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 1.5k

System / cell line: genomic ✕ Clear

p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

PMID 11875738 · PMC2375302 · British journal of cancer · 2002 · 8 claims · 6 setups

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p53 status can be reliably determined by yeast functional assay from single frozen sections of trucut biopsies

frozen plasmids single extracted p53 sanger laser
Analyses of apoptotic regulators CASP9 and DFFA at 1P36.2, reveal rare allele variants in human neuroblastoma tumours.

PMID 11870543 · PMC2375272 · British journal of cancer · 2002 · 8 claims · 5 setups

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DFFA is localized within the 1p36.2-3 smallest region of overlap (SRO) of deletions defined in Scandinavian neuroblastoma tumours, distal to marker D1S244

scandinavian chromosome unfinished neuroblastoma pcr bac-library in-silico
Getting positive about selection.

PMID 12914654 · PMC193638 · Genome biology · 2003 · 8 claims · 4 setups

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Purifying selection is the predominant form of molecular evolution, preserving fitness by eliminating deleterious mutations, while positive selection is rare but critical for adaptation.

genome chimpanzee human-chimpanzee humans whole-genome ratio maximum-likelihood
Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

PMID 15601538 · PMC3525068 · Human genomics · 2004 · 8 claims · 8 setups

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An integrated system combining Ensembl, ACeDB, Gbrowse and custom relational databases provides a scalable genome informatics and workflow infrastructure for complex disease gene discovery.

pcr candidate embl clinical snp manual homology
A genome annotation-driven approach to cloning the human ORFeome.

PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

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Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

chromosome pooled t-tailed naga comparative rt-pcr sanger
Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

PMID 15361934 · PMC515368 · PLoS biology · 2004 · 7 claims · 8 setups

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The HIF-1/VHL-1/EGL-9 hydroxylase pathway is tightly conserved in C. elegans

elegans whole-genome rnase pharmacological
TP73 allelic expression in human brain and allele frequencies in Alzheimer's disease.

PMID 15175114 · PMC420466 · BMC medical genetics · 2004 · 8 claims · 6 setups

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A -386G/A SNP in the TP73 P3 promoter is weakly but significantly associated with AD risk in a tri-ethnic elderly population.

brain peripheral sk-nsh-n genomic rt-pcr direct snp
Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

Has reproduction · 80

BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr
Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

PMID 15018647 · PMC365025 · BMC genomics · 2004 · 8 claims · 8 setups

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Combined SSH subtractive cloning and array CGH is an efficient strategy to identify overexpressed genes located within DNA amplicons.

imr-32 subtracted mycn-amplified suppression differential array
Novel and de novo PKD1 mutations identified by multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP).

PMID 15018634 · PMC356914 · BMC medical genetics · 2004 · 6 claims · 7 setups

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MRF-SSCP method (using combined restriction digestion plus SSCP with silver staining) was developed to screen PKD1 mutations in full-length cDNA fractionated into nine overlapping nested-PCR segments

blood pkd1 pcr-purified genomic long nested-pcr mrf-sscp
X-linked severe combined immunodeficiency syndrome: the first Korean case with gamma c chain gene mutation and subsequent genetic counseling.

PMID 14966353 · PMC2822247 · Journal of Korean medical science · 2004 · 8 claims · 7 setups

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The patient's X-SCID is caused by a C690T point mutation in exon 5 of the γc chain gene, producing an R226C amino acid substitution.

pbmcs mother serum fetal flow direct pcr-rflp
Molecular variants of the ATM gene in Hodgkin's disease in children.

PMID 14735203 · PMC2409549 · British journal of cancer · 2004 · 8 claims · 4 setups

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Missense variants of the ATM gene occur in childhood Hodgkin lymphoma but at low frequency (9%), and thus do not play a major role in oncogenesis of the disease

frozen matched paired rt-pcr germ-line sscp
Germline truncating mutations in both MSH2 and BRCA2 in a single kindred.

