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 17

System / cell line: donor ✕ Assay: snp ✕ Clear

Silhouette scores for assessment of SNP genotype clusters.

PMID 15760469 · PMC555759 · BMC genomics · 2005 · 7 claims · 5 setups

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Silhouette scores provide a relevant, objective numeric measure of SNP genotype cluster quality, condensing tightness and separation into a single value from -1.0 to 1.0.

genomic blood extended hybridized single genomic multiplex
Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

PMID 18334959 · PMC2268850 · Molecular vision · 2008 · 7 claims · 5 setups

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A homozygous c.955G>A mutation at the last base of exon 6 of LCA5 disrupts the normal splice donor site.

genomic lca5 lymphocyte affected snp sanger splice
The diploid genome sequence of an individual human.

PMID 17803354 · PMC1964779 · PLoS biology · 2007 · 7 claims · 6 setups

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Generated an independently assembled diploid human genome sequence (HuRef) from both chromosome sets of a single individual using whole-genome shotgun Sanger sequencing

donor huref whole-genome assembly-to-assembly snp
High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

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WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

genomic whole-genome same call snp technical genotype
Inferring human colonization history using a copying model.

PMID 18497854 · PMC2367454 · PLoS genetics · 2008 · 8 claims · 6 setups

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A copying-model approach using SNP haplotype sharing can infer both the order of population founding and the donor populations contributing ancestry to each new population.

simulated populations coalescent snp ascertainment
The diploid genome sequence of an Asian individual.

PMID 18987735 · PMC2716080 · Nature · 2008 · 8 claims · 8 setups

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First diploid genome sequence of an Asian (Han Chinese) individual generated using massively parallel Illumina sequencing

han donor genome genomic whole-genome g-banded snp
Genome-wide survey of allele-specific splicing in humans.

PMID 18518984 · PMC2427040 · BMC genomics · 2008 · 8 claims · 5 setups

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A genome-wide computational scan identified 30,977 SNPs located within predicted splicing regulatory sequences (donor sites, acceptor sites, branch points, and ESEs)

genome cdna hapmap computational est exon
Genetic and functional association of FAM5C with myocardial infarction.

PMID 18430236 · PMC2383879 · BMC medical genetics · 2008 · 8 claims · 5 setups

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SNPs within FAM5C show genetic linkage to and association with myocardial infarction in the GENECARD family-based sample

genecard cathgen donor aortic genome-wide case-control expression
Calibration-free NGS quantitation of mutations below 0.01% VAF.

PMID 34675197 · PMC8531361 · Nature communications · 2021 · 8 claims · 6 setups

Has reproduction · 96

QBDA (Quantitative Blocker Displacement Amplification) integrates UMI molecular barcoding with BDA variant enrichment to enable calibration-free VAF quantitation

h37rv repository healthy same single-plex 10-plex 22-plex
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
Frequent loss of the AXIN1 locus but absence of AXIN1 gene mutations in adenocarcinomas of the gastro-oesophageal junction with nuclear beta-catenin expression.

PMID 14970870 · PMC3215949 · British journal of cancer · 2004 · 8 claims · 7 setups

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Nuclear β-catenin expression in GEJ adenocarcinoma cell lines correlates with enhanced TCF-mediated reporter gene transcription

gej paired showing tumours tcf pcr-sscp bidirectional
Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

PMID 17052327 · PMC1626071 · BMC medical genetics · 2006 · 8 claims · 8 setups

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RSTS is caused by chromosomal microdeletions and point mutations in one copy of CREBBP (16p13.3), consistent with haploinsufficiency of this dosage-sensitive gene

peripheral patient-parent genomic crebbp karyotyping bac microsatellite
Intrinsic genetic characteristics determine tumor-modifying capacity of fibroblasts: matrix metalloproteinase-3 5A/5A genotype enhances breast cancer cell invasion.

PMID 17922906 · PMC2242664 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Tumor-derived fibroblasts promote higher levels of breast cancer cell invasion than normal fibroblasts

breast conditioned mda-mb-468 genomic invasion immunofluorescence pcr-rflp
Evolutionary toggling of the MAPT 17q21.31 inversion region.

PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups

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The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31

chimpanzee lymphoblastoid donor whole-genome reciprocal bac
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
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 87

Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

airway asm most single rna-seq quantitative qrt-pcr
Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.

PMID 33849442 · PMC8042899 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

Has reproduction · 23

Whole-genome resequencing reveals three geographically distinct genetic groups: local Chinese, wild, and local Southeast/South Asian duck populations

newly duck southeast chinese whole-genome phylogenetic population

Experiments

Silhouette scores for assessment of SNP genotype clusters.

Identification of a novel splice-site mutation in the Lebercilin (LCA5) gene causing Leber congenital amaurosis.

The diploid genome sequence of an individual human.

High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

Inferring human colonization history using a copying model.

The diploid genome sequence of an Asian individual.

Genome-wide survey of allele-specific splicing in humans.

Genetic and functional association of FAM5C with myocardial infarction.

Calibration-free NGS quantitation of mutations below 0.01% VAF.

Identification of common genetic variation that modulates alternative splicing.

Frequent loss of the AXIN1 locus but absence of AXIN1 gene mutations in adenocarcinomas of the gastro-oesophageal junction with nuclear beta-catenin expression.

Rubinstein-Taybi Syndrome: spectrum of CREBBP mutations in Italian patients.

Intrinsic genetic characteristics determine tumor-modifying capacity of fibroblasts: matrix metalloproteinase-3 5A/5A genotype enhances breast cancer cell invasion.

Evolutionary toggling of the MAPT 17q21.31 inversion region.

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

RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations.