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 392

Assay: rt-pcr ✕ Clear

A well-conserved Plasmodium falciparum var gene shows an unusual stage-specific transcript pattern.

PMID 12787360 · PMC2869446 · Molecular microbiology · 2003 · 8 claims · 8 setups

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Full-length var transcripts (detected by the complex var exon 2 probe) are present only in ring stages, not in pigmented trophozoites, across multiple parasite lines

falciparum red northern static rt-pcr
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

PMID 15534692 · PMC526178 · PLoS biology · 2004 · 8 claims · 6 setups

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Intramolecular pairs of oppositely oriented Alu elements within the same pre-mRNA form dsRNA foldback structures that are major substrates for A-to-I RNA editing

huge brain pre-mrna greater genomic rt-pcr quantitative
Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene.

PMID 16429166 · PMC1342637 · PLoS genetics · 2005 · 8 claims · 5 setups

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PANTHER subPSEC scores correctly predicted the functional impact of >94% (16/17) of tested naturally occurring ABCA1 variants

abca1 stably subpsec cholesterol rt-pcr
Mutation analysis of FANCD2, BRIP1/BACH1, LMO4 and SFN in familial breast cancer.

PMID 16280053 · PMC1410737 · Breast cancer research : BCR · 2005 · 8 claims · 8 setups

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There is no evidence that highly penetrant exonic or splice site mutations in FANCD2, BRIP1/BACH1, LMO4 or SFN contribute to familial breast cancer

germline lymphoblastoid dhplc sequencing rt-pcr
High proportion of recurrent germline mutations in the BRCA1 gene in breast and ovarian cancer patients from the Prague area.

PMID 16168118 · PMC1242140 · Breast cancer research : BCR · 2005 · 8 claims · 4 setups

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BRCA1 c.5266dupC (5382insC) is the dominant recurrent mutation driving hereditary breast/ovarian cancer in this Czech population

genomic pcr-amplified cdna truncation direct 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
Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

PMID 15804357 · PMC1129089 · BMC genomics · 2005 · 8 claims · 6 setups

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MagT1 is a novel mammalian Mg2+ transporter with channel-like properties, showing no amino acid sequence identity to other known transporters

kidney mdct tissues xenopus oligonucleotide northern real-time
Genomic sequencing of the severe acute respiratory syndrome-coronavirus.

PMID 16916263 · PMC7121524 · Methods in molecular biology (Clifton, N.J.) · 2006 · 7 claims · 7 setups

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PCR-based amplification and direct sequencing of SARS-CoV genome fragments is feasible from uncultured clinical specimens (serum, nasopharyngeal aspirate, stool), avoiding culture-derived artifacts and biohazard risk.

sars-cov extracted cdna pcr viral reverse real-time
The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

PMID 16859552 · PMC1538596 · BMC genomics · 2006 · 7 claims · 7 setups

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Numts co-amplified with mtDNA during PCR generate false heteroplasmic signals at specific nucleotide positions.

143b ffpe blood cloned southern pcr rt-pcr
Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

PMID 16536879 · PMC1479377 · BMC bioinformatics · 2006 · 8 claims · 6 setups

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ENACE, a cross-species EST-to-genome comparison algorithm, can identify novel cassette-on exons and retained introns for EST-scanty species and distinguish conserved vs lineage-specific exons

presumably orthologous enace genes cross-species rt-pcr-sequencing nonsynonymous-to-synonymous
MRPS18CP2 alleles and DEFA3 absence as putative chromosome 8p23.1 modifiers of hearing loss due to mtDNA mutation A1555G in the 12S rRNA gene.

