry western gel
Mutational analysis of human CEACAM1: the potential of receptor polymorphism in increasing host susceptibility to bacterial infection.

PMID 16953805 · PMC1859983 · Cellular microbiology · 2007 · 7 claims · 8 setups

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Ile-91 is the primary docking residue required for binding of all tested Nm and Hi strains to CEACAM1, despite structural diversity of bacterial ligands

ceacam1 meningitidis influenzae ha3 homology site-directed receptor
Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

PMID 16934001 · PMC1550284 · PLoS genetics · 2006 · 7 claims · 6 setups

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The E320Q, Q463H, and L706S STAT1 alleles are intrinsically deleterious for both IFNG/GAF-mediated and IFNA/ISGF3-mediated immunity when tested in STAT1-deficient transfected cells

ebv-transformed sv40-transformed nuclear stat1-deficient cdna western immunofluorescence
Genetic diversity among Enterococcus faecalis.

PMID 17611618 · PMC1899230 · PloS one · 2007 · 7 claims · 7 setups

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Virulence and antibiotic resistance traits are distributed across many diverse E. faecalis lineages rather than confined to one clade

faecalis multi-locus dot pcr
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
The loss of transcriptional inhibition by the photoreceptor-cell specific nuclear receptor (NR2E3) is not a necessary cause of enhanced S-cone syndrome.

PMID 17438525 · PMC2669504 · Molecular vision · 2007 · 8 claims · 8 setups

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NR2E3 LBD fused to a heterologous Gal4 DBD mediates dose-dependent transcriptional repression on Gal4-responsive reporters.

cos-1 hela luciferase western electrophoretic
Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

PMID 19011008 · PMC2719557 · Investigative ophthalmology & visual science · 2009 · 6 claims · 5 setups

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TGFBIp (multiple molecular weight forms) is significantly overexpressed in FECD HCEC-DM complex compared to normal endothelium

pooled hcec-dm corneal 2-d western real-time
Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements.

PMID 18942891 · PMC2570425 · PLoS biology · 2008 · 8 claims · 5 setups

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An unbiased SILAC-based proteomic screen identified a relatively small cohort of γ-secretase substrates among thousands of proteins in HeLa cells, all of which are type I transmembrane proteins.

hela presenilin-1 hek silac western
The spectrum of parkinsonian manifestations associated with glucocerebrosidase mutations.

PMID 18852351 · PMC2629407 · Archives of neurology · 2008 · 8 claims · 8 setups

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GBA mutations are associated with a spectrum of parkinsonian phenotypes ranging from Parkinson disease to Lewy body dementia

patients sequencing southern targeted
Tuberculosis vaccine strain Mycobacterium bovis BCG Russia is a natural recA mutant.

PMID 18637199 · PMC2483709 · BMC microbiology · 2008 · 8 claims · 5 setups

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A RecA- phenotype increases genetic stability and may help restrict ongoing genome evolution of BCG substrains while maintaining protective efficacy

bovis bcg genomic cell-free allelic southern sequencing
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 50

A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

erwinia intergenic candidate wounded small northern race
A novel role for mitochondria in regulating epigenetic modification in the nucleus.

PMID 18458531 · PMC2639623 · Cancer biology & therapy · 2008 · 8 claims · 6 setups

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Mitochondria regulate epigenetic (DNA methylation) modification in the nucleus

mcf12a mda-mb-435 143b restriction western bisulfite
Identification of beta-secretase (BACE1) substrates using quantitative proteomics.

PMID 20041192 · PMC2793532 · PloS one · 2009 · 7 claims · 5 setups

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Quantitative proteomics of conditioned medium from BACE1-overexpressing HEK and HeLa cells identified 68 putative β-secretase substrates

hek293 hela hek concentrated silac western sds-page
H-DBAS: human-transcriptome database for alternative splicing: update 2010.

PMID 19969536 · PMC2808982 · Nucleic acids research · 2010 · 8 claims · 4 setups

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RNA-Seq tags from the polysome fraction identify AS exons that are very likely used for protein synthesis

dld-1 rna-seq western real-time
Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth.

