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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Has reproduction · 100
Analysis of a photosynthetic cyanobacterium rich in internal membrane systems via gradient profiling by sequencing (Grad-seq).
PMID 33793824 · PMC8136920 · The Plant cell · 2021 · 8 claims · 6 setups
Grad-seq resolves complexes with overlapping subunits, such as CpcG1-type versus CpcL-type phycobilisomes or PsaK1 versus PsaK2 photosystem I (pre)complexes, validating the approach.
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Has reproduction · 71
Spatial organization shapes the turnover of a bacterial transcriptome.
PMID 27198188 · PMC4874777 · eLife · 2016 · 7 claims · 6 setups
The E. coli transcriptome is spatially organized genome-wide: mRNAs encoding inner-membrane proteins are enriched at the membrane, while mRNAs encoding cytoplasmic, periplasmic and outer-membrane proteins are distributed throughout the cytoplasm.
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Has reproduction · 71
A method for selectively enriching microbial DNA from contaminating vertebrate host DNA.
PMID 24204593 · PMC3810253 · PloS one · 2013 · 8 claims · 7 setups
MBD-Fc bound to Protein A paramagnetic beads selectively binds methylated (vertebrate host) DNA, depleting it from mixed samples
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Has reproduction · 77
Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.
PMID 28398514 · PMC5499547 · Nucleic acids research · 2017 · 6 claims · 6 setups
A sequence-independent biotin–streptavidin (SAv) roadblocking strategy using randomly biotinylated DNA templates can stall TECs across all template positions for cotranscriptional SHAPE-Seq, simplifying template preparation and reducing cost.
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Has reproduction · 89
Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.
PMID 27092297 · PMC4820441 · Frontiers in cellular and infection microbiology · 2016 · 7 claims · 7 setups
STEC are prevalent in surface waters of four Lower Mainland BC watersheds, recovered from 21.6, 23.2, 19.5, and 9.2% of samples across sites, with seasonal variation (13.3% in fall to 34.3% in winter).
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Has reproduction · 77
spotter: a single-nucleotide resolution stochastic simulation model of supercoiling-mediated transcription and translation in prokaryotes.
PMID 37602419 · PMC10516669 · Nucleic acids research · 2023 · 8 claims · 4 setups
spotter is the first simulation model to integrate transcription, DNA supercoiling, and translation simultaneously in a single stochastic framework for prokaryotes.
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Strategies for folding of affinity tagged proteins using GroEL and osmolytes.
PMID 19082872 · PMC3693453 · Journal of structural and functional genomics · 2009 · 8 claims · 8 setups
GroEL/osmolyte mixtures can be used to refold difficult-to-fold chimeric affinity-tagged proteins by exploiting intrinsic chaperonin binding.
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Has reproduction · 74
L-Arabinose Alters the E. coli Transcriptome to Favor Biofilm Growth and Enhances Survival During Fluoroquinolone Stress.
PMID 40732174 · PMC12299780 · Microorganisms · 2025 · 8 claims · 6 setups
L-arabinose increases planktonic growth rate but reduces total growth of E. coli at both 28°C and 37°C
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Has reproduction · 100
Structure of a mitochondrial ribosome with fragmented rRNA in complex with membrane-targeting elements.
PMID 36253367 · PMC9576764 · Nature communications · 2022 · 8 claims · 4 setups
The P. magna mitoribosome contains rRNA split into 13 fragments (LSU1-8, SSU1-4, mt-5S)
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The use of multiple displacement amplification to amplify complex DNA libraries.
PMID 18285362 · PMC2275127 · Nucleic acids research · 2008 · 7 claims · 8 setups
MDA alone cannot select against/remove plasmid ligation multimers, unlike bacterial propagation
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Has reproduction · 67
Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions.
PMID 32959884 · PMC7689298 · Human molecular genetics · 2020 · 8 claims · 8 setups
Trem2 promotes/drives the IL-4-induced anti-inflammatory gene expression program (e.g. Arg1, Ap1b1) in microglia, and reduced Trem2 attenuates this response.
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Identification of novel citrullinated autoantigens of synovium in rheumatoid arthritis using a proteomic approach.
PMID 17125526 · PMC1794520 · Arthritis research & therapy · 2006 · 8 claims · 6 setups
51 citrullinated protein spots were detected in RA synovial tissue, of which 30 (58.8%) were autoantigenic (reactive with RA sera)
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Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.
PMID 17659072 · PMC1950510 · Malaria journal · 2007 · 7 claims · 6 setups
PfMAD20 is the predominant PfMSP-1 allelic type among Indian field isolates
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Contributions of proteomics to understanding phagosome maturation.
PMID 18331591 · PMC2613258 · Cellular microbiology · 2008 · 8 claims · 8 setups
Proteomic studies across many species have identified hundreds of proteins associated with phagosomes, revealing conserved functional classes (vATPase subunits, GTPases, hydrolases, SNAREs, Rabs, cytoskeletal proteins).