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 58

System / cell line: locus ✕ Assay: region ✕ Clear

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

species genomic jmjd6 jmjc reciprocal comparative est
Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

PMID 16680197 · PMC1456318 · PLoS genetics · 2006 · 7 claims · 7 setups

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SNPs in the Affymetrix 100K set are undersampled from coding regions (both synonymous and nonsynonymous) and oversampled from regions outside genes, relative to HapMap SNPs

genome autosomal hapmap chromosome snp chromosomal minor
High-density SNP genotyping to define beta-globin locus haplotypes.

PMID 18829352 · PMC4251776 · Blood cells, molecules & diseases · 2009 · 8 claims · 5 setups

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RFLP analysis lacks sufficient site density/coverage to accurately reflect the genomic complexity of the β-locus

genomic rflp subset rflp high-density haploview
Sequencing the regulatory genome.

PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

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Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

interphase nine beta-globin drosophila nuclear digital chip
Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

PMID 30010758 · PMC6065499 · GigaScience · 2018 · 8 claims · 6 setups

Has reproduction · 91

A draft genome (Ogye_1.1) was assembled using a hybrid de novo method combining high-depth Illumina short reads (376.6X) and low-depth PacBio long reads (9.7X)

yeonsan ogye_1.1 locus tissues whole-genome genome structural
Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

PMID 15790396 · PMC1087472 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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Paircomp, FamilyRelationsII, and Cartwheel together form an integrated system for comparing, viewing, and managing analyses of BAC-sized (~100 kb) genomic sequence pairs.

otx sea elegans endo16 windowed reporter comparative
Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

PMID 18692127 · PMC3341170 · Genomics · 2008 · 8 claims · 7 setups

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Autozygosity mapping identified a highly significant homozygous region on chromosome 13q14.11-q14.3 (Z/LOD=10.41)

family p2ry5 affected snp microsatellite sanger
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
Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

PMID 20023659 · PMC2980844 · Nature genetics · 2010 · 8 claims · 8 setups

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Mutations in INF2, a formin family actin-regulating protein, cause autosomal dominant focal segmental glomerulosclerosis (FSGS)

families genes individuals kidney genome-wide sanger resequencing
Stable in a genome of instability: an interview with Evan Eichler. Interview by Jane Gitschier.

PMID 18654618 · PMC2442658 · PLoS genetics · 2008 · 8 claims · 5 setups

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Loss of AGG interruptions in CGG repeat tracts predisposes FMR1 alleles to instability and faster progression toward premutation/disease state

fmr1 xq28 genome agg fluorescence genome-wide
Association of replication error positive phenotype with lymphocyte infiltration in endometrial cancers.

PMID 9818024 · PMC5921952 · Japanese journal of cancer research : Gann · 1998 · 7 claims · 4 setups

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RER+ phenotype (microsatellite instability at ≥2 of 7 loci) occurs in a subset (21-23%) of sporadic endometrioid endometrial adenocarcinomas but not in other histological types or endometrial hyperplasia

paired tumor hematoxylin-eosin-stained pcr sequencing histopathological
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
Software for tag single nucleotide polymorphism selection.

PMID 16004730 · PMC3525260 · Human genomics · 2005 · 8 claims · 3 setups

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Pairwise R2 methods tend to pick more tagging SNPs than strictly needed because they miss redundancy where two or more tag SNPs jointly predict an untagged SNP with no single direct surrogate.

tgfbr1 encode candidate tag haplotype
Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

PMID 15608239 · PMC539999 · Nucleic acids research · 2005 · 8 claims · 8 setups

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GALA is now a set of interlinked relational databases covering five vertebrate species: human, chimpanzee, mouse, rat and chicken.

chromosome genomic comparative phylohmmcons conserved
Significance of the parkin and PINK1 gene in Jordanian families with incidences of young-onset and juvenile parkinsonism.

PMID 19087301 · PMC2635385 · BMC neurology · 2008 · 8 claims · 8 setups

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A parkin exon 4 deletion segregates with disease in a three-generation family (Family F), homozygous in both affected individuals

consanguineous same affected family sanger multiplex microsatellite
Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

PMID 19004867 · PMC2602793 · Nucleic acids research · 2008 · 7 claims · 4 setups

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Methylation patterns of the five GR promoters activated in PBMCs are highly variable between individuals.

chromosome genomic pbmc multi-species phylogenetic bisulphite
Genetic diversity of vaccine candidate antigens in Plasmodium falciparum isolates from the Amazon basin of Peru.

PMID 18505558 · PMC2432069 · Malaria journal · 2008 · 8 claims · 7 setups

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CSP (Th2R/Th3R region) is polymorphic in Peruvian isolates, with four distinct alleles identified, none identical to the 3D7 vaccine strain

pfcsp pfmsp-1 pfama-1 pflsa-1 pcr polymorphism multilocus
mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences.

PMID 16381973 · PMC1347373 · Nucleic acids research · 2006 · 8 claims · 3 setups

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mtDB is a comprehensive, actively maintained database of published human mitochondrial genome sequences, providing a common resource for population genetics and medical research

mitochondrial aligned compilation sequence multi-locus
Mutational analyses of multiple target genes in histologically heterogeneous gastric cancer with microsatellite instability.

PMID 10081489 · PMC5921733 · Japanese journal of cancer research : Gann · 1998 · 7 claims · 5 setups

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MSI frequency in gastric cancers with histological heterogeneity was 35% (7/20 cases) and 28% (11/40 tumor DNAs), consistent with prior gastric cancer MSI studies.

formalin-fixed msi-positive surgically microsatellite pcr-sscp histopathological
Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

bac genome metaphase overlapping manual repeat fluorescence

Experiments

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

Coverage and characteristics of the Affymetrix GeneChip Human Mapping 100K SNP set.

High-density SNP genotyping to define beta-globin locus haplotypes.

Sequencing the regulatory genome.

Whole genome and transcriptome maps of the entirely black native Korean chicken breed Yeonsan Ogye.

Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

Genome-wide linkage analysis of an autosomal recessive hypotrichosis identifies a novel P2RY5 mutation.

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

Mutations in the formin gene INF2 cause focal segmental glomerulosclerosis.

Stable in a genome of instability: an interview with Evan Eichler. Interview by Jane Gitschier.

Association of replication error positive phenotype with lymphocyte infiltration in endometrial cancers.

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

Software for tag single nucleotide polymorphism selection.

Improvements to GALA and dbERGE II: databases featuring genomic sequence alignment, annotation and experimental results.

Significance of the parkin and PINK1 gene in Jordanian families with incidences of young-onset and juvenile parkinsonism.

Highly individual methylation patterns of alternative glucocorticoid receptor promoters suggest individualized epigenetic regulatory mechanisms.

Genetic diversity of vaccine candidate antigens in Plasmodium falciparum isolates from the Amazon basin of Peru.

mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences.

Mutational analyses of multiple target genes in histologically heterogeneous gastric cancer with microsatellite instability.

Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.