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 31

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

Alternative splicing and bioinformatic analysis of human U12-type introns.

PMID 17332017 · PMC1874599 · Nucleic acids research · 2007 · 8 claims · 6 setups

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The long, evolutionarily conserved polypyrimidine (Py) tract of the JNK2 U2-U12 hybrid intron provides the signal for default inclusion of the downstream alternative exon 6b in non-neuronal cells

hela hek293 genome jnk2 rt-pcr minigene bioinformatic
A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.

PMID 19860899 · PMC2774331 · BMC genomics · 2009 · 8 claims · 6 setups

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HaloCHIP is a functional antibody-free alternative to ChIP that uses covalent capture of HaloTag-fusion protein-DNA complexes on HaloLink resin

hela computational living halochip halochip-chip chip-chip
Point mutations in GLI3 lead to misregulation of its subcellular localization.

PMID 19829694 · PMC2758996 · PloS one · 2009 · 6 claims · 8 setups

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The MID1-α4-PP2A complex regulates the subcellular localization and transcriptional activity of GLI3.

hela immunofluorescence real-time luciferase
Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length.

PMID 34871442 · PMC8682771 · Nucleic acids research · 2021 · 8 claims · 8 setups

Has reproduction · 58

RPS6 becomes progressively dephosphorylated on ribosomes as they translate along an mRNA CDS

hela mef phospho-rps6-selective 80s immunoblotting
A high throughput method for genome-wide analysis of retroviral integration.

PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

hela ht3 genome chromosomes isf vita sanger
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 clinical course and genetic defect in the PCFT gene in a 27-year-old woman with hereditary folate malabsorption.

PMID 18718264 · PMC3835188 · The Journal of pediatrics · 2008 · 6 claims · 5 setups

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The patient carries two identical homozygous mutations (GC>AA at positions 197/198) in exon 1 of PCFT, causing a premature stop codon (C66X)

parental rfc hela blood genomic [3h]5-methyltetrahydrofolate northern
No direct effect of the -521 C/T polymorphism in the human dopamine D4 receptor gene promoter on transcriptional activity.

PMID 16723017 · PMC1481588 · BMC molecular biology · 2006 · 8 claims · 3 setups

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The -521 C/T SNP has no significant effect on transcriptional activity of the DRD4 promoter in any of three neural cell lines tested

sk-n-f1 rt-pcr luciferase
Mutations of the beta- and gamma-catenin genes are uncommon in human lung, breast, kidney, cervical and ovarian carcinomas.

PMID 11437403 · PMC2363927 · British journal of cancer · 2001 · 7 claims · 4 setups

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β-catenin and γ-catenin gene mutations are uncommon in human lung, breast, kidney, cervical and ovarian carcinomas

lung carcinoma lines pcr-sscp rt-pcr-sscp direct
Deletion of dinucleotide repeat (Delta 14 allele) in the methylthioadenosine phosphorylase (MTAP) promoter and the allelotype of MTAP promoter in the Japanese population.

PMID 11985785 · PMC5927014 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 4 setups

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DHL-9 lymphoma cells lack detectable MTAP enzyme activity despite possessing an intact (non-deleted) MTAP gene

dhl-9 genomic lymphoblastoid hela pcr allele-specific luciferase
Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

PMID 18988625 · PMC2602766 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Thermodynamic stability (Tm and standard free-energy change, ΔG) of the seed duplex is a major determinant of siRNA off-target effect efficiency

hela protein-free dual-luciferase reporter thermodynamic
A missense mutation (Q279R) in the fumarylacetoacetate hydrolase gene, responsible for hereditary tyrosinemia, acts as a splicing mutation.

