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 67

System / cell line: presence ✕ Assay: chromosome ✕ Clear

An efficient method for multi-locus molecular haplotyping.

PMID 17158153 · PMC1802573 · Nucleic acids research · 2007 · 7 claims · 6 setups

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A novel molecular haplotyping method using limiting dilution, aliquot pre-screening, and tiling reconstruction can resolve haplotypes spanning many loci over long distances from a single individual's DNA.

single agarose-embedded genotyping multiplexed monoplex primer-extension
Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

PMID 16822311 · PMC1553470 · Retrovirology · 2006 · 8 claims · 6 setups

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CTLL cells stably expressing wild-type Tax (CTLL/WT) show higher aneuploidy than a CREB-transactivation-deficient Tax clone (CTLL/703)

ctll gene promoter metaphase microarray bioinformatics
Analysis of X chromosome inactivation in autism spectrum disorders.

PMID 18361425 · PMC4867005 · American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics · 2008 · 6 claims · 5 setups

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No significant excess of skewed XCI was found in mothers of children with ASD or in affected girls compared to controls

genomic multiplex mecp2 four chromosome non-parametric mutation
Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

PMID 19650893 · PMC2728732 · BMC evolutionary biology · 2009 · 8 claims · 7 setups

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Autochthonous Berber Y-chromosome lineages E-M81, E-M78 and J-M267 were detected in indigenous Canary Island remains, confirming a North West African origin for the aboriginal ancestors.

prehispanic indigenous ancient modern y-chromosome nested real-time
Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

PMID 16469098 · PMC1409804 · BMC bioinformatics · 2006 · 7 claims · 3 setups

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AUGUSTUS+ extends the AUGUSTUS GHMM by combining intrinsic sequence information with extrinsic hints via an extended emission alphabet, so the GHMM jointly models the DNA sequence, gene structure, and hint collection.

chromosome genomic training ghmm-based sequence parameter
Candidate target genes for loss of heterozygosity on human chromosome 17q21.

PMID 15187990 · PMC2409524 · British journal of cancer · 2004 · 8 claims · 5 setups

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JUP (plakoglobin) is the only identified gene physically located between the D17S746 and D17S846 markers that define the smallest common region of LOH on chromosome 17q21

genomic normal breast p1-phage nucleotide rt-pcr cold
Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

PMID 17026745 · PMC1630699 · BMC genetics · 2006 · 8 claims · 6 setups

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Identified 32 male-specific Y-chromosome sequences totaling 24159 bp via combined Blast (human Y chromosome match, absence from female dog genome) and PCR male-specificity screening of a male poodle shotgun genome.

poodle dogs y-chromosome blast pcr nested
TEMP: a computational method for analyzing transposable element polymorphism in populations.

PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

Has reproduction · 61

TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

drosophila five four melanogaster simulated comparative whole-genome
Skittle: a 2-dimensional genome visualization tool.

PMID 20042093 · PMC2817707 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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Skittle is a 2D genome visualization tool combining a color-coded Nucleotide Display, a Repeat Map, a Repeat Overview, and an Alignment Cylinder to reveal genomic patterns at multiple scales

chromosome random alpha genome nucleotide repeat alignment
Loss of cyclin-dependent kinase inhibitor genes and chromosome 9 karyotypic abnormalities in human bladder cancer cell lines.

PMID 7577470 · PMC2033929 · British journal of cancer · 1995 · 8 claims · 4 setups

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Homozygous deletion of both p15 and p16 occurred in 7 of 13 (54%) independent bladder cancer cell lines tested

bladder pcr pcr cytogenetic arbitrary
The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer.

PMID 12381271 · PMC134458 · BMC genetics · 2002 · 7 claims · 8 setups

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UNC93A maps within the minimal region of allele loss on 6q27 between D6S264 and D6S149, centromeric to D6S149

panel 293-t malignant same rt-pcr northern fluorescence
Novel CYP1B1 mutations in consanguineous Pakistani families with primary congenital glaucoma.

PMID 18989382 · PMC2579935 · Molecular vision · 2008 · 7 claims · 6 setups

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Missense mutations in CYP1B1 are most likely responsible for PCG in these three Pakistani families

genomic family ethnically affected genotyping two-point sanger
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups

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Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster

c57bl orthologous alpha-defensin defensin manual comparative sequence
NOD-like receptor repertoire in the chromosome-level genome of the demosponge Dysidea avara (Schmidt, 1862).

PMID 41710890 · PMC12909245 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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Dysidea avara has a chromosome-level genome assembly of 575 Mb, N50 41 Mb, 162 scaffolds, and 15 chromosomes.

dysidea avara translated nlrs long-read hi-c genome
Chromosome-Scale Assembly of the Complete Genome Sequence of Porcisia hertigi, Isolate C119, Strain LV43.

PMID 34647802 · PMC8515887 · Microbiology resource announcements · 2021 · 6 claims · 8 setups

Has reproduction · 88

The complete, chromosome-scale genome sequence of Porcisia hertigi (isolate C119, strain LV43) was assembled using combined short- and long-read sequencing technologies.

porcisia hertigi parasite extraction short-read
Analysis of human sarcospan as a candidate gene for CFEOM1.

PMID 11180757 · PMC29083 · BMC genetics · 2001 · 7 claims · 5 setups

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Sarcospan sequence is unmutated in all six CFEOM1 families studied

yac genomic extraocular genome pcr direct immunofluorescence
Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.

PMID 17704778 · PMC2872770 · Nature genetics · 2007 · 8 claims · 6 setups

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Mutations in UPF3B cause syndromic (Lujan-Fryns syndrome, FG syndrome) and nonsyndromic X-linked mental retardation

probands lymphoblastoid lcls tissues gene quantitative cycloheximide
Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

PMID 17480121 · PMC1865561 · PLoS genetics · 2007 · 7 claims · 8 setups

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KLF14 is a novel imprinted gene showing monoallelic maternal expression in embryonic and extra-embryonic tissues of both human and mouse

embryonic fetal monochromosomal fibroblasts allele-specific rt-pcr chromatin
A missense mutation in the nuclear localization signal sequence of CERKL (p.R106S) causes autosomal recessive retinal degeneration.

PMID 18978954 · PMC2576480 · Molecular vision · 2008 · 8 claims · 6 setups

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A C>A transversion in exon 2 of CERKL (c.316C>A) causes a missense change p.R106S in the nuclear localization signal sequence (KLKRR) of the protein.

patients genomic family cerkl ophthalmic homozygosity multipoint
A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

cetacea amel-y amel-x cetartiodactyla pcr sanger molecular

Experiments

An efficient method for multi-locus molecular haplotyping.

Involvement of HTLV-I Tax and CREB in aneuploidy: a bioinformatics approach.

Analysis of X chromosome inactivation in autism spectrum disorders.

Demographic history of Canary Islands male gene-pool: replacement of native lineages by European.

Gene prediction in eukaryotes with a generalized hidden Markov model that uses hints from external sources.

Candidate target genes for loss of heterozygosity on human chromosome 17q21.

Dog Y chromosomal DNA sequence: identification, sequencing and SNP discovery.

TEMP: a computational method for analyzing transposable element polymorphism in populations.

Skittle: a 2-dimensional genome visualization tool.

Loss of cyclin-dependent kinase inhibitor genes and chromosome 9 karyotypic abnormalities in human bladder cancer cell lines.

The human homologue of unc-93 maps to chromosome 6q27 - characterisation and analysis in sporadic epithelial ovarian cancer.

Novel CYP1B1 mutations in consanguineous Pakistani families with primary congenital glaucoma.

Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.

NOD-like receptor repertoire in the chromosome-level genome of the demosponge Dysidea avara (Schmidt, 1862).

Chromosome-Scale Assembly of the Complete Genome Sequence of Porcisia hertigi, Isolate C119, Strain LV43.

Analysis of human sarcospan as a candidate gene for CFEOM1.

Mutations in UPF3B, a member of the nonsense-mediated mRNA decay complex, cause syndromic and nonsyndromic mental retardation.

Identification of the imprinted KLF14 transcription factor undergoing human-specific accelerated evolution.

A missense mutation in the nuclear localization signal sequence of CERKL (p.R106S) causes autosomal recessive retinal degeneration.

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.