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: frequency ✕ Assay: amplicon ✕ Clear

Nimbus: a design-driven analyses suite for amplicon-based NGS data.

PMID 29538618 · PMC6084620 · Bioinformatics (Oxford, England) · 2018 · 7 claims · 5 setups

Has reproduction · 64

Nimbus tracks the source amplicon of reads throughout alignment and SNP/InDel calling

blood na15510 twin haloplex haloplex spiked-in humanexome-12
EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

PMID 35561186 · PMC9113274 · Bioinformatics (Oxford, England) · 2022 · 7 claims · 5 setups

Has reproduction · 49

EDGE COVID-19 (EC-19) is a web-based platform that automates QC, reference-based variant/consensus calling, lineage determination, and submission of SARS-CoV-2 genomes and metadata to GenBank, GISAID and INSDC for both Illumina and ONT data.

sars-cov-2 srr illumina ont amplicon lineage cross-workflow
High frequency of deletions at the hypoxanthine-guanine phosphoribosyltransferase locus in an ataxia-telangiectasia lymphoblastoid cell line irradiated with gamma-rays.

PMID 11714443 · PMC5926665 · Japanese journal of cancer research : Gann · 2001 · 7 claims · 5 setups

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A high proportion (12/15, 80%) of gamma-ray-induced HPRT-deficient mutants in A-T (GM2783) cells are deletions

gm2783 mutant multiplex pcr long
Identification of STRA6 and SKI sequence variants in patients with anophthalmia/microphthalmia.

PMID 19112531 · PMC2610290 · Molecular vision · 2008 · 8 claims · 4 setups

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A novel STRA6 missense variant (p.G217E, exon 8) and a novel STRA6 nonsense variant (p.Q592X, exon 18) were identified in one A/M subject and absent from 89 controls, implicating STRA6 in this subject's A/M phenotype.

genomic stra6 direct variant
Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

PMID 19650893 · PMC2728732 · BMC evolutionary biology · 2009 · 8 claims · 7 setups

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Autochthonous Berber Y-chromosome lineages E-M81, E-M78 and J-M267 were detected in indigenous Canary Island remains, confirming a North West African origin for the aboriginal ancestors.

prehispanic indigenous ancient modern y-chromosome nested real-time
Massively parallel pyrosequencing in HIV research.

PMID 18614863 · PMC4221253 · AIDS (London, England) · 2008 · 8 claims · 8 setups

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Massively parallel pyrosequencing platforms (454/Roche, Solexa/Illumina) enable very high-throughput DNA sequencing, up to ~1 billion bases per run

mammoth hiv hiv-infected honey pyrosequencing pcr 16s
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

aml tumor novo additional genome snp comparative
Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

genomic commercial plco unrelated targeted long-range genotyping
Familial Wolfram syndrome due to compound heterozygosity for two novel WFS1 mutations.

PMID 18660851 · PMC2483297 · Molecular vision · 2008 · 8 claims · 6 setups

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The four affected siblings are compound heterozygotes for two novel WFS1 mutations, one from each parent, causing Wolfram syndrome.

genomic affected microsatellite pcr allele-specific
Genotypic analysis of two hypervariable human cytomegalovirus genes.

PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

hcmv clinical pcr ul146 pcr nested molecular
Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

PMID 18418848 · PMC6668724 · Genes, chromosomes & cancer · 2008 · 6 claims · 5 setups

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Emulsion PCR combined with picotiter plate pyrosequencing (454 sequencing) enables high-resolution, high-throughput detection of low-frequency sequence variants among the many individual copies of an amplified gene.

erbb2-amplified erbb2-positive plasmid cos-7 emulsion serial immune-complex
DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.

PMID 17576693 · PMC1934997 · Nucleic acids research · 2007 · 6 claims · 7 setups

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DNA bar coding combined with pyrosequencing allows parallel, deep characterization of drug resistance mutations across many HIV populations in a single experiment

hiv pooled plasma pyrosequencing conventional rt-pcr
A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

PMID 19763161 · PMC2730533 · PLoS genetics · 2009 · 7 claims · 8 setups

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A heterozygous SCN9A missense mutation (p.N641Y) cosegregates with febrile seizures in the large K4425 family and is absent from ethnically matched population controls

family k4425 embryonic scn9a-n641y linkage copy deletion
Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.

PMID 19760750 · PMC2784016 · Human mutation · 2009 · 8 claims · 6 setups

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Two-round fast COLD-PCR followed by Sanger sequencing detects TP53 mutations at abundances as low as ~1%, below the sensitivity of conventional Sanger sequencing (~20-25%)

lung wild-type matched paired two-round real-time airs-rflp

Experiments

Nimbus: a design-driven analyses suite for amplicon-based NGS data.

EDGE COVID-19: a web platform to generate submission-ready genomes from SARS-CoV-2 sequencing efforts.

High frequency of deletions at the hypoxanthine-guanine phosphoribosyltransferase locus in an ataxia-telangiectasia lymphoblastoid cell line irradiated with gamma-rays.

Identification of STRA6 and SKI sequence variants in patients with anophthalmia/microphthalmia.

Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

Massively parallel pyrosequencing in HIV research.

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

Familial Wolfram syndrome due to compound heterozygosity for two novel WFS1 mutations.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

DNA bar coding and pyrosequencing to identify rare HIV drug resistance mutations.

A role of SCN9A in human epilepsies, as a cause of febrile seizures and as a potential modifier of Dravet syndrome.

Two-round coamplification at lower denaturation temperature-PCR (COLD-PCR)-based sanger sequencing identifies a novel spectrum of low-level mutations in lung adenocarcinoma.