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: real ✕ Assay: coding ✕ Clear

Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

PMID 18826599 · PMC2576242 · BMC evolutionary biology · 2008 · 7 claims · 4 setups

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CpG/non-CpG assignment based on presence/absence of a CpG dinucleotide seriously biases substitution rate estimates, overestimating CpG changes and underestimating non-CpG changes.

randomly real human-chimpanzee simulated simulation comparative
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

PMID 16381612 · PMC1360673 · BMC bioinformatics · 2005 · 7 claims · 7 setups

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A 32-dimensional triplet structure-sequence feature vector combined with SVM (triplet-SVM) can distinguish real human pre-miRNAs from pseudo pre-miRNA hairpins with ~90% accuracy.

pre-mirnas test conserved-hairpin cross-species secondary svm cross-species
miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

PMID 18029362 · PMC2238982 · Nucleic acids research · 2008 · 8 claims · 6 setups

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miRNAMap 2.0 is a resource collecting experimentally verified miRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes

major tissues conserved predicted quantitative bead-based microarray
Genetic variation in an individual human exome.

PMID 18704161 · PMC2493042 · PLoS genetics · 2008 · 8 claims · 7 setups

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The ~12,500 nonsilent coding variants in the HuRef exome can be reduced ~8-fold to a set of ~1,600 variants most likely to affect protein function.

huref genes subset whole-genome allele functional
Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

PMID 19133980 · PMC4303606 · British journal of haematology · 2009 · 7 claims · 6 setups

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Downregulation of GR mRNA in the resistant myeloma cell line is caused by a block to transcriptional elongation within intron B of the GR gene

mm.1s pcr demethylating quantitative
A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

PMID 19890225 · PMC6177227 · Pharmacogenetics and genomics · 2009 · 7 claims · 6 setups

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Extensive sequencing of UGT1A4 (promoter to exon 1+2000bp) identified numerous novel polymorphisms: 13 intronic, 39 promoter, and 14 exonic variants (10 causing amino acid changes)

genomic hek293 hepg2 microsomes pcr site-directed luciferase
Exon deletions and intragenic insertions are not rare in ataxia with oculomotor apraxia 2.

PMID 19744353 · PMC2749023 · BMC medical genetics · 2009 · 8 claims · 6 setups

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Gross mutations (exon deletions and intragenic insertions) are a frequent, not rare, cause of AOA2

genomic peripheral setx sanger dosage long-range
Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing.

PMID 30208848 · PMC6134632 · BMC genomics · 2018 · 8 claims · 7 setups

Has reproduction · 50

2867 circRNAs were identified in soybean flower buds via high-throughput sequencing with RNase R enrichment, of which 1009 were differentially expressed between NJCMS1A and NJCMS1B

flower roots analysis parental high-throughput quantitative pcr
The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

PMID 12036445 · PMC5927037 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 5 setups

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SNI (elevated spontaneous point mutation rate without microsatellite instability) is present in rat mammary carcinoma cell lines and human breast cancer cell lines

mammary same normal pcr-sscp direct quantitative
Novel SCN1A frameshift mutation with absence of truncated Nav1.1 protein in severe myoclonic epilepsy of infancy.

PMID 18680191 · PMC3708306 · American journal of medical genetics. Part A · 2008 · 8 claims · 3 setups

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A novel heterozygous SCN1A frameshift mutation, c.3608delA (p.Gln1203HisfsX4), was identified in a postmortem SMEI patient, located in the D2-D3 intracellular linker of NaV1.1.

postmortem cdna western quantitative
Gene expression study on peripheral blood identifies progranulin mutations.

PMID 18551524 · PMC2773201 · Annals of neurology · 2008 · 7 claims · 3 setups

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PGRN is highly expressed in peripheral blood (97th percentile of all array genes)

peripheral blood-derived microarray direct real-time
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups

Has reproduction · 67

binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)

cami real-world metagenomic binned genome binning mag
MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.

PMID 36386613 · PMC9651917 · Frontiers in microbiology · 2022 · 7 claims · 4 setups

Has reproduction · 83

MetaGT is a pipeline that combines metatranscriptomic and metagenomic data from the same sample to assemble complete transcript sequences

simulated mock16 real snailgut novo transcript gene
WNT10B mutations in human obesity.

PMID 16477437 · PMC4304000 · Diabetologia · 2006 · 8 claims · 8 setups

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The WNT10B C256Y missense mutation abrogates the protein's ability to activate canonical WNT signalling and block adipogenesis

genomic 3t3-l1 subject proband dhplc top-flash western
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
Genome assembly comparison identifies structural variants in the human genome.

PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

genome ceph unrelated individuals whole-genome pcr quantitative
Nucleosome regulatory dynamics in response to TGFβ.

PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups

Has reproduction · 59

SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.

hepatocellular hepg2 130-bp mnase strand-specific taqman
Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.

PMID 19844255 · PMC2824775 · European journal of human genetics : EJHG · 2010 · 7 claims · 7 setups

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A locus on chromosome 16q23-24 affects HDL-C levels in two independent French-Canadian family studies (QUE and SLSJ)

que slsj candidate skin genome-wide sanger tagging
Severe insulin resistance and intrauterine growth deficiency associated with haploinsufficiency for INSR and CHN2: new insights into synergistic pathways involved in growth and metabolism.

PMID 19720790 · PMC2780873 · Diabetes · 2009 · 7 claims · 8 setups

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INSR is disrupted by the chromosome 19 breakpoint, causing INSR haploinsufficiency (monoallelic expression) that explains the insulin resistance/dysglycemia phenotype

metaphase genomic ebv-transformed serum fluorescence multiplex sanger

Experiments

Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals.

Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine.

miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

Genetic variation in an individual human exome.

Glucocorticoid resistance in a multiple myeloma cell line is regulated by a transcription elongation block in the glucocorticoid receptor gene (NR3C1).

A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.

Exon deletions and intragenic insertions are not rare in ataxia with oculomotor apraxia 2.

Comparative analysis of circular RNAs between soybean cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B by high-throughput sequencing.

The absence of Mth1 inactivation and DNA polymerase kappa overexpression in rat mammary carcinomas with frequent A:T to C:G transversions.

Novel SCN1A frameshift mutation with absence of truncated Nav1.1 protein in severe myoclonic epilepsy of infancy.

Gene expression study on peripheral blood identifies progranulin mutations.

binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.

MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.

WNT10B mutations in human obesity.

Analysis of X chromosome inactivation in autism spectrum disorders.

Genome assembly comparison identifies structural variants in the human genome.

Nucleosome regulatory dynamics in response to TGFβ.

Fine mapping and association studies of a high-density lipoprotein cholesterol linkage region on chromosome 16 in French-Canadian subjects.

Severe insulin resistance and intrauterine growth deficiency associated with haploinsufficiency for INSR and CHN2: new insights into synergistic pathways involved in growth and metabolism.