PMID 11476670 · PMC35353 · BMC genetics · 2001 · 8 claims · 7 setups

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The Q279R missense mutation acts as a splicing mutation in vivo, causing skipping of exon 9 (alone or with exon 8) rather than simply altering the encoded amino acid.

microdissected resected non-tumor liver pcr-rflp immunohistochemistry western
Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

PMID 18267968 · PMC2367719 · Nucleic acids research · 2008 · 6 claims · 8 setups

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The seed arm (guide strand positions 2-8), its complementary passenger-strand sequence, the 5' end of the guide strand, and the 3' overhang of the passenger strand can be simultaneously replaced with DNA without substantial loss of gene-silencing activity.

cho-k1 e14tg2a recombinant hela dual-luciferase rt-pcr electrophoresis
Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

PMID 16034026 · PMC1179734 · Nucleic acids research · 2005 · 8 claims · 6 setups

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L1 insertions are directly responsible for genomic deletions (L1IMDs) confirmed in both human and chimpanzee genomes

hg16 genomic individuals element computational pcr pcr-based
P19 H-ras induces G1/S phase delay maintaining cells in a reversible quiescence state.

PMID 20046837 · PMC2798614 · PloS one · 2009 · 8 claims · 8 setups

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p19 regulates telomerase activity through its interaction with p73α/β proteins

yeast hela yeast facs pkc
Translation affects mRNA stability in a codon-dependent manner in human cells.

PMID 31012849 · PMC6529216 · eLife · 2019 · 8 claims · 8 setups

Has reproduction · 87

Translation strongly affects mRNA stability in a codon-dependent manner in human cells, with specific codons stabilizing or destabilizing mRNAs.

293t incl endogenous time-course orfome slam-seq
Histone deacetylase SIRT6 regulates tryptophan catabolism and prevents metabolite imbalance associated with neurodegeneration.

PMID 41345108 · PMC12789597 · Nature communications · 2025 · 7 claims · 8 setups

Has reproduction · 93

SIRT6 is an evolutionarily conserved regulator of tryptophan catabolism that balances tryptophan usage between the kynurenine and serotonin/melatonin pathways

embryonic brains sirt6 serum untargeted rna-seq microarray
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
Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

PMID 17945002 · PMC2242669 · Breast cancer research : BCR · 2007 · 8 claims · 7 setups

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-26G>A polymorphism in the BRCA2 5' UTR is functional: the A allele drives roughly twice the reporter gene expression of the G allele in MCF-7 and HeLa cells

mcf-7 hela brca2 peripheral luciferase transcription genotyping
Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.

PMID 17705821 · PMC2045109 · BMC molecular biology · 2007 · 8 claims · 8 setups

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Multiple alternatively spliced 5'-UTR isoforms of human PPARdelta mRNA differ in translation efficiency

placenta five lines huh7 5'-race rt-pcr real-time

Experiments

Alternative splicing and bioinformatic analysis of human U12-type introns.

A functional analysis of the CREB signaling pathway using HaloCHIP-chip and high throughput reporter assays.

Point mutations in GLI3 lead to misregulation of its subcellular localization.

Phosphorylation of ribosomal protein S6 differentially affects mRNA translation based on ORF length.

A high throughput method for genome-wide analysis of retroviral integration.

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

The clinical course and genetic defect in the PCFT gene in a 27-year-old woman with hereditary folate malabsorption.

No direct effect of the -521 C/T polymorphism in the human dopamine D4 receptor gene promoter on transcriptional activity.

Mutations of the beta- and gamma-catenin genes are uncommon in human lung, breast, kidney, cervical and ovarian carcinomas.

Deletion of dinucleotide repeat (Delta 14 allele) in the methylthioadenosine phosphorylase (MTAP) promoter and the allelotype of MTAP promoter in the Japanese population.

Thermodynamic stability and Watson-Crick base pairing in the seed duplex are major determinants of the efficiency of the siRNA-based off-target effect.

A missense mutation (Q279R) in the fumarylacetoacetate hydrolase gene, responsible for hereditary tyrosinemia, acts as a splicing mutation.

Functional dissection of siRNA sequence by systematic DNA substitution: modified siRNA with a DNA seed arm is a powerful tool for mammalian gene silencing with significantly reduced off-target effect.

Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

P19 H-ras induces G1/S phase delay maintaining cells in a reversible quiescence state.

Translation affects mRNA stability in a codon-dependent manner in human cells.

Histone deacetylase SIRT6 regulates tryptophan catabolism and prevents metabolite imbalance associated with neurodegeneration.

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

Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

Alternative splicing of human peroxisome proliferator-activated receptor delta (PPAR delta): effects on translation efficiency and trans-activation ability.