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 23

System / cell line: transcripts ✕ Assay: genome-wide ✕ Clear

Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice.

PMID 27655631 · PMC5175363 · Nucleic acids research · 2016 · 8 claims · 8 setups

Has reproduction · 10

Embryonic ATZ exposure affects meiosis, spermiogenesis and reduces spermatozoa number in F3 generation male mice

testis dissociated epididymis chip-seq strand-specific h&e
Distribution and effects of nonsense polymorphisms in human genes.

PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

genome genes nonsense snps genome-wide snp codon
Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

PMID 19903332 · PMC3091321 · Genome biology · 2009 · 6 claims · 5 setups

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A candidate 37-transcript diagnostic signature distinguishes septicemic melioidosis from sepsis caused by other organisms with 100% accuracy in the training set and 78%/80% accuracy in two independent validation sets

blood whole-genome unsupervised class
A third approach to gene prediction suggests thousands of additional human transcribed regions.

PMID 16543943 · PMC1391917 · PLoS computational biology · 2006 · 8 claims · 7 setups

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A third basic concept for gene prediction exists, based on detecting strand-specific 'transcription footprints' (mutational and selectional biases) rather than gene structure or sequence similarity.

genome 4.4-mb known nucleotide repeat polyadenylation
Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.

PMID 41738778 · PMC12962854 · Genome biology and evolution · 2026 · 8 claims · 8 setups

Has reproduction · 89

Eight sericin genes were identified in the Actias luna genome, including two clusters of closely related paralogs.

actias genomes translated luna genome hmm manual
Tandem repeats modify the structure of human genes hosted in segmental duplications.

PMID 19954527 · PMC2812944 · Genome biology · 2009 · 8 claims · 6 setups

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Around 7% of primate-specific genes located within segmental duplications contain variable internal tandem repeats (ITRs).

genome genomic est paired genome-wide comparative cnv
Gene duplication: the genomic trade in spare parts.

PMID 15252449 · PMC449868 · PLoS biology · 2004 · 8 claims · 7 setups

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Gene duplication relaxes selective constraint on one copy, allowing exploration of evolutionary space that is otherwise forbidden in single-copy genes, making duplication the major opportunity for new gene function evolution.

great genome recently yeast genome-wide molecular comparative
Genome Network and FANTOM3: assessing the complexity of the transcriptome.

PMID 16683037 · PMC1449904 · PLoS genetics · 2006 · 8 claims · 7 setups

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63% of the genome is transcribed from at least one strand, versus the earlier belief that only 2% is transcribed into protein-coding mRNA

fantom3 genome large-scale mammalian cage full-length genome
miRBase: tools for microRNA genomics.

PMID 17991681 · PMC2238936 · Nucleic acids research · 2008 · 8 claims · 6 setups

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miRBase release 10.0 contains 5071 miRNA hairpin loci from 58 species, expressing 5922 distinct mature miRNA sequences, a growth of over 2000 sequences in 2 years

species utrs genomic chromosome genome-wide target transcription
Relative impact of nucleotide and copy number variation on gene expression phenotypes.

PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

lymphoblastoid same computational subset gene snp array
HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

PMID 18978773 · PMC2597294 · Nature · 2008 · 8 claims · 8 setups

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HITS-CLIP, combining CLIP with high-throughput sequencing, provides a genome-wide, unbiased method to map protein-RNA interactions in vivo.

neocortex brain 293t hits-clip traditional exon
Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

PMID 18930150 · PMC2774125 · Methods (San Diego, Calif.) · 2008 · 8 claims · 8 setups

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Data integration of multiple functional genomics datasets effectively predicts mitochondrial gene function and prioritizes candidate mitochondrial disease genes.

saccharomyces higher yeast mitochondria genome-wide rnai gene
Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production.

PMID 37223250 · PMC10117727 · microLife · 2021 · 8 claims · 9 setups

Has reproduction · 50

Grad-seq resolves in-gradient sedimentation profiles for ~87-88% of annotated C. difficile transcripts and ~50% of annotated proteins, providing a comprehensive RNA-protein complexome resource

difficile grad-seq rna-seq lc-ms
Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

PMID 18793467 · PMC2537574 · BMC bioinformatics · 2008 · 8 claims · 7 setups

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Inter-species conservation is the strongest single predictor of disease-associated coding mutations among the factors tested.

hgmd refseq aligned svm svm reciprocal inter-species
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
Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.

PMID 36543858 · PMC9772385 · Communications biology · 2022 · 8 claims · 7 setups

Has reproduction · 100

Compiled the largest human embryonic A-to-I editome to date from 2071 RNA-seq transcriptomes and identified thousands of per-stage Recurrent Embryonic Edits (REEs, present in ≥50% of samples per stage)

preimplantation single uniparental embryos rna-seq paired gene
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
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

PMID 19773805 · PMC2958924 · Nature reviews. Molecular cell biology · 2009 · 8 claims · 6 setups

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Alternative splicing occurs in the expression of nearly 95% of human multi-exon genes

gria2 drosophila nova1 cd45 splicing sirna hits-clip
Gene expression profiles of HIV-1-infected glia and brain: toward better understanding of the role of astrocytes in HIV-1-associated neurocognitive disorders.

PMID 19697136 · PMC3107560 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2010 · 8 claims · 6 setups

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Astrocyte gene expression dysregulation resulting from HIV-1 exposure may contribute to HIV-1 neuropathogenesis

fetal astrocytes brain macaque rapid microarray correlational
Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.

PMID 36645269 · PMC9927211 · Microbiology spectrum · 2023 · 8 claims · 8 setups

Has reproduction · 93

An enhancer-like element in OriLyt (RNA4.9 promoter) is extraordinarily enriched in H3K27Ac compared to other viral loci.

hff mrc5 chip-qpcr rt-qpcr chipseq

Experiments

Exposure to the widely used herbicide atrazine results in deregulation of global tissue-specific RNA transcription in the third generation and is associated with a global decrease of histone trimethylation in mice.

Distribution and effects of nonsense polymorphisms in human genes.

Genomic transcriptional profiling identifies a candidate blood biomarker signature for the diagnosis of septicemic melioidosis.

A third approach to gene prediction suggests thousands of additional human transcribed regions.

Evolution of Highly Repetitive Silk Genes in the Luna Moth, Actias luna.

Tandem repeats modify the structure of human genes hosted in segmental duplications.

Gene duplication: the genomic trade in spare parts.

Genome Network and FANTOM3: assessing the complexity of the transcriptome.

miRBase: tools for microRNA genomics.

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

Identification of mitochondrial disease genes through integrative analysis of multiple datasets.

Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production.

Exhaustive prediction of disease susceptibility to coding base changes in the human genome.

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

Recurrent RNA edits in human preimplantation potentially enhance maternal mRNA clearance.

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.

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches.

Gene expression profiles of HIV-1-infected glia and brain: toward better understanding of the role of astrocytes in HIV-1-associated neurocognitive disorders.

Critical Role for the Human Cytomegalovirus Major Immediate Early Proteins in Recruitment of RNA Polymerase II and H3K27Ac To an Enhancer-Like Element in OriLyt.