PMID 19920251 · PMC2812789 · Science signaling · 2009 · 7 claims · 8 setups

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Oncogenic FGFR1 directly phosphorylates PKM2 at tyrosine 105 (Y105), inhibiting its enzymatic activity

293t kg-1a recombinant h1299 ms-based co-transfection enzymatic
Expression patterns of cardiac myofilament proteins: genomic and protein analysis of surgical myectomy tissue from patients with obstructive hypertrophic cardiomyopathy.

PMID 19808356 · PMC2765062 · Circulation. Heart failure · 2009 · 8 claims · 4 setups

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Myofilament protein levels (MYBPC3 and MYH7) are increased, not decreased, in HCM patients carrying a mutation in either gene compared to healthy heart tissue

genomic lysate formalin-fixed myectomy mutational western immunohistochemistry
Malarial hemozoin activates the NLRP3 inflammasome through Lyn and Syk kinases.

PMID 19696895 · PMC2722371 · PLoS pathogens · 2009 · 7 claims · 8 setups

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Hemozoin induces IL-1β maturation and secretion in an NLRP3-, ASC- and caspase-1-dependent, but NLRC4-independent, manner

pma-differentiated bone-marrow-derived asc nlrp3 elisa western peritoneal
Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

PMID 19674479 · PMC2743674 · Molecular brain · 2009 · 7 claims · 8 setups

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R125M, R127L, and R125M/R127L BDNF SNP variants are poorly cleaved, resulting in predominant secretion of proBDNF (CR-proBDNF)

bdnf hippocampal cortical cerebellar bioinformatic western immunoprecipitation
CTCF/cohesin-binding sites are susceptible to replication-associated DNA damage and genomic instability in cancer cells.

PMID 41630911 · PMC12860730 · iScience · 2026 · 8 claims · 8 setups

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CTCF and cohesin (RAD21) remain co-bound to DNA throughout interphase, including during the S (replication) phase, in HeLa cells

hela tumors flow chromatin frap
Stress Responsive bZIP Transcription Factors ATF4 and BACH1 Cooperate With MAF-Family bZIP Protein NRL to Fine-Tune Rod Photoreceptor Gene Expression.

PMID 42246540 · PMC13249099 · Investigative ophthalmology & visual science · 2026 · 8 claims · 7 setups

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ATF4 and BACH1 are identified as bZIP protein interactors of NRL

y2hgold hek293 p28 flow-sorted yeast co-immunoprecipitation immunofluorescence

Experiments

Tissue MicroArray (TMA) analysis of normal and persistent Chlamydophila pneumoniae infection.

Mutational analysis of human CEACAM1: the potential of receptor polymorphism in increasing host susceptibility to bacterial infection.

Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

Genetic diversity among Enterococcus faecalis.

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

The loss of transcriptional inhibition by the photoreceptor-cell specific nuclear receptor (NR2E3) is not a necessary cause of enhanced S-cone syndrome.

Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements.

The spectrum of parkinsonian manifestations associated with glucocerebrosidase mutations.

Tuberculosis vaccine strain Mycobacterium bovis BCG Russia is a natural recA mutant.

Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

A novel role for mitochondria in regulating epigenetic modification in the nucleus.

Identification of beta-secretase (BACE1) substrates using quantitative proteomics.

H-DBAS: human-transcriptome database for alternative splicing: update 2010.

Tyrosine phosphorylation inhibits PKM2 to promote the Warburg effect and tumor growth.

Expression patterns of cardiac myofilament proteins: genomic and protein analysis of surgical myectomy tissue from patients with obstructive hypertrophic cardiomyopathy.

Malarial hemozoin activates the NLRP3 inflammasome through Lyn and Syk kinases.

Multiple functions of precursor BDNF to CNS neurons: negative regulation of neurite growth, spine formation and cell survival.

CTCF/cohesin-binding sites are susceptible to replication-associated DNA damage and genomic instability in cancer cells.

Stress Responsive bZIP Transcription Factors ATF4 and BACH1 Cooperate With MAF-Family bZIP Protein NRL to Fine-Tune Rod Photoreceptor Gene Expression.