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 36

System / cell line: sanger ✕ Assay: amplicon ✕ Clear

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
Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

PMID 18606010 · PMC2464579 · BMC medical genetics · 2008 · 6 claims · 4 setups

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Methylation of the MHC2TA promoter pIV is not associated with MS susceptibility; no methylation was detected in any twin sample regardless of disease status

peripheral mhc2ta pcr sanger bisulfite cpg
Probing the cancer genome.

PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups

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Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level

mcf-7 tumor lung oral sanger solexa gistic
Evaluating sequence data quality from the Swift Accel-Amplicon CFTR Panel.

PMID 31913291 · PMC6949293 · Scientific data · 2020 · 6 claims · 7 setups

Has reproduction · 89

The Accel-Amplicon CFTR panel generates sequencing data with high coverage depth and near 100% on-target reads.

genomic adapted aligned pcr amplicon multiplex qpcr
Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval.

PMID 18510646 · PMC2689154 · Annals of human genetics · 2008 · 7 claims · 5 setups

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Direct sequencing of 43 candidate genes in 7 Spanish arRP families identified 244 sequence variants (76 novel), none pathogenic, excluding these genes as disease-causing.

spanish rp5 population candidate direct comparative pcr
Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

PMID 18842124 · PMC2569949 · BMC genomics · 2008 · 7 claims · 7 setups

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GS-FLX pyrosequencing of pooled amplicons detects sequence variants with high specificity (99.95%) and no false negatives at ≥30× coverage

pools pcr genomic gs-flx massively sanger pcr
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.

PMID 18413340 · PMC2425484 · Nucleic acids research · 2008 · 8 claims · 8 setups

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CpG-rich regions (CpG islands) show low and similar methylation levels across individuals, but the sequential order of the few methylated CpGs among the many unmethylated ones varies randomly between individuals.

cd4+ computational hep direct simulation epigraph
Identification of the first intragenic deletion of the PITX2 gene causing an Axenfeld-Rieger Syndrome: case report.

PMID 17134502 · PMC1684248 · BMC medical genetics · 2006 · 8 claims · 8 setups

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An intragenic deletion of 3,059 bp within the PITX2 gene, spanning the end of exon 5 through the start of exon 6, causes this family's severe ARS phenotype

genomic lymphoblastoid i-2 patients pcr quantitative long-range
Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

PMID 16545110 · PMC1475604 · BMC cancer · 2006 · 8 claims · 4 setups

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Smoking is associated with adenoma and CRC development, with the association strongest in tumors lacking APC truncation mutations

formalin-fixed ffpe paired study direct pcr restriction
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups

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The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.

pooled 16s sequenced topo 16s primer taxonomic
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
Genomics--from Neanderthals to high-throughput sequencing.

PMID 16934106 · PMC1779599 · Genome biology · 2006 · 8 claims · 8 setups

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Next-generation sequencing platforms (GS20/454 and Solexa) can deliver the throughput and cost reductions needed for population-scale and medical resequencing.

bacterial ion-channel drosophila arrays next-generation pooled multiplex
Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).

PMID 32463383 · PMC7734503 · Journal of integrative bioinformatics · 2020 · 6 claims · 5 setups

Has reproduction · 78

The MycoDiversity DataBase (MDDB) is a curated repository integrating public fungal metabarcoding data of environmental samples to study fungal biodiversity patterns in space and time.

fungal pubmed pdf sra metabarcoding acquisition regular-expression
Segregation of a M404V mutation of the p62/sequestosome 1 (p62/SQSTM1) gene with polyostotic Paget's disease of bone in an Italian family.

PMID 16277682 · PMC1297578 · Arthritis research & therapy · 2005 · 6 claims · 4 setups

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The M404V mutation in p62/SQSTM1 exon 8 segregates with the polyostotic form of PDB in the F01 Italian family

genomic serum affected pcr pcr biochemical clinical
Two novel missense mutations in the myostatin gene identified in Japanese patients with Duchenne muscular dystrophy.

PMID 17428346 · PMC1855920 · BMC medical genetics · 2007 · 7 claims · 5 setups

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Two novel missense mutations in the myostatin gene (p.95D>H and p.156L>I) were identified in Japanese DMD patients

genomic pcr elbow peripheral pcr subcloning gel
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
Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons.

PMID 18448472 · PMC2425497 · Nucleic acids research · 2008 · 7 claims · 8 setups

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Internal oligonucleotide calibration improves homozygote genotyping accuracy for base-pair neutral small amplicons from 91.7% to 99.7% across five of six targets

genomic high-resolution sanger probe-based
No significant role for beta tubulin mutations and mismatch repair defects in ovarian cancer resistance to paclitaxel/cisplatin.

PMID 16095531 · PMC1199587 · BMC cancer · 2005 · 6 claims · 4 setups

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TUBB exon 4 mutations are not found in primary ovarian carcinomas treated with paclitaxel/cisplatin

ovarian same pcr agarose microsatellite
External contamination in single cell mtDNA analysis.

PMID 17668059 · PMC1930155 · PloS one · 2007 · 8 claims · 6 setups

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External DNA contamination is a real and non-negligible problem in single-cell mtDNA sequence analysis

single current laboratory reagent mtdna two-step nested
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

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

Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis.

Probing the cancer genome.

Evaluating sequence data quality from the Swift Accel-Amplicon CFTR Panel.

Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval.

Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping.

Identification of the first intragenic deletion of the PITX2 gene causing an Axenfeld-Rieger Syndrome: case report.

Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.

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

Genomics--from Neanderthals to high-throughput sequencing.

Fungal metabarcoding data integration framework for the MycoDiversity DataBase (MDDB).

Segregation of a M404V mutation of the p62/sequestosome 1 (p62/SQSTM1) gene with polyostotic Paget's disease of bone in an Italian family.

Two novel missense mutations in the myostatin gene identified in Japanese patients with Duchenne muscular dystrophy.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

Base-pair neutral homozygotes can be discriminated by calibrated high-resolution melting of small amplicons.

No significant role for beta tubulin mutations and mismatch repair defects in ovarian cancer resistance to paclitaxel/cisplatin.

External contamination in single cell mtDNA analysis.

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