PMID 14735197 · PMC2409581 · British journal of cancer · 2004 · 8 claims · 8 setups

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Kindred MON1080 carries germline truncating mutations in both MSH2 and BRCA2, with two family members being double heterozygotes

colonic astrocytoma breast microdissected immunohistochemistry microsatellite truncation
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

PMID 16381612 · PMC1360673 · BMC bioinformatics · 2005 · 7 claims · 7 setups

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A 32-dimensional triplet structure-sequence feature vector combined with SVM (triplet-SVM) can distinguish real human pre-miRNAs from pseudo pre-miRNA hairpins with ~90% accuracy.

pre-mirnas test conserved-hairpin cross-species secondary svm cross-species
Two novel mutations in the aquaporin 2 gene in a girl with congenital nephrogenic diabetes insipidus.

PMID 16361827 · PMC2779314 · Journal of Korean medical science · 2005 · 8 claims · 5 setups

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The patient carries a compound heterozygous missense mutation in AQP2: A70D (exon 1, paternal) and R187H (exon 3, maternal)

3-year-old serum genomic clinical hormone water
Introduction of in vitro transcribed ENO1 mRNA into neuroblastoma cells induces cell death.

PMID 16359544 · PMC1327688 · BMC cancer · 2005 · 8 claims · 6 setups

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ENO1 has tumour suppressor activity

sk-n-as neuroblastoma genomic growth tunel real-time
Allele quantification using molecular inversion probes (MIP).

PMID 16314297 · PMC1301601 · Nucleic acids research · 2005 · 8 claims · 5 setups

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MIP technology at high multiplex (>20,000 SNPs) can provide copy number measurements while simultaneously obtaining allele information

reference ffpe lines na18573 mip restriction quantitative
Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

PMID 16280054 · PMC1410740 · Breast cancer research : BCR · 2005 · 8 claims · 7 setups

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None of the six candidate genes (CBFA2T3, TERF2, TERF2IP, FBXL8, LRRC29, FANCA) showed inactivating mutations or expression differences clearly associated with 16q LOH status

breast quantitative fragment gene-expression
Polymorphism in the tumour necrosis factor receptor II gene is associated with circulating levels of soluble tumour necrosis factor receptors in rheumatoid arthritis.

PMID 16277675 · PMC1297570 · Arthritis research & therapy · 2005 · 8 claims · 6 setups

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The TNF-RII T676G polymorphism is associated with circulating levels of sTNF-RI and sTNF-RII in RA, with a trend TT > TG > GG

serum genomic peripheral synovial elisa pcr-rflp clinical
SNPdetector: a software tool for sensitive and accurate SNP detection.

PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

inbred unrelated zebra same pcr manual comparative

Experiments

p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

Analyses of apoptotic regulators CASP9 and DFFA at 1P36.2, reveal rare allele variants in human neuroblastoma tumours.

Getting positive about selection.

Development of an integrated genome informatics, data management and workflow infrastructure: a toolbox for the study of complex disease genetics.

A genome annotation-driven approach to cloning the human ORFeome.

Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

TP73 allelic expression in human brain and allele frequencies in Alzheimer's disease.

Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

Novel and de novo PKD1 mutations identified by multiple restriction fragment-single strand conformation polymorphism (MRF-SSCP).

X-linked severe combined immunodeficiency syndrome: the first Korean case with gamma c chain gene mutation and subsequent genetic counseling.

Molecular variants of the ATM gene in Hodgkin's disease in children.

Germline truncating mutations in both MSH2 and BRCA2 in a single kindred.

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

Two novel mutations in the aquaporin 2 gene in a girl with congenital nephrogenic diabetes insipidus.

Introduction of in vitro transcribed ENO1 mRNA into neuroblastoma cells induces cell death.

Allele quantification using molecular inversion probes (MIP).

Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

Polymorphism in the tumour necrosis factor receptor II gene is associated with circulating levels of soluble tumour necrosis factor receptors in rheumatoid arthritis.

SNPdetector: a software tool for sensitive and accurate SNP detection.