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 79

System / cell line: clone ✕ Assay: sequencing ✕ Clear

Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

PMID 18282289 · PMC2270265 · BMC genomics · 2008 · 8 claims · 6 setups

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The sheep TRG1 and TRG2 loci evolved through a series of duplication events involving either entire V-J-J-C recombinational cassettes or single V genes

sheep bac dot tandem
Molecular analysis of Plasmodium ovale variants.

PMID 15324543 · PMC3323326 · Emerging infectious diseases · 2004 · 8 claims · 5 setups

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P. ovale isolates separate into two genetically distinct types, classic (Nigerian I/CDC) and variant (LS), consistent across four independent gene loci.

ovale plasmodium pcr first comparative
The DNA sequence and analysis of human chromosome 13.

PMID 15057823 · PMC2665288 · Nature · 2004 · 8 claims · 8 setups

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95.5 Mb of finished sequence from chromosome 13 was completed, containing 633 genes and 296 pseudogenes.

chromosome rpci-11 genomic comparative fluorescence
Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

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DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

extremely families genome sanger case-control family-based
Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design.

PMID 18515352 · PMC2447791 · Nucleic acids research · 2008 · 7 claims · 7 setups

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Uprobe provides new predesigned whole-genome universal overgo probe sets for screening marsupial, rodent, and carnivore BAC libraries.

wallaby squirrel deer clouded overgo bac comparative
A high throughput method for genome-wide analysis of retroviral integration.

PMID 17028098 · PMC1636494 · Nucleic acids research · 2006 · 8 claims · 8 setups

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VITA uses MmeI to cleave DNA at a fixed distance from its recognition site, generating 21-22 bp genomic tags that serve as signatures of lentiviral integration sites.

hela ht3 genome chromosomes isf vita sanger
Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

PMID 17784912 · PMC2169797 · Molecular microbiology · 2007 · 8 claims · 6 setups

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MG192 is highly variable among and within M. genitalium strains both in vitro and in vivo

genitalium clinical urine pairwise pcr serial
Molecular dissection of ALS-associated toxicity of SOD1 in transgenic mice using an exon-fusion approach.

PMID 18424447 · PMC2465800 · Human molecular genetics · 2008 · 6 claims · 8 setups

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Nonsense-mediated mRNA decay (NMD) degrades mutant SOD1 mRNA carrying a PTC in non-terminal exons (1-4), explaining why ALS-associated PTC mutations are found only in exon 5

transgenic nih hsod1 lumbar southern northern rt-pcr
GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

PMID 16698959 · PMC3303178 · Nucleic acids research · 2006 · 7 claims · 5 setups

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GREM enables genome-wide isolation and quantitative analysis of transcriptionally active (promoter-active) repetitive elements while excluding read-through transcript background

testicular genomic coli grem rt-pcr race
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
Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

pediatric tumor eight desmoplastic aprimes bisulfite quantitative
Accurate whole human genome sequencing using reversible terminator chemistry.

PMID 18987734 · PMC2581791 · Nature · 2008 · 8 claims · 7 setups

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A novel sequencing platform using fluorescent reversible terminator nucleotides on clonally amplified single-molecule DNA clusters generates several billion bases of accurate sequence per experiment at low cost.

bac flow-sorted same yoruba reversible snp targeted
A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

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A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

domestic red same white partial comparative pcr
Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

PMID 15169551 · PMC441375 · BMC genomics · 2004 · 8 claims · 8 setups

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A very large, previously uncharacterized gene, AHI1, containing WD40 and SH3 domains was discovered in the candidate interval

cdna image hbs1l ahi1 rt-pcr est northern
Aerobic nonylphenol degradation and nitro-nonylphenol formation by microbial cultures from sediments.

PMID 20043151 · PMC2825322 · Applied microbiology and biotechnology · 2010 · 8 claims · 8 setups

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Aerobic biodegradation of branched NP in polluted river sediment occurs within 8 days after a 2-day lag phase at 30°C

np-polluted sediment-derived fourth-generation extracted biodegradation serial metabolite
DNA sequence and analysis of human chromosome 9.

PMID 15164053 · PMC2734081 · Nature · 2004 · 8 claims · 8 setups

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The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs, representing >99.6% of the region.

bac chromosome fibres chimpanzee clone-based restriction computational
Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

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Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

qbl pgf classical ceph bac comparative gene
Twin peaks: the draft human genome sequence.

PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups

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The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.

genome genomic genes yeast whole-genome bac computational
A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

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Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

serum plasmids coli pcr oligonucleotide chip
DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

PMID 16625196 · PMC2610434 · Nature · 2006 · 8 claims · 7 setups

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A finished sequence of human chromosome 17 (78,839,971 bases, ~2.8% of the euchromatic genome) was generated.

chromosome dog macaque genomic comparative segmental

Experiments

Genomic organization and recombinational unit duplication-driven evolution of ovine and bovine T cell receptor gamma loci.

Molecular analysis of Plasmodium ovale variants.

The DNA sequence and analysis of human chromosome 13.

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

Uprobe 2008: an online resource for universal overgo hybridization-based probe retrieval and design.

A high throughput method for genome-wide analysis of retroviral integration.

Mycoplasma genitalium: an efficient strategy to generate genetic variation from a minimal genome.

Molecular dissection of ALS-associated toxicity of SOD1 in transgenic mice using an exon-fusion approach.

GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

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

Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

Accurate whole human genome sequencing using reversible terminator chemistry.

A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Genome annotation of a 1.5 Mb region of human chromosome 6q23 encompassing a quantitative trait locus for fetal hemoglobin expression in adults.

Aerobic nonylphenol degradation and nitro-nonylphenol formation by microbial cultures from sediments.

DNA sequence and analysis of human chromosome 9.

Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

Twin peaks: the draft human genome sequence.

A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.