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 256

System / cell line: individual ✕ Clear

Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales).

PMID 36674965 · PMC9866071 · International journal of molecular sciences · 2023 · 8 claims · 8 setups

Has reproduction · 51

K. uniflora shows high allelic heterozygosity (negative F_IS) consistent with theoretical expectations under asexual evolution

uniflora whole-genome phylogenomic population
Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.

PMID 34177835 · PMC8221242 · Frontiers in microbiology · 2021 · 8 claims · 6 setups

Has reproduction · 79

Viral metagenomics of liver tissue from rats, mice, shrews, and bats revealed a diverse set of sequences related to herpesviruses, orthomyxoviruses, anelloviruses, hepeviruses, hepadnaviruses, flaviviruses, parvoviruses, and picornaviruses

pooled individual liver serum viral pcr strand-specific
A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.

PMID 34545398 · PMC8527503 · G3 (Bethesda, Md.) · 2021 · 8 claims · 8 setups

Has reproduction · 79

A chromosome-scale genome assembly of H. californensis spans 110 Mb in 44 scaffolds, with 99.47% of bases in 13 scaffolds

californensis chromosome pacbio illumina
Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

PMID 36295018 · PMC9605557 · Life (Basel, Switzerland) · 2022 · 8 claims · 7 setups

Has reproduction

Retrotransposons mobilize via a copy-and-paste mechanism involving transcription of an RNA intermediate and reinsertion as a cDNA copy, unlike DNA transposons which cut-and-paste.

drosophila normal genomic genome synthetic whole-genome computational
N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

PMID 36422864 · PMC9731578 · eLife · 2022 · 8 claims · 8 setups

Has reproduction · 55

Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo

cerevisiae diploid yeast recombinant affinity rt-qpcr chip-seq
Genetic variants of Ehrlichia phagocytophila, Rhode Island and Connecticut.

PMID 11996680 · PMC3369764 · Emerging infectious diseases · 2002 · 7 claims · 6 setups

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All 50 E. phagocytophila-positive samples from Bridgeport, CT (1996-1998) had 16S rRNA sequences identical to the human agent (EP-ha).

ixodes white-footed eastern pcr-positive nested sequencing cloning
Sources of variability and effect of experimental approach on expression profiling data interpretation.

PMID 11936955 · PMC65691 · BMC bioinformatics · 2002 · 8 claims · 7 setups

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Intra-patient tissue heterogeneity (different regions of the same biopsy) is often the greatest source of variability in expression profiling

skeletal muscle spleen myogenic affymetrix duplicate unsupervised
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
Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

PMID 15534692 · PMC526178 · PLoS biology · 2004 · 8 claims · 6 setups

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Intramolecular pairs of oppositely oriented Alu elements within the same pre-mRNA form dsRNA foldback structures that are major substrates for A-to-I RNA editing

huge brain pre-mrna greater genomic rt-pcr quantitative
RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

PMID 24324815 · PMC3855774 · PloS one · 2013 · 8 claims · 8 setups

Has reproduction · 38

A total of 1,530 transcripts were differentially expressed between well-watered and water-deficit stressed field-grown upland cotton root tissues (913 up-regulated, 617 down-regulated).

gossypium uppermost root reads bulk leaf rt-qpcr
A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid.

PMID 16321154 · PMC1326206 · BMC neurology · 2005 · 7 claims · 6 setups

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CFS, PGI and fibromyalgia are highly overlapping symptom complexes likely reflecting a shared underlying pathophysiological mechanism rather than distinct diseases

pooled individual cerebrospinal subjects capillary trypsin elisa
PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

PMID 16199750 · PMC1240117 · Nucleic acids research · 2005 · 7 claims · 6 setups

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The PPC algorithm, which applies a probe-pair-specific second-degree polynomial correction, increases the accuracy of allele frequency estimates from pooled DNA compared with previously described algorithms

individually reference equimolar independently snp reference pooled
Coxiella burnetii genotyping.

PMID 16102309 · PMC3320512 · Emerging infectious diseases · 2005 · 8 claims · 5 setups

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Multispacer sequence typing (MST) is the first reliable method for typing Coxiella burnetii isolates

coxiella burnetii matrix sequence pcr molecular pcr-based
Evolutionarily conserved human targets of adenosine to inosine RNA editing.

PMID 15731336 · PMC549564 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Identified four novel human ADAR editing substrates causing amino acid changes: FLNA, BLCAP, CYFIP2 and IGFBP7

panel brain chicken flna comparative rt-pcr homology
Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

PMID 15722479 · PMC549431 · Nucleic acids research · 2005 · 7 claims · 4 setups

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Two base deletion probes display the highest average hybridization specificity, followed by single base substitution, single base deletion, and single base insertion probes.

atm hybridized probe oligonucleotide transcription microarray
Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

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Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

postmortem genes gene proteins microarray protein-protein hierarchical
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
Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats.

PMID 17142224 · PMC1669776 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Pure (GAA·TTC)44+ alleles at the FXN locus are unstable in human somatic cells in vivo, showing both expansions and contractions.

blood v34a cos1 cv1 small genome-wide strip
NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region.

PMID 16998187 · PMC1636422 · Nucleic acids research · 2006 · 8 claims · 8 setups

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The major BCL2 promoter G-quadruplex (bcl2Mid) is a well-defined, mixed parallel/antiparallel-stranded intramolecular structure with three G-tetrads, two lateral loops, one side loop, and four grooves of different widths

synthetic bcl2mid bcl2pu39 nmr 31p site-specific
Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.

PMID 16719907 · PMC1513570 · BMC genomics · 2006 · 8 claims · 5 setups

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A 2 Mb BAC contig of 78 clones was assembled covering the entire bovine FHIT locus

bovine pcr-based comparative rt-pcr

Experiments

Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales).

Detection of Virus-Related Sequences Associated With Potential Etiologies of Hepatitis in Liver Tissue Samples From Rats, Mice, Shrews, and Bats.

A chromosome-scale genome assembly and karyotype of the ctenophore Hormiphora californensis.

Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.

Genetic variants of Ehrlichia phagocytophila, Rhode Island and Connecticut.

Sources of variability and effect of experimental approach on expression profiling data interpretation.

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

Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

RNA-Seq transcriptome profiling of upland cotton (Gossypium hirsutum L.) root tissue under water-deficit stress.

A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid.

PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

Coxiella burnetii genotyping.

Evolutionarily conserved human targets of adenosine to inosine RNA editing.

Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

An efficient method for multi-locus molecular haplotyping.

Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats.

NMR solution structure of the major G-quadruplex structure formed in the human BCL2 promoter region.

Comparative genomic mapping of the bovine Fragile Histidine Triad (FHIT) tumour suppressor gene: characterization of a 2 Mb BAC contig covering the locus, complete annotation of the gene, analysis of cDNA and of physiological expression profiles.