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 20

System / cell line: reference ✕ Assay: cgh ✕ Clear

Human and mouse oligonucleotide-based array CGH.

PMID 16361265 · PMC1316119 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Oligo array CGH detects single copy gains, multi-copy amplifications, and homozygous/heterozygous deletions as small as 100 kb

bt474 normal gm01750 mda-mb-468 array fish
Genome-wide analysis of subependymomas shows underlying chromosomal copy number changes involving chromosomes 6, 7, 8 and 14 in a proportion of cases.

PMID 18397339 · PMC2659379 · Brain pathology (Zurich, Switzerland) · 2008 · 8 claims · 2 setups

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Whole-genome aCGH reveals chromosomal copy number abnormalities in 5 of 12 (42%) subependymoma cases

subependymoma whole-genome chromosome
Exploiting noise in array CGH data to improve detection of DNA copy number change.

PMID 17272296 · PMC1994778 · Nucleic acids research · 2007 · 7 claims · 4 setups

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When aberrations are present, noise in BAC, 19k oligo, and 385k oligo array-CGH data is highly non-Gaussian and shows long-range spatial correlations.

atm-deficient normal simulated array simulated
Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups

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Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer

large-insert patients test genomic array-cgh manual automated
CGHPRO -- a comprehensive data analysis tool for array CGH.

PMID 15807904 · PMC1274268 · BMC bioinformatics · 2005 · 8 claims · 3 setups

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CGHPRO is a user-friendly, versatile, stand-alone Java tool for normalization, visualization, breakpoint detection and comparative analysis of array-CGH data

tiling artificially array
High resolution array-CGH analysis of single cells.

PMID 17178751 · PMC1807964 · Nucleic acids research · 2007 · 7 claims · 7 setups

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Single copy number changes as small as 8.3 Mb can be detected reliably in single cells using GenomePlex WGA combined with high-resolution tiling-path array-CGH.

769p hct116 peripheral single array-cgh gel fish
Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

PMID 17565693 · PMC1920519 · BMC genomics · 2007 · 8 claims · 4 setups

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42 different CNVs were detected in 27 phenotypically normal individuals using 1 Mb resolution BAC array-CGH

genomic metaphase computational array-cgh fish real-time
Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

genomic normalized simulated tiling-resolution snp oligonucleotide
CGH-Profiler: data mining based on genomic aberration profiles.

PMID 16042799 · PMC1183191 · BMC bioinformatics · 2005 · 8 claims · 3 setups

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CGH-Profiler circumvents ISCN nomenclature by importing CGH data from different vendor systems and converting it into a table format suitable for statistical analysis.

tumour cgh metaphase comparative metaphase
Challenges and standards in integrating surveys of structural variation.

PMID 17597783 · PMC2698291 · Nature genetics · 2007 · 7 claims · 5 setups

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There is no standard approach to collecting, assessing the quality of, or describing structural variants, risking the entire genome eventually being labeled 'structurally variant' based on uncurated nondisease-sample data.

genomic hapmap reference independent comparative snp fosmid
Recurrent DNA copy number changes in 1q, 4q, 6q, 9p, 13q, 14q and 22q detected by comparative genomic hybridization in malignant mesothelioma.

PMID 9052404 · PMC2063309 · British journal of cancer · 1997 · 7 claims · 2 setups

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This is the first genome-wide screening for DNA sequence gains and losses using CGH in malignant pleural mesothelioma tumours.

pleural cgh comparative statistical
Paired-end mapping reveals extensive structural variation in the human genome.

PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

genomic na15510 stretched reference paired-end pcr array
Pathogenesis of vestibular schwannoma in ring chromosome 22.

PMID 19772601 · PMC2758865 · BMC medical genetics · 2009 · 8 claims · 7 setups

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Tumours in ring chromosome 22 patients arise from the combination of loss of the ring chromosome (first hit) and a pathogenic somatic NF2 mutation on the remaining chromosome 22 (second hit)

peripheral schwann skin-biopsy vestibular karyotyping fish array
Integration of cytogenetic landmarks into the draft sequence of the human genome.

PMID 11237021 · PMC7845515 · Nature · 2001 · 8 claims · 6 setups

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7,600 cytogenetically defined landmarks (from a set of 8,877 clones) were placed on the draft sequence of the human genome as a public resource

large-insert bac ml-2 dgap012 fluorescence sts array
Relative impact of nucleotide and copy number variation on gene expression phenotypes.

PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

lymphoblastoid same computational subset gene snp array
Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

PMID 18410676 · PMC2375447 · BMC genomics · 2008 · 8 claims · 7 setups

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Chicken and turkey genomes differ by only two inter-chromosomal rearrangements (GGA2 orthologous to MGA3+6; GGA4 orthologous to MGA4+9), both involving centromeres.

chicken turkey broiler chromosome single fish
Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.

PMID 19922635 · PMC2784474 · BMC microbiology · 2009 · 8 claims · 6 setups

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S. Enteritidis isolates show a high degree of genetic homogeneity/uniformity across typing methods and CGH despite geographic, temporal and source differences.

enteritidis selected uruguayan caco-2 rapd-pcr pfge comparative
Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

PMID 18831773 · PMC3226104 · BMC genomics · 2008 · 8 claims · 8 setups

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Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare

mcf7 arabidopsis specified different chip-seq microarray array-based
Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

PMID 18655731 · PMC2515324 · BMC genomics · 2008 · 7 claims · 6 setups

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A collection of 132,577 ESTs from four Actinidia species was generated and clustered into 41,858 non-redundant clusters (18,070 TCs and 23,788 singletons)

cdna full-length tentative non-redundant est codon snp
Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains.

PMID 18590534 · PMC2481270 · BMC genomics · 2008 · 8 claims · 6 setups

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B. pertussis strains carrying the ptxP3 allele gradually replaced ptxP1 strains and became predominant from 1998, coinciding with the Dutch pertussis resurgence

dutch additional pertussis ptxp3 multi-locus multiple-locus microarray-based

Experiments

Human and mouse oligonucleotide-based array CGH.

Genome-wide analysis of subependymomas shows underlying chromosomal copy number changes involving chromosomes 6, 7, 8 and 14 in a proportion of cases.

Exploiting noise in array CGH data to improve detection of DNA copy number change.

Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

CGHPRO -- a comprehensive data analysis tool for array CGH.

High resolution array-CGH analysis of single cells.

Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

CGH-Profiler: data mining based on genomic aberration profiles.

Challenges and standards in integrating surveys of structural variation.

Recurrent DNA copy number changes in 1q, 4q, 6q, 9p, 13q, 14q and 22q detected by comparative genomic hybridization in malignant mesothelioma.

Paired-end mapping reveals extensive structural variation in the human genome.

Pathogenesis of vestibular schwannoma in ring chromosome 22.

Integration of cytogenetic landmarks into the draft sequence of the human genome.

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

Genomic and phenotypic variation in epidemic-spanning Salmonella enterica serovar Enteritidis isolates.

Genomics, molecular imaging, bioinformatics, and bio-nano-info integration are synergistic components of translational medicine and personalized healthcare research.

Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains.