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 16

System / cell line: across ✕ Assay: southern ✕ Clear

A reliable method to display authentic DNase I hypersensitive sites at long-ranges in single-copy genes from large genomes.

PMID 16510851 · PMC1388096 · Nucleic acids research · 2006 · 6 claims · 3 setups

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MDHA extends the range of classical DHA from ~20 kb increments to intervals approaching 100 kb using agarose-embedded nuclei, FIGE, and long-range Southern blotting

jurkat specified mdha northern
Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).

PMID 41490125 · PMC12768360 · PloS one · 2026 · 6 claims · 5 setups

Has reproduction · 69

The original BRAKER3-based NWR annotation was of poor quality: only 51% of transcripts were correctly called, many were assigned uninformative protein names, and some were misassigned to incorrect or bacterial sequences.

granulosa nwr aligned unassigned bulk reference transcript
BRCA1 mutations in southern England.

PMID 9649133 · PMC2150412 · British journal of cancer · 1998 · 7 claims · 4 setups

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Early age of onset combined with a strong family history is the most effective selection criterion for detecting BRCA1 mutations, more so than bilaterality alone

genomic pcr clinical heteroduplex sequencing pcr
Extreme conservation of noncoding DNA near HoxD complex of vertebrates.

PMID 15462684 · PMC524357 · BMC genomics · 2004 · 7 claims · 7 setups

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Three blocks of extremely conserved non-coding DNA (CR1, CR2, CR3) exist within 7 kb upstream of the HoxD complex, 3' of Evx-2, conserved from fish to human.

hoxd genomic pcr pcr-amplified comparative pcr southern
Tracing human genetic histories and natural selection with precise local ancestry inference.

PMID 40379651 · PMC12084304 · Nature communications · 2025 · 7 claims · 7 setups

Has reproduction · 76

Orchestra, a two-stage LAI method combining a recombination-distance base layer with a deep learning (convolutional + attention) smoothing module, outperforms RFmix, FLARE and Gnomix in precision and recall across simulated admixture generations.

1kgp-16pops independent simulated 1kgp simulated population-level local
Geographical genomics of human leukocyte gene expression variation in southern Morocco.

PMID 19966804 · PMC2798927 · Nature genetics · 2010 · 8 claims · 8 setups

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Gene expression differs substantially between locations (up to 38% of transcripts), driven largely by a rural-versus-urban lifestyle contrast rather than ethnicity or gender.

peripheral blood genotype randomly genome-wide population admixture
Inter- and Intraspecific Venom Variation in the Reclusive Rear-Fanged Black-Striped Snakes (Coniophanes).

PMID 41745774 · PMC12945099 · Toxins · 2026 · 8 claims · 4 setups

Has reproduction

Coniophanes DVG transcriptomes contain 18 toxin families, with toxins comprising 38.8% to 66% of total transcriptome expression depending on species

duvernoy's fissidens venom imperialis rna-seq dicect quantitative
Mutation analysis of the Fanconi anaemia A gene in breast tumours with loss of heterozygosity at 16q24.3.

PMID 10098735 · PMC2362253 · British journal of cancer · 1999 · 7 claims · 6 setups

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The FAA gene is not the gene targeted by LOH at 16q24.3 in breast cancer

breast tumour sscp exon-by-exon southern
Fusion of short telomeres in human cells is characterized by extensive deletion and microhomology, and can result in complex rearrangements.

PMID 20026586 · PMC2847243 · Nucleic acids research · 2010 · 8 claims · 5 setups

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Telomere fusion in human cells is characterized by extensive sub-telomeric deletion of at least one telomere, extending up to 5.6-6.1 kb

hek293 mrc5 pcr single single-molecule southern direct
Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

PMID 7606775 · PMC3730239 · Cell · 1995 · 6 claims · 8 setups

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Expression of a specific var gene (A4var) correlates with A4 antigenic type and with binding to ICAM-1

falciparum cdna c18 genomic rt-pcr southern genomic
New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

PMID 16340004 · PMC1310899 · Nucleic acids research · 2005 · 7 claims · 8 setups

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Long pure palindromes (>~200 bp) cannot be stably cloned in E.coli due to cruciform-driven instability, and no E.coli mutant fully overcomes this cloning block.

individuals e.coli cerevisiae yeast pcr plasmid phi-29
Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

PMID 18818683 · PMC2756756 · Kidney international · 2008 · 8 claims · 8 setups

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Developed an MLPA assay with PKD1 exon 1-33 probes designed at single base-pair mismatches with the six PKD1 pseudogenes to achieve locus specificity

blood-derived blood crisp father mlpa long-range field
Loss of heterozygosity at the 5,10-methylenetetrahydrofolate reductase locus in human ovarian carcinomas.

PMID 9099956 · PMC2222800 · British journal of cancer · 1997 · 8 claims · 7 setups

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No sequence mutations were found in the MTHFR gene in ovarian tumors and cell lines despite extensive SSCP screening

ovarian non-mucinous informative rt-pcr immunohistochemistry pcr-rflp
mtDNA nt13708A variant increases the risk of multiple sclerosis.

PMID 18270557 · PMC2217590 · PloS one · 2008 · 8 claims · 5 setups

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The mtDNA nt13708 G/A polymorphism (nt13708A allele) is significantly associated with increased risk of MS (OR=1.71, P=0.0002) across three well-matched European cohorts.

peripheral pooled mtdna snp meta-analysis complete
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

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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
Functional characterisation of the TSC1-TSC2 complex to assess multiple TSC2 variants identified in single families affected by tuberous sclerosis complex.

PMID 18302728 · PMC2291454 · BMC medical genetics · 2008 · 8 claims · 8 setups

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Functional assays of TSC1–TSC2 complex activity can distinguish pathogenic TSC2 mutations from rare polymorphisms when multiple variants segregate in one family

hek immunoprecipitated tsc2 peripheral coimmunoprecipitation rheb s6k-t389

Experiments

A reliable method to display authentic DNase I hypersensitive sites at long-ranges in single-copy genes from large genomes.

Manual curation for improved genome annotation of the functionally extinct northern white rhinoceros (Ceratotherium simum cottoni).

BRCA1 mutations in southern England.

Extreme conservation of noncoding DNA near HoxD complex of vertebrates.

Tracing human genetic histories and natural selection with precise local ancestry inference.

Geographical genomics of human leukocyte gene expression variation in southern Morocco.

Inter- and Intraspecific Venom Variation in the Reclusive Rear-Fanged Black-Striped Snakes (Coniophanes).

Mutation analysis of the Fanconi anaemia A gene in breast tumours with loss of heterozygosity at 16q24.3.

Fusion of short telomeres in human cells is characterized by extensive deletion and microhomology, and can result in complex rearrangements.

Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

Loss of heterozygosity at the 5,10-methylenetetrahydrofolate reductase locus in human ovarian carcinomas.

mtDNA nt13708A variant increases the risk of multiple sclerosis.

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

Functional characterisation of the TSC1-TSC2 complex to assess multiple TSC2 variants identified in single families affected by tuberous sclerosis complex.