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 119

System / cell line: primer ✕ Clear

A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

PMID 16351727 · PMC1327677 · BMC genomics · 2005 · 8 claims · 5 setups

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A qPCR method using unique-sequence primers can reproducibly detect chromosomal microdeletions and microduplications

genomic genome pcr real-time fluorescence sequence
Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

PMID 16288651 · PMC1314899 · BMC genomics · 2005 · 8 claims · 6 setups

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Human genomic DNA sequence can be leveraged to obtain 3' end sequence of NHP orthologs, which can then be used to generate NHP oligonucleotide microarrays

refseq macaca genomic rhesus exon pcr molecular
Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

PMID 24131564 · PMC3875859 · Genome research · 2014 · 8 claims · 8 setups

Has reproduction · 100

TSscan, a computational pipeline integrating long- and short-read transcriptome sequencing from multiple hESC lines, can detect trans-splicing while minimizing false positives from experimental artifacts and genetic rearrangements.

hesc hescs long-read short-read rt-pcr
A chromosomally integrated bacteriophage in invasive meningococci.

PMID 15967821 · PMC2212043 · The Journal of experimental medicine · 2005 · 8 claims · 7 setups

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An 8-kb genetic island (NMA1792-NMA1799) is specifically associated with hyperinvasive meningococcal clonal complexes

meningitidis culture czech patients comparative pcr nuclease
Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs.

PMID 15811185 · PMC1079828 · BMC genomics · 2005 · 8 claims · 4 setups

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Relative Allele Signal (RAS) values from SNP microarrays provide a quantitative index of allele frequencies in pooled DNA

pooled pool snps snp snapshot individual
An efficient method for multi-locus molecular haplotyping.

PMID 17158153 · PMC1802573 · Nucleic acids research · 2007 · 7 claims · 6 setups

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A novel molecular haplotyping method using limiting dilution, aliquot pre-screening, and tiling reconstruction can resolve haplotypes spanning many loci over long distances from a single individual's DNA.

single agarose-embedded genotyping multiplexed monoplex primer-extension
Gefitinib for non-small-cell lung cancer patients with epidermal growth factor receptor gene mutations screened by peptide nucleic acid-locked nucleic acid PCR clamp.

PMID 17106442 · PMC2360739 · British journal of cancer · 2006 · 5 claims · 4 setups

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NSCLC patients with EGFR mutations detected by PNA-LNA PCR clamp show significantly higher response rates and longer survival with gefitinib than EGFR wild-type patients.

clinical nsclc pna-lna direct phase
PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

PMID 17105657 · PMC1657037 · BMC bioinformatics · 2006 · 6 claims · 5 setups

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PathogenMIPer designs unique, target-specific MIP probes, assembling all probe components (target-specific sequences, barcodes, universal primers, restriction sites) into ready-to-order probes for any genome.

hpv clinical biotinylated pcr mip molecular microarray
Deletion of the V2 vasopressin receptor gene in two Chinese patients with nephrogenic diabetes insipidus.

PMID 17101063 · PMC1657029 · BMC genetics · 2006 · 7 claims · 6 setups

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The two NDI patients carry a 5,995-bp genomic deletion combined with a 3-bp (GAG) insertion at Xq28 that removes the entire AVPR2 gene and the last exon (exon 22) of the C1 (ARHGAP4) gene.

genomic proband blood patients pcr long-range combined
High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

genomic ecotilling non-synonymous ecotilling sanger universal-primer
Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups

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Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.

parahaemolyticus vulnificus clinical ecori-digested bioinformatic comparative pcr
Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.

PMID 16582098 · PMC1421508 · Nucleic acids research · 2006 · 6 claims · 5 setups

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TnT enables parallel amplification of 75 SNPs from sub-nanogram amounts of genomic DNA

genomic dbsnp tnt duplex bioinformatic
Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe.

PMID 16432256 · PMC1345699 · Nucleic acids research · 2006 · 8 claims · 5 setups

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A 17mer PNA spanning K-ras codons 12/13 can serve as both PCR clamp and sensor probe in a single-tube reaction, differentiating all 12 possible point mutations from wild-type by melting temperature shift

wild-type mixture mutant serial melting real-time limit-of-detection
Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups

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QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker

paired colorectal genome normal quma auma bioinformatic
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence
Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans.

PMID 17900363 · PMC2098775 · BMC evolutionary biology · 2007 · 8 claims · 4 setups

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M. ulcerans has evolved into five InDel haplotypes that separate into two distinct phylogenetic lineages: a 'classical' lineage (Africa, Australia, South East Asia) and an 'ancestral' lineage (Asia, South America, Mexico)

ulcerans marinum plasmid-based pcr genome
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

PMID 17299583 · PMC1797623 · PloS one · 2007 · 6 claims · 4 setups

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5′-tagged PCR primers enable pooling of homologous PCR products from multiple sources into a single GS20 run with accurate post-hoc assignment of sequences to source

extracts pooled same non-assigned pcr parallel conventional
A missense mutation in the nuclear localization signal sequence of CERKL (p.R106S) causes autosomal recessive retinal degeneration.

PMID 18978954 · PMC2576480 · Molecular vision · 2008 · 8 claims · 6 setups

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A C>A transversion in exon 2 of CERKL (c.316C>A) causes a missense change p.R106S in the nuclear localization signal sequence (KLKRR) of the protein.

patients genomic family cerkl ophthalmic homozygosity multipoint
Pathogenic mitochondrial DNA mutations are common in the general population.

PMID 18674747 · PMC2495064 · American journal of human genetics · 2008 · 7 claims · 6 setups

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At least 1 in 200 healthy humans harbors a pathogenic mtDNA mutation with potential to cause disease in offspring of female carriers

neonatal independent m.1555a→g-positive mutation-positive high-throughput last-cycle cloning
Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.

PMID 18616294 · PMC2646719 · Biochemistry · 2008 · 8 claims · 6 setups

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Both G[8,5-Me]T and T[5-Me,8]G intrastrand cross-links are strongly mutagenic in COS-7 and 293T mammalian cells

cos-7 293t synthetic pms2 shuttle primer steady-state

Experiments

A method for accurate detection of genomic microdeletions using real-time quantitative PCR.

Leveraging human genomic information to identify nonhuman primate sequences for expression array development.

Integrative transcriptome sequencing identifies trans-splicing events with important roles in human embryonic stem cell pluripotency.

A chromosomally integrated bacteriophage in invasive meningococci.

Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs.

An efficient method for multi-locus molecular haplotyping.

Gefitinib for non-small-cell lung cancer patients with epidermal growth factor receptor gene mutations screened by peptide nucleic acid-locked nucleic acid PCR clamp.

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

Deletion of the V2 vasopressin receptor gene in two Chinese patients with nephrogenic diabetes insipidus.

High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.

Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.

Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe.

Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

Evolution of two distinct phylogenetic lineages of the emerging human pathogen Mycobacterium ulcerans.

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing.

A missense mutation in the nuclear localization signal sequence of CERKL (p.R106S) causes autosomal recessive retinal degeneration.

Pathogenic mitochondrial DNA mutations are common in the general population.

Mutational specificity of gamma-radiation-induced guanine-thymine and thymine-guanine intrastrand cross-links in mammalian cells and translesion synthesis past the guanine-thymine lesion by human DNA polymerase eta.