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 1.9k

System / cell line: sequencing ✕ Clear

High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

PMID 20037647 · PMC2793016 · PloS one · 2009 · 7 claims · 7 setups

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A dirty genome approach using unfinished, unclosed genome sequences combined with proteomics can rapidly identify immunogenic proteins useful for diagnostic tool development

parachlamydia spots coli recombinant pyrosequencing solexa gel
Scapuloperoneal spinal muscular atrophy and CMT2C are allelic disorders caused by alterations in TRPV4.

PMID 20037587 · PMC3786192 · Nature genetics · 2010 · 8 claims · 6 setups

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SPSMA and CMT2C are allelic disorders caused by mutations in TRPV4

spsma spsma-affected hek293 candidate histopathology confocal
Complex landscapes of somatic rearrangement in human breast cancer genomes.

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

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

breast subset confirmed paired-end fish exon-exon
Mutational analysis of TARDBP in neurodegenerative diseases.

PMID 20031275 · PMC2889148 · Neurobiology of aging · 2011 · 8 claims · 4 setups

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TARDBP mutations are not a significant cause of AD or PD

als tdp-43 pcr pathogenicity
Melusin gene (ITGB1BP2) nucleotide variations study in hypertensive and cardiopathic patients.

PMID 20017903 · PMC2803168 · BMC medical genetics · 2009 · 6 claims · 5 setups

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Only three nucleotide variations in ITGB1BP2 were found among 928 screened subjects, indicating a high degree of conservation of the gene in the populations analyzed

genomic hela itgb1bp2 melusin direct minigene in-silico
A small-cell lung cancer genome with complex signatures of tobacco exposure.

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

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

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

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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
Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

PMID 20011630 · PMC2790479 · Molecular vision · 2009 · 8 claims · 5 setups

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MDH1 is not the causative gene for RP28-linked autosomal recessive retinitis pigmentosa

genomic lr-pcr uhts v-4 long-range ultra sanger
PALB2 variants in hereditary and unselected Finnish prostate cancer cases.

PMID 20003494 · PMC2806404 · Journal of negative results in biomedicine · 2009 · 8 claims · 6 setups

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None of the detected PALB2 variants, including 1592delT, show significant association with PRCA at the population level in Finland

blood finnish combined formalin-fixed direct additional statistical
Novel syntaxin 11 gene (STX11) mutation in three Argentinean patients with hemophagocytic lymphohistiocytosis.

PMID 19967551 · PMC7370861 · Journal of clinical immunology · 2010 · 8 claims · 8 setups

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Three unrelated Argentinean HLH patients carry an identical novel homozygous 4-bp deletion (c.581_584delTGCC; p.Leu194ProfsX2) in STX11

genomic peripheral blood fresh direct snp rt-pcr
Non-imprinted allele-specific DNA methylation on human autosomes.

PMID 19958531 · PMC2812945 · Genome biology · 2009 · 8 claims · 7 setups

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SNPs within CpG islands are associated with allele-specific DNA methylation differences between alleles.

leukocytes leukocyte hek293 bisulfite methylation-sensitive cdna
A rare de novo nonsense mutation in OTX2 causes early onset retinal dystrophy and pituitary dysfunction.

PMID 19956411 · PMC2786888 · Molecular vision · 2009 · 6 claims · 7 setups

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A novel de novo heterozygous nonsense mutation (c.413C>G, p.S138X) in OTX2 causes an early onset retinal dystrophy accompanied by pituitary dysfunction (growth hormone deficiency)

genomic anonymous single direct lca mismatch
Characterization of the influenza A H5N1 viruses of the 2008-09 outbreaks in India reveals a third introduction and possible endemicity.

