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 14

System / cell line: sequencing ✕ Assay: primer-extension ✕ Clear

Ultra-deep multi-oncopanel sequencing of benchmarking samples with a wide range of variant allele frequencies.

PMID 35680918 · PMC9184574 · Scientific data · 2022 · 8 claims · 8 setups

Has reproduction · 82

Four reference samples (Sample A, Sample B, Sample C, Sample Spike-in/AC5) were developed with large numbers of high-confidence positive and negative small variant positions to serve as known content for oncopanel performance assessment.

agilent burning integrated igenetech targeted
The minisequencing method: a simple strategy for genetic screening of MEN 2 families.

PMID 12042015 · PMC116428 · BMC genetics · 2002 · 6 claims · 4 setups

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Minisequencing reproduces the same mutation information obtained by direct sequencing of PCR products at RET codons 634 and 918 in all tested MEN 2 family members.

genomic pcr same white pcr minisequencing direct
Proposed methods for testing and selecting the ERCC external RNA controls.

PMID 16266432 · PMC1325234 · BMC genomics · 2005 · 8 claims · 5 setups

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A consortium-developed, standardized set of external RNA control transcripts can be used to assess technical performance in gene expression assays (microarray and QRT-PCR)

candidate linearized transcripts pools sequence transcription quality
Screening of common CYP1B1 mutations in Iranian POAG patients using a microarray-based PrASE protocol.

PMID 19096718 · PMC2603445 · Molecular vision · 2008 · 7 claims · 5 setups

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CYP1B1 mutations are implicated in POAG among Iranians, notably in the juvenile-onset form

genomic cyp1b1 poag microarray-based dideoxy sanger
Minisequencing mitochondrial DNA pathogenic mutations.

PMID 18402672 · PMC2377236 · BMC medical genetics · 2008 · 7 claims · 7 setups

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A minisequencing multiplex assay can interrogate 25 pathogenic mtDNA mutations across the whole mtDNA genome in a single reaction using 13 amplicons.

blood-derived same genomic pcr minisequencing automatic multiplex
Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

PMID 16895448 · PMC1523240 · PLoS genetics · 2006 · 8 claims · 8 setups

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MALDI-TOF MS-based primer extension assays (hME, iPLEX) enable cost-effective, high-throughput multiplexed SNP genotyping

genomic domestic pooled colorectal snp pooling microsatellite
Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

PMID 18622261 · PMC2680356 · Pharmacogenetics and genomics · 2008 · 7 claims · 7 setups

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UGT2B7 haplotype 4 is associated with increased enzyme activity (M3G and M6G formation)

liver caucasian ugt2b7 gene snp enzymatic
Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions.

PMID 15958788 · PMC1150895 · Nucleic acids research · 2005 · 6 claims · 4 setups

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SNaPshot primers with mismatches to upstream bisulfite-induced C/T or G/A polymorphisms produce a position-dependent biasing effect of up to 70%, decreasing as the mismatch moves farther upstream of the target cytosine

comt synthetic genomic snapshot
Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei.

PMID 35714765 · PMC9283944 · The Journal of biological chemistry · 2022 · 8 claims · 4 setups

Has reproduction · 80

Genome-wide Ψ mapping using HydraPsiSeq and small RNA Ψ-seq identifies Ψ sites on snoRNA, 7SL RNA, vtRNA, SL RNA, and tRNA in T. brucei

brucei hydrapsiseq small primer
Heterozygous CAV1 frameshift mutations (MIM 601047) in patients with atypical partial lipodystrophy and hypertriglyceridemia.

PMID 18237401 · PMC2276215 · Lipids in health and disease · 2008 · 8 claims · 4 setups

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Two distinct heterozygous frameshift mutations in CAV1 (I134fsdelA-X137 and -88delC) were identified in patients with atypical partial lipodystrophy and severe hypertriglyceridemia

genomic sequence restriction allele-specific
Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

PMID 15640441 · PMC546178 · Nucleic acids research · 2005 · 8 claims · 7 setups

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NCL aggregation of DNA-modified gold nanoparticles shows extraordinary selectivity against terminal mismatches at the free ends of surface-bound duplexes

probe-modified probe-gnp synthetic four uv-vis ssdna pcr
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
Mutations at codons 178, 200-129, and 232 contributed to the inherited prion diseases in Korean patients.

PMID 19698114 · PMC2749045 · BMC infectious diseases · 2009 · 8 claims · 7 setups

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Three PRNP mutations—D178N, E200K, and M232R—were identified in heterozygosity in Korean probable CJD patients, marking their first report in this population.

csf 293t genomic pcr western recombinant sequencing
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

Ultra-deep multi-oncopanel sequencing of benchmarking samples with a wide range of variant allele frequencies.

The minisequencing method: a simple strategy for genetic screening of MEN 2 families.

Proposed methods for testing and selecting the ERCC external RNA controls.

Screening of common CYP1B1 mutations in Iranian POAG patients using a microarray-based PrASE protocol.

Minisequencing mitochondrial DNA pathogenic mutations.

Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

Single nucleotide polymorphism discovery and functional assessment of variation in the UDP-glucuronosyltransferase 2B7 gene.

Single nucleotide extension technology for quantitative site-specific evaluation of metC/C in GC-rich regions.

Identification and functional implications of pseudouridine RNA modification on small noncoding RNAs in the mammalian pathogen Trypanosoma brucei.

Heterozygous CAV1 frameshift mutations (MIM 601047) in patients with atypical partial lipodystrophy and hypertriglyceridemia.

Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

An efficient method for multi-locus molecular haplotyping.

Mutations at codons 178, 200-129, and 232 contributed to the inherited prion diseases in Korean patients.

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.