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 69

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

MutScreener: primer design tool for PCR-direct sequencing.

PMID 16845093 · PMC1538803 · Nucleic acids research · 2006 · 8 claims · 4 setups

Full-text index only

MutScreener is a web-based application that automates PCR-direct sequencing assay design by annotating gene structure and designing PCR and sequencing primers.

sim4 cdna gene comparative sequence pcr
SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.

PMID 15980532 · PMC1160243 · Nucleic acids research · 2005 · 7 claims · 3 setups

Full-text index only

SOP 3 v2 is a web-based application that outputs recommended forward/reverse PCR primers plus a sequencing primer optimized for sequence-based genotyping of human and mouse polymorphisms

genomic ncbi laboratory primer genomic
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
Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.

PMID 16670016 · PMC1513378 · Lipids in health and disease · 2006 · 8 claims · 6 setups

Full-text index only

A -987C>T polymorphism located 4bp from the 3' end of the MseI RFLP forward primer causes allelic drop-out, producing incorrect -1131T>C genotypes.

asian random subjects unrelated arms-pcr msei sanger
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 38

A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

gossypium uppermost root reads bulk leaf rt-qpcr
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

Full-text index only

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

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

Full-text index only

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
Somatic mutation of epidermal growth factor receptor in a small subset of cutaneous squamous cell carcinoma.

PMID 19812598 · PMC2825112 · The Journal of investigative dermatology · 2010 · 8 claims · 5 setups

Full-text index only

EGFR is activated by somatic mutation in a small subset of cutaneous SCC

archival scc sanger array-based fluorescence
Proposed methods for testing and selecting the ERCC external RNA controls.

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

Full-text index only

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
Paternal imprinting of the SLC22A1LS gene located in the human chromosome segment 11p15.5.

PMID 15175115 · PMC425576 · BMC genetics · 2004 · 6 claims · 3 setups

Full-text index only

The SLC22A1LS gene is paternally imprinted (i.e., only the maternal allele is expressed).

genomic pcr cdna pcr-sscp sequencing
Prevalence and penetrance of BRCA1 and BRCA2 mutations in a population-based series of breast cancer cases. Anglian Breast Cancer Study Group.

PMID 11044354 · PMC2408797 · British journal of cancer · 2000 · 6 claims · 4 setups

Full-text index only

BRCA1 and BRCA2 mutations are rare in the general population and account for only a small fraction of all breast cancer in the UK

genomic pedigrees first-degree study pcr pedigree-based age
Relationship between cyclooxygenase 8473T>C polymorphism and the risk of lung cancer: a case-control study.

PMID 16542464 · PMC1468421 · BMC cancer · 2006 · 8 claims · 4 setups

Full-text index only

The COX-2 8473T>C genotype distribution did not differ significantly between overall lung cancer cases and controls.

peripheral selected lung pcr-based sequencing questionnaire-based
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

Full-text index only

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

Full-text index only

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
Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes.

PMID 16202172 · PMC1260020 · BMC medical genetics · 2005 · 8 claims · 3 setups

Full-text index only

HA-1 allele and genotype frequencies were determined in 131 unrelated Italian subjects (HA-1H=0.43, HA-1R=0.57), consistent with Hardy-Weinberg equilibrium and prior North American Caucasian data.

genomic sequence-specific direct melting
CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification.

PMID 36304334 · PMC9580850 · Frontiers in bioinformatics · 2022 · 8 claims · 5 setups

Has reproduction · 88

CIRCprimerXL is a high-throughput, user-friendly circRNA RT-qPCR primer design pipeline available as both a web tool and a standalone Nextflow/Docker pipeline

synthetic sw480 circrnas rt-qpcr circrna primer
Characterization of 954 bovine full-CDS cDNA sequences.

PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

Full-text index only

954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

bovine translated bflic sequence est primer-walking blastp
Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

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

Full-text index only

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

Full-text index only

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

liver caucasian ugt2b7 gene snp enzymatic
New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.

PMID 19948351 · PMC2813930 · Virology · 2010 · 8 claims · 8 setups

Full-text index only

The new CUT primer system detects a broader range of HPV genera/species and novel putative types than the FAP primer system (p<0.01)

skin cloned mixed-type gene nested sequencing molecular

Experiments

MutScreener: primer design tool for PCR-direct sequencing.

SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms.

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

Allelic drop-out may occur with a primer binding site polymorphism for the commonly used RFLP assay for the -1131T>C polymorphism of the Apolipoprotein AV gene.

RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

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

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

Somatic mutation of epidermal growth factor receptor in a small subset of cutaneous squamous cell carcinoma.

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

Paternal imprinting of the SLC22A1LS gene located in the human chromosome segment 11p15.5.

Prevalence and penetrance of BRCA1 and BRCA2 mutations in a population-based series of breast cancer cases. Anglian Breast Cancer Study Group.

Relationship between cyclooxygenase 8473T>C polymorphism and the risk of lung cancer: a case-control study.

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

Minisequencing mitochondrial DNA pathogenic mutations.

Sequence diversity within the HA-1 gene as detected by melting temperature assay without oligonucleotide probes.

CIRCprimerXL: Convenient and High-Throughput PCR Primer Design for Circular RNA Quantification.

Characterization of 954 bovine full-CDS cDNA sequences.

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.

New generic primer system targeting mucosal/genital and cutaneous human papillomaviruses leads to the characterization of HPV 115, a novel Beta-papillomavirus species 3.