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 19

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

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
A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups

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SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters

bac kidney genomic marathon genomic cdna pcr
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
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
Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

PMID 19039135 · PMC2746051 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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Diagnosis and relapse ALL samples show different patterns of CNAs, with relapse-acquired abnormalities preferentially affecting cell cycle regulation and B-cell development genes

matched bone leukemia diagnosis snp flow 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
Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

genomic normalized simulated tiling-resolution snp oligonucleotide
The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

PMID 12361482 · PMC131051 · BMC genetics · 2002 · 8 claims · 7 setups

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The human TDH gene is located at chromosome 8p23-22, spans 10 kb, and has 8 exons that would be expected to encode a 369-residue ORF.

genomic predicted cdna tissues genomic sequence pcr
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
EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.

PMID 34805989 · PMC8598301 · NAR genomics and bioinformatics · 2021 · 8 claims · 5 setups

Has reproduction · 54

EpiDiverse Toolkit provides Nextflow-based pipelines for WGBS mapping, methylation calling, variant calling, differential methylation, and EWAS tailored to non-model plant ecology

populus nigra genome variant clustering
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
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
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
Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

genome transcriptome gene genes full-length genome cdna
Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

chimpanzee retrofitted primate aspm tar restriction genomic
Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

PMID 16336695 · PMC1325232 · Respiratory research · 2005 · 6 claims · 8 setups

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There is overall little sequence variation in the conserved non-coding elements (CNEs) on 5q31, including none detected in CNE-B/CNS-1

genomic pcr large outbred comparative denaturing pcr
High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer.

PMID 16432260 · PMC1345698 · Nucleic acids research · 2006 · 8 claims · 5 setups

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A 96-well high-throughput bisulfite modification (HTBM) method was developed and validated against single-sample bisulfite modification (SSBM), producing comparable methylation results even from as little as 3 ng DNA.

genomic normal advanced bisulfite-treated methylation-specific bisulfite snp
Searching for genes for cleft lip and/or palate based on breakpoint analysis of a balanced translocation t(9;17)(q32;q12).

PMID 19929093 · PMC2945731 · The Cleft palate-craniofacial journal : official publication of the American Cleft Palate-Craniofacial Association · 2009 · 8 claims · 4 setups

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The translocation breakpoints disrupt SLC31A1 (intron 1) on chromosome 9 and a predicted gene containing CCL2 (5'UTR/exons) on chromosome 17

family genomic case-control case fluorescence long-range mutation
A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

PMID 16626494 · PMC1459863 · Malaria journal · 2006 · 8 claims · 5 setups

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Pyrosequencing, after adjustment to a standard curve, provides accurate and precise estimates of allele frequencies in mixed MSP-1_19 infections

falciparum cloned pyrosequencing pcr

Experiments

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

A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

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

DNA sequence and analysis of human chromosome 9.

Genomic analysis of the clonal origins of relapsed acute lymphoblastic leukemia.

Accurate whole human genome sequencing using reversible terminator chemistry.

Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

The human L-threonine 3-dehydrogenase gene is an expressed pseudogene.

The DNA sequence and analysis of human chromosome 13.

EpiDiverse Toolkit: a pipeline suite for the analysis of bisulfite sequencing data in ecological plant epigenetics.

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

Twin peaks: the draft human genome sequence.

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

Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy.

High throughput detection of M6P/IGF2R intronic hypermethylation and LOH in ovarian cancer.

Searching for genes for cleft lip and/or palate based on breakpoint analysis of a balanced translocation t(9;17)(q32;q12).

A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.