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 43

System / cell line: cell-line ✕ Assay: exon ✕ Clear

Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

PMID 19811662 · PMC2766370 · Molecular cancer · 2009 · 7 claims · 6 setups

Full-text index only

LCN-HRM enables detection and sequencing-based characterisation of low-level mutations that are undetectable by direct sequencing alone

hct116 ffpe genomic tx84 dideoxynucleotide high lcn-hrm
Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

PMID 18366763 · PMC2292204 · BMC molecular biology · 2008 · 8 claims · 8 setups

Full-text index only

Transcription start sites of human DYRK1A are distributed over an 800 bp region within an unmethylated CpG island

pc3 saos2 resting phoenix 5'-race-pcr rt-pcr chip-seq
Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain.

PMID 15737014 · PMC549606 · PLoS medicine · 2005 · 7 claims · 6 setups

Full-text index only

A secondary EGFR exon 20 mutation (T790M) is found in tumors from patients with acquired resistance to gefitinib or erlotinib

tumor 293t nsclc direct fluorescent rt-pcr
X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

PMID 17932061 · PMC2238884 · Nucleic acids research · 2008 · 7 claims · 4 setups

Full-text index only

X:Map is a genome annotation database that maps every Affymetrix exon array probeset to Ensembl genome features (genes, ESTs, GenScan predictions) and supports both high-throughput and gene-centric analysis.

ensembl breast mcf7 25-mer probe-to-transcript microarray
A small-cell lung cancer genome with complex signatures of tobacco exposure.

PMID 20016488 · PMC2880489 · Nature · 2010 · 8 claims · 7 setups

Full-text index only

22,910 somatic substitutions, including 132 in coding exons, were identified genome-wide in the NCI-H209 SCLC genome.

nci-h209 sclc lu-135 massively pcr multiplex
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
Rare-type mutations of MMAC1 tumor suppressor gene in human glioma cell lines and their tumors of origin.

PMID 10551321 · PMC5926156 · Japanese journal of cancer research : Gann · 1999 · 8 claims · 6 setups

Full-text index only

6 of 10 glioma cell lines examined showed MMAC1 mutations with presumed loss of heterozygosity (LOH)

glioma pcr northern rt-pcr sscp
CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

PMID 11556834 · PMC2375081 · British journal of cancer · 2001 · 7 claims · 6 setups

Full-text index only

Germ line CDKN2A mutations were found in 5 of 15 (33.3%) Italian melanoma-prone families, including one novel mutation (P48T) and three known pathogenic mutations (R24P, G101W, N71S)

genomic radiolabelled tig-er u2os sscp protein-protein retroviral
High resolution melting for mutation scanning of TP53 exons 5-8.

PMID 17764544 · PMC2025602 · BMC cancer · 2007 · 7 claims · 5 setups

Full-text index only

HRM is an effective technique for rapid scanning of TP53 mutations that can markedly reduce required sequencing

tp53-mutant ovarian breast high hrm dideoxy
Complex landscapes of somatic rearrangement in human breast cancer genomes.

PMID 20033038 · PMC3398135 · Nature · 2009 · 8 claims · 6 setups

Full-text index only

There are more somatic rearrangements in some breast cancers than previously appreciated by cytogenetic methods.

breast subset confirmed paired-end fish exon-exon
H-DBAS: human-transcriptome database for alternative splicing: update 2010.

PMID 19969536 · PMC2808982 · Nucleic acids research · 2010 · 8 claims · 4 setups

Full-text index only

RNA-Seq tags from the polysome fraction identify AS exons that are very likely used for protein synthesis

dld-1 rna-seq western real-time
Mutation analysis of genes that control the G1/S cell cycle in melanoma: TP53, CDKN1A, CDKN2A, and CDKN2B.

PMID 15819981 · PMC1097717 · BMC cancer · 2005 · 7 claims · 4 setups

Full-text index only

TP53 gene shows heterozygous defects in 8 of 39 (20.5%) melanoma tumors, including novel point mutations and novel SNPs in intronic sequences

metastatic melanoma genomic pcr-sscp sequencing pcr
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

Full-text index only

Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

liver genomic tissues embryos rt-pcr genomic secondary
BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH).

PMID 16439806 · PMC1356528 · Nucleic acids research · 2006 · 8 claims · 7 setups

Full-text index only

oaCGH, not BAC CGH arrays, is the platform that will prevail in the future

genomic lung genetics bt474 array exon
A comprehensive catalogue of somatic mutations from a human cancer genome.

PMID 20016485 · PMC3145108 · Nature · 2010 · 8 claims · 7 setups

Full-text index only

Whole-genome sequencing of COLO-829 melanoma cells and matched COLO-829BL normal cells produced the first comprehensive catalogue of somatic mutations from an individual cancer genome

colo-829 additional whole-genome conventional pcr
Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

PMID 15018647 · PMC365025 · BMC genomics · 2004 · 8 claims · 8 setups

Full-text index only

Combined SSH subtractive cloning and array CGH is an efficient strategy to identify overexpressed genes located within DNA amplicons.

imr-32 subtracted mycn-amplified suppression differential array
Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

PMID 16327884 · PMC1298935 · PLoS genetics · 2005 · 8 claims · 8 setups

Full-text index only

Point mutations in FOXE1, GLI2, JAG2, LHX8, MSX1, MSX2, SATB2, SKI, SPRY2, and TBX10 may be rare causes of isolated CL/P

family additional unrelated mutant direct linkage targeted
In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

PMID 16995940 · PMC1590028 · BMC genomics · 2006 · 8 claims · 6 setups

Full-text index only

In silico ESE-prediction algorithms (ESEfinder, RescueESE, PESX) do not reliably predict actual in vivo splicing behavior of missense mutations

hmlh1 same cos-7 hela ese splice minigene
Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

PMID 17945002 · PMC2242669 · Breast cancer research : BCR · 2007 · 8 claims · 7 setups

Full-text index only

-26G>A polymorphism in the BRCA2 5' UTR is functional: the A allele drives roughly twice the reporter gene expression of the G allele in MCF-7 and HeLa cells

mcf-7 hela brca2 peripheral luciferase transcription genotyping
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

Full-text index only

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

Experiments

Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1.

Acquired resistance of lung adenocarcinomas to gefitinib or erlotinib is associated with a second mutation in the EGFR kinase domain.

X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

A small-cell lung cancer genome with complex signatures of tobacco exposure.

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.

Rare-type mutations of MMAC1 tumor suppressor gene in human glioma cell lines and their tumors of origin.

CDKN2A and CDK4 mutation analysis in Italian melanoma-prone families: functional characterization of a novel CDKN2A germ line mutation.

High resolution melting for mutation scanning of TP53 exons 5-8.

Complex landscapes of somatic rearrangement in human breast cancer genomes.

H-DBAS: human-transcriptome database for alternative splicing: update 2010.

Mutation analysis of genes that control the G1/S cell cycle in melanoma: TP53, CDKN1A, CDKN2A, and CDKN2B.

Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH).

A comprehensive catalogue of somatic mutations from a human cancer genome.

Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

Medical sequencing of candidate genes for nonsyndromic cleft lip and palate.

In silico and in vivo splicing analysis of MLH1 and MSH2 missense mutations shows exon- and tissue-specific effects.

Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

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