PMID 18154640 · PMC2233610 · BMC medical genetics · 2007 · 8 claims · 6 setups

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Chromosome 8p23.1 has previously been proposed as a nuclear modifier locus for A1555G-associated hearing loss phenotype

blood a1555g lymphoblastoid nuclear pcr-rflp direct rt-pcr
Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

PMID 17967058 · PMC2042017 · PLoS pathogens · 2007 · 8 claims · 8 setups

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APOBEC3C is necessary and sufficient to induce G-to-A mutation in some HIV-1 strains despite Vif expression

magi pbmc 293t supt1 sensitive rt-pcr western
Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

PMID 17598913 · PMC1929078 · BMC genomics · 2007 · 8 claims · 4 setups

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Standard Affymetrix expression GeneChips (MOE430, HG-U133) contain probe sets that detect natural antisense transcripts (NATs)

moe430 pooled organs probe strand-specific microarray
Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

PMID 18654835 · PMC4973579 · Biogerontology · 2009 · 8 claims · 7 setups

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Treatment of HCA3 human diploid fibroblasts with a mild dose of H2O2 (600 μM) induces premature senescence without killing the cells.

hca3 differentially mudpit cdna semi-quantitative
CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

neuroblastoma nlf athymic methylation-specific quantitative soft
Molecular dissection of ALS-associated toxicity of SOD1 in transgenic mice using an exon-fusion approach.

PMID 18424447 · PMC2465800 · Human molecular genetics · 2008 · 6 claims · 8 setups

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Nonsense-mediated mRNA decay (NMD) degrades mutant SOD1 mRNA carrying a PTC in non-terminal exons (1-4), explaining why ALS-associated PTC mutations are found only in exon 5

transgenic nih hsod1 lumbar southern northern rt-pcr
ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

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Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

ductal same sporadic paired cdna quantitative genotyping
Melusin gene (ITGB1BP2) nucleotide variations study in hypertensive and cardiopathic patients.

PMID 20017903 · PMC2803168 · BMC medical genetics · 2009 · 6 claims · 5 setups

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Only three nucleotide variations in ITGB1BP2 were found among 928 screened subjects, indicating a high degree of conservation of the gene in the populations analyzed

genomic hela itgb1bp2 melusin direct minigene in-silico
Novel syntaxin 11 gene (STX11) mutation in three Argentinean patients with hemophagocytic lymphohistiocytosis.

PMID 19967551 · PMC7370861 · Journal of clinical immunology · 2010 · 8 claims · 8 setups

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Three unrelated Argentinean HLH patients carry an identical novel homozygous 4-bp deletion (c.581_584delTGCC; p.Leu194ProfsX2) in STX11

genomic peripheral blood fresh direct snp rt-pcr
Genetic analysis of 10 unrelated Korean families with p22-phox-deficient chronic granulomatous disease: an unusually identical mutation of the CYBA gene on Jeju Island, Korea.

PMID 19949658 · PMC2775850 · Journal of Korean medical science · 2009 · 8 claims · 4 setups

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All 12 analyzed CGD patients from 10 unrelated Jeju families carry an identical homozygous c.7C>T substitution in exon 1 of CYBA, predicted to cause a nonsense mutation (p.Q3X)

peripheral genomic dhr western rt-pcr

Experiments

A well-conserved Plasmodium falciparum var gene shows an unusual stage-specific transcript pattern.

Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene.

Mutation analysis of FANCD2, BRIP1/BACH1, LMO4 and SFN in familial breast cancer.

High proportion of recurrent germline mutations in the BRCA1 gene in breast and ovarian cancer patients from the Prague area.

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

Identification and characterization of a novel mammalian Mg2+ transporter with channel-like properties.

Genomic sequencing of the severe acute respiratory syndrome-coronavirus.

The pseudo-mitochondrial genome influences mistakes in heteroplasmy interpretation.

Identification and evolutionary analysis of novel exons and alternative splicing events using cross-species EST-to-genome comparisons in human, mouse and rat.

MRPS18CP2 alleles and DEFA3 absence as putative chromosome 8p23.1 modifiers of hearing loss due to mtDNA mutation A1555G in the 12S rRNA gene.

Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

Genomic and proteomic profiling of oxidative stress response in human diploid fibroblasts.

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

Molecular dissection of ALS-associated toxicity of SOD1 in transgenic mice using an exon-fusion approach.

ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

Melusin gene (ITGB1BP2) nucleotide variations study in hypertensive and cardiopathic patients.

Novel syntaxin 11 gene (STX11) mutation in three Argentinean patients with hemophagocytic lymphohistiocytosis.

Genetic analysis of 10 unrelated Korean families with p22-phox-deficient chronic granulomatous disease: an unusually identical mutation of the CYBA gene on Jeju Island, Korea.