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).
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Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.
PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups
QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker
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Has reproduction · 55
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
Pho92 specifically binds m6A-modified RNA via its YTH domain, both in vitro and in vivo
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Has reproduction · 69
High-resolution transcriptome and genome-wide dynamics of RNA polymerase and NusA in Mycobacterium tuberculosis.
PMID 23222129 · PMC3553938 · Nucleic acids research · 2013 · 8 claims · 7 setups
NusA interacts with RNAP ubiquitously throughout the M. tuberculosis chromosome and its ChIP-seq profile mirrors RNAP distribution in both exponential and stationary phase, despite NusA not binding DNA directly.
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Increased DNA microarray hybridization specificity using sscDNA targets.
PMID 15847692 · PMC1090574 · BMC genomics · 2005 · 7 claims · 5 setups
A single round of ribo-SPIA amplification produces sufficient sscDNA for microarray hybridization from as little as 5 ng of starting total RNA
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Nitrosothiol reactivity profiling identifies S-nitrosylated proteins with unexpected stability.
PMID 19101475 · PMC2628636 · Chemistry & biology · 2008 · 8 claims · 7 setups
Most protein nitrosothiols are rapidly denitrosylated by physiological GSH, but a small subset show markedly reduced GSH reactivity and remain stably S-nitrosylated
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Shaken not stirred: a global research cocktail served in Hinxton.
PMID 18036269 · PMC2258181 · Genome biology · 2007 · 8 claims · 8 setups
Network-guided reverse genetics using probabilistic functional gene networks (e.g. YeastNet, WormNet) reduces the search space for identifying genes in a given biological process
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Has reproduction · 50
The HCV Envelope Glycoprotein Down-Modulates NF-κB Signalling and Associates With Stimulation of the Host Endoplasmic Reticulum Stress Pathway.
PMID 35371105 · PMC8964954 · Frontiers in immunology · 2022 · 8 claims · 8 setups
HCV E1E2 glycoproteins, and more so E2, down-modulate HIV-1 LTR activation in 293T, TZM-bl and Huh7 cells
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Has reproduction · 78
TRIM28 repression of retrotransposon-based enhancers is necessary to preserve transcriptional dynamics in embryonic stem cells.
PMID 23233547 · PMC3589534 · Genome research · 2013 · 8 claims · 8 setups
TRIM28 repression of ERVs protects cellular gene expression in early embryos from perturbation by cis-acting activators contained within these retroelements.
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Sequencing the regulatory genome.
PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups
Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)