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 11

System / cell line: regions ✕ Assay: cnv ✕ Clear

A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

Has reproduction · 61

T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided
Impact of short-read sequencing on the misassembly of a plant genome.

PMID 33530937 · PMC7852129 · BMC genomics · 2021 · 7 claims · 6 setups

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Short-read tomato assembly has substantial high-coverage (0.6%, 5.1 Mb) and low-coverage (9.7%, 79.6 Mb) regions relative to background coverage

tomato whole-genome cnv machine
Bias of selection on human copy-number variants.

PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

genome human-mouse cnv-encompassed inbred comparative randomization molecular
Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

PMID 37216666 · PMC10411599 · G3 (Bethesda, Md.) · 2023 · 7 claims · 8 setups

Has reproduction · 86

CAGE sequencing of 24 tissues from 3 cattle populations (dairy, beef-dairy cross, Kinsella composite) defines TSS and coexpressed short-range enhancers in the ARS-UCD1.2 reference genome

tissues predicted tss-enhancer cattle cage extraction coexpression
Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

PMID 17608949 · PMC1934372 · BMC genomics · 2007 · 7 claims · 5 setups

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Developed a statistical model-fitting method to infer generalized (multi-allelic, copy-number-aware) genotypes from raw SNP microarray data

individuals mother-father-child transcribed snp quantitative multiplex
Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.

PMID 19949810 · PMC2865568 · Journal of neurology · 2010 · 7 claims · 4 setups

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CNVs are a rare cause of non-CMT1A Charcot-Marie-Tooth disease

unrelated genomic mtmr2 array quantitative sanger
Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

PMID 18784189 · PMC2577347 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Genomic waves are present in both Illumina and Affymetrix SNP genotyping arrays, confirming they are not platform-specific

representative illumina six snp serial concentration
Current status and the future for the genetics of type I diabetes.

PMID 19956094 · PMC2805458 · Genes and immunity · 2009 · 8 claims · 7 setups

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A T1DGC genome-wide association meta-analysis of >7500 cases and >9000 controls identified 42 distinct genomic locations associated with T1D at P<10^-6.

asp subjects t1dgc cases genome-wide mhc candidate
Single-molecule sequencing of an individual human genome.

PMID 19668243 · PMC4117198 · Nature biotechnology · 2009 · 8 claims · 7 setups

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Single-molecule sequencing without cloning, amplification or ligation can sequence an individual human genome on one instrument by a single operator in four runs

genome staphylococcus single-molecule snp sanger
In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

genomic genome pan blood snp sequence cross-species
Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

PMID 20018283 · PMC2845297 · Atherosclerosis · 2010 · 8 claims · 7 setups

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The ADIPOQ locus is the only major gene locus for plasma adiponectin, reaching genome-wide significance in combined and sex-stratified analyses

population-based cohorts gwa plasma genome-wide replication candidate

Experiments

A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

Impact of short-read sequencing on the misassembly of a plant genome.

Bias of selection on human copy-number variants.

Improving the annotation of the cattle genome by annotating transcription start sites in a diverse set of tissues and populations using Cap Analysis Gene Expression sequencing.

Toward accurate high-throughput SNP genotyping in the presence of inherited copy number variation.

Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.

Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

Current status and the future for the genetics of type I diabetes.

Single-molecule sequencing of an individual human genome.

In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.