PMID 19924254 · PMC2775943 · PloS one · 2009 · 7 claims · 5 setups

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All 2008-09 Indian H5N1 isolates belong to the EMA3 sublineage of clade 2.2

h5n1 gene genome phylogenetic bayesian
Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

PMID 19922672 · PMC2789746 · Malaria journal · 2009 · 8 claims · 8 setups

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Two distinctive COI haplotype groups were consistently detected, corresponding to the Caribbean and Pacific regions.

anopheles mtdna microsatellite population
Novel SOX2 mutations and genotype-phenotype correlation in anophthalmia and microphthalmia.

PMID 19921648 · PMC2787970 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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SOX2 coding-region mutations were identified in 10 of 51 (19.6%) unrelated individuals with anophthalmia/microphthalmia

blood parents sox2-mutation-positive pcr parental clinical
Tumor mapping in 2 large multigenerational families with CYLD mutations: implications for disease management and tumor induction.

PMID 19917957 · PMC2935681 · Archives of dermatology · 2009 · 8 claims · 4 setups

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The clinical distinction between FC, BSS, and MFT has little prognostic or clinical utility, even within the same family, warranting a unifying diagnosis of 'CYLD cutaneous syndrome'.

blood-derived individuals patients excised genomic structured tumor
A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

PMID 19911041 · PMC2766639 · PLoS genetics · 2009 · 8 claims · 7 setups

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Padlock probes combined with high-throughput sequencing enable accurate, quantitative, low-bias digital RNA allelotyping of allele-specific expression

genomic pgp1 skin fibroblasts padlock quantitative gene
DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

PMID 19910371 · PMC2808897 · Nucleic acids research · 2010 · 8 claims · 8 setups

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DBTSS update adds ~330 million new TSS Seq tags from 31 different human/mouse cell types or culture conditions.

normal dld1 beas2b ramos tss comparative
MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome.

PMID 19906696 · PMC2811030 · Nucleic acids research · 2010 · 6 claims · 4 setups

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MiGS combines MBD2 MBD-domain precipitation of methylated DNA with massively parallel sequencing to enable unbiased, high-throughput genome-wide DNA methylation profiling

hct116 migs mbd-isolated bisulfite gene
Mutational hot spot potential of a novel base pair mutation of the CSPG2 gene in a family with Wagner syndrome.

PMID 19901218 · PMC3514888 · Archives of ophthalmology (Chicago, Ill. : 1960) · 2009 · 8 claims · 4 setups

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No COL2A1 mutations were found, making ocular Stickler syndrome an unlikely diagnosis for this family

genomic family complete pcr clinical

Experiments

High throughput sequencing and proteomics to identify immunogenic proteins of a new pathogen: the dirty genome approach.

Scapuloperoneal spinal muscular atrophy and CMT2C are allelic disorders caused by alterations in TRPV4.

Complex landscapes of somatic rearrangement in human breast cancer genomes.

Mutational analysis of TARDBP in neurodegenerative diseases.

Melusin gene (ITGB1BP2) nucleotide variations study in hypertensive and cardiopathic patients.

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

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

Ultra high throughput sequencing excludes MDH1 as candidate gene for RP28-linked retinitis pigmentosa.

PALB2 variants in hereditary and unselected Finnish prostate cancer cases.

Novel syntaxin 11 gene (STX11) mutation in three Argentinean patients with hemophagocytic lymphohistiocytosis.

Non-imprinted allele-specific DNA methylation on human autosomes.

A rare de novo nonsense mutation in OTX2 causes early onset retinal dystrophy and pituitary dysfunction.

Characterization of the influenza A H5N1 viruses of the 2008-09 outbreaks in India reveals a third introduction and possible endemicity.

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

Novel SOX2 mutations and genotype-phenotype correlation in anophthalmia and microphthalmia.

Tumor mapping in 2 large multigenerational families with CYLD mutations: implications for disease management and tumor induction.

A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

DBTSS provides a tissue specific dynamic view of Transcription Start Sites.

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome.

Mutational hot spot potential of a novel base pair mutation of the CSPG2 gene in a family with Wagner syndrome.