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 18

System / cell line: cloned ✕ Assay: fragment ✕ Clear

Prediction and assessment of splicing alterations: implications for clinical testing.

PMID 18951448 · PMC2832470 · Human mutation · 2008 · 8 claims · 5 setups

Full-text index only

Bioinformatic prediction alone is insufficient; in vitro analysis is needed to confirm or establish splicing aberrations for clinical variant classification

brca1 lymphocytes mammalian large bioinformatic cycloheximide mini-gene
Association between telomere length and V(H) gene mutation status in chronic lymphocytic leukaemia: clinical and biological implications.

PMID 12592375 · PMC2377180 · British journal of cancer · 2003 · 7 claims · 5 setups

Full-text index only

Unmutated VH gene CLL cases have significantly shorter telomeres than mutated VH gene CLL cases

cll subset pcr southern real-time
Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer.

PMID 15686596 · PMC549029 · Molecular cancer · 2005 · 8 claims · 5 setups

Full-text index only

A chromatin library coupled with experimental validation can productively identify novel in vivo Stat5 chromatin binding sites in cancer, including abnormal regulatory sites in tumor-specific neochromatin.

t-47d agarose chromatin cloning
Assisted large fragment insertion by Red/ET-recombination (ALFIRE)--an alternative and enhanced method for large fragment recombineering.

PMID 17517785 · PMC1904275 · Nucleic acids research · 2007 · 6 claims · 7 setups

Full-text index only

ALFIRE allows insertion of any fragment into small or large episomes without requiring an antibiotic selection gene in the final construct

coli psc101badγβαa[hygro] psc101badγβαa-i-scei[amp] i-scei-cs-hmlhcgr-bac bacterial restriction pcr
New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

PMID 16340004 · PMC1310899 · Nucleic acids research · 2005 · 7 claims · 8 setups

Full-text index only

Long pure palindromes (>~200 bp) cannot be stably cloned in E.coli due to cruciform-driven instability, and no E.coli mutant fully overcomes this cloning block.

individuals e.coli cerevisiae yeast pcr plasmid phi-29
Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups

Full-text index only

A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.

inhbb cloned same fresh-frozen rnase masscleave clonal
Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

PMID 15935100 · PMC1164406 · BMC cancer · 2005 · 8 claims · 4 setups

Full-text index only

B-raf exon 15 somatic mutations occur in 24/60 (40%) of cutaneous/subcutaneous melanoma metastases, similar to the frequency in primary melanomas

paraffin-embedded cloned same predicted pcr cloning blastx
Differentiating human from animal isolates of Cryptosporidium parvum.

PMID 9866750 · PMC2640237 · Emerging infectious diseases · 1998 · 7 claims · 5 setups

Full-text index only

Two distinct genotypes of C. parvum (human/anthroponotic and bovine/zoonotic) exist, distinguishable by TRAP-C2 gene sequence differences at five nucleotide positions.

parvum cloned aligned fecal pcr pcr-rflp sequencing
PAX6 gene variations associated with aniridia in south India.

PMID 15086958 · PMC419353 · BMC medical genetics · 2004 · 7 claims · 5 setups

Full-text index only

Mutations in PAX6 cause the aniridia phenotype via haploinsufficiency (loss-of-function/null alleles)

genomic pcr aniridia sscp automated allele-specific
Genetic distance and heterogenecity between quasispecies is a critical predictor to IFN response in Egyptian patients with HCV genotype-4.

PMID 17300723 · PMC1805740 · Virology journal · 2007 · 7 claims · 7 setups

Full-text index only

Genetic distance and heterogeneity between HCV quasispecies is a critical predictor of IFN response in Egyptian genotype-4 patients

serum pcr cloned 5'utr rt-pcr molecular sequencing
The use of multiple displacement amplification to amplify complex DNA libraries.

PMID 18285362 · PMC2275127 · Nucleic acids research · 2008 · 7 claims · 8 setups

Full-text index only

MDA alone cannot select against/remove plasmid ligation multimers, unlike bacterial propagation

hes3 hes3-derived coli plasmids isolation flcdna gis-pet
Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13).

PMID 15234325 · PMC7129141 · International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2004 · 7 claims · 3 setups

Full-text index only

Human aminopeptidase N (APN/CD13/ANPEP) is the receptor for human coronavirus 229E (HCoV-229E)

genomic cloned consensus pcr molecular sequence
52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart.

PMID 7561701 · PMC2192297 · The Journal of experimental medicine · 1995 · 7 claims · 7 setups

Full-text index only

The 52-kD SS-A/Ro gene spans 10 kb of DNA and is composed of seven exons, with the translation initiation codon in exon 2 and the leucine zipper encoded by exon 4.

molt-4 placental placenta fetal cdna genomic race
A genome annotation-driven approach to cloning the human ORFeome.

PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups

Full-text index only

Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%

chromosome pooled t-tailed naga comparative rt-pcr sanger
Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

PMID 18513421 · PMC2426714 · Retrovirology · 2008 · 7 claims · 6 setups

Full-text index only

HIV-1 quasispecies in PBMCs are more genetically heterogeneous than in plasma

plasma proviral cloned pbmc hiv-1 nested clonal
DNA sequencing: bench to bedside and beyond.

PMID 17855400 · PMC2094077 · Nucleic acids research · 2007 · 8 claims · 7 setups

Full-text index only

DNA sequencing methods derived from Sanger's 1977 dideoxy method have dominated sequencing for 30 years despite being only incrementally refined.

bacteriophage double-stranded single-stranded cloned plus maxam-gilbert dideoxy
Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

PMID 15860770 · PMC1087791 · Nucleic acids research · 2005 · 8 claims · 4 setups

Full-text index only

A Geniom One-synthesized oligonucleotide microarray can determine the methylation status of individual CpG dinucleotides in parallel, combining high throughput with single-base resolution

hct116 p16 genomic methylation-specific combined oligonucleotide
A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

Full-text index only

A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

cetacea amel-y amel-x cetartiodactyla pcr sanger molecular

Experiments

Prediction and assessment of splicing alterations: implications for clinical testing.

Association between telomere length and V(H) gene mutation status in chronic lymphocytic leukaemia: clinical and biological implications.

Evaluation of genome-wide chromatin library of Stat5 binding sites in human breast cancer.

Assisted large fragment insertion by Red/ET-recombination (ALFIRE)--an alternative and enhanced method for large fragment recombineering.

New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

Preponderance of the oncogenic V599E and V599K mutations in B-raf kinase domain is enhanced in melanoma cutaneous/subcutaneous metastases.

Differentiating human from animal isolates of Cryptosporidium parvum.

PAX6 gene variations associated with aniridia in south India.

Genetic distance and heterogenecity between quasispecies is a critical predictor to IFN response in Egyptian patients with HCV genotype-4.

The use of multiple displacement amplification to amplify complex DNA libraries.

Identification of six new polymorphisms in the human coronavirus 229E receptor gene (aminopeptidase N/CD13).

52-kD SS-A/Ro: genomic structure and identification of an alternatively spliced transcript encoding a novel leucine zipper-minus autoantigen expressed in fetal and adult heart.

A genome annotation-driven approach to cloning the human ORFeome.

Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

DNA sequencing: bench to bedside and beyond.

Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.