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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Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.
PMID 18560825 · PMC2493868 · Immunogenetics · 2008 · 8 claims · 8 setups
Neither transcriptional profiling alone nor genetic linkage analysis alone has been an effective approach to identify genes or gene networks that specify stemness or initiate differentiation/lineage specification.
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Has reproduction · 67
NET-prism enables RNA polymerase-dedicated transcriptional interrogation at nucleotide resolution.
PMID 31156037 · PMC6693550 · RNA biology · 2019 · 8 claims · 7 setups
NET-prism, an adapted NET-seq protocol using immunoprecipitation of Pol II-associated factors, enables strand-specific, nucleotide-resolution interrogation of transcription dynamics for any Pol II-interacting protein.
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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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A large-scale proteomic analysis of human embryonic stem cells.
PMID 18162134 · PMC2211323 · BMC genomics · 2007 · 8 claims · 5 setups
Two large-scale western blot systems (PowerBlot, Kinexus) identify over 600 proteins expressed in undifferentiated hESCs across 18 functional classes
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Has reproduction · 87
Translation affects mRNA stability in a codon-dependent manner in human cells.
PMID 31012849 · PMC6529216 · eLife · 2019 · 8 claims · 6 setups
Translation affects mRNA stability in a codon-dependent manner in human cells
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Has reproduction · 94
A multiple super-enhancer region establishes inter-TAD interactions and controls Hoxa function in cranial neural crest.
PMID 37277355 · PMC10241789 · Nature communications · 2023 · 8 claims · 8 setups
2232 genome-wide putative super-enhancers (SEs) were identified in mouse cranial neural crest cell (CNCC) subpopulations
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Has reproduction · 75
Dynamic reversal of random X-Chromosome inactivation during iPSC reprogramming.
PMID 31515287 · PMC6771397 · Genome research · 2019 · 7 claims · 6 setups
XCR during iPSC reprogramming is hierarchical, with distinct subsets of X-linked genes reactivating early, intermediate, late, and very late
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An intergenic non-coding rRNA correlated with expression of the rRNA and frequency of an rRNA single nucleotide polymorphism in lung cancer cells.
PMID 19838300 · PMC2759515 · PloS one · 2009 · 8 claims · 7 setups
An nc-rRNA is transcribed from the intergenic spacer upstream of the rRNA transcription start site in human lung epithelial and lung cancer cells, spanning roughly -1000 to at least +203/+300.
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With the finished human genome in hand, what next?
PMID 12844356 · PMC193627 · Genome biology · 2003 · 8 claims · 8 setups
Gene Ontology (GO) provides a syntax/query framework for functional classification of genes, expanding beyond E. coli origins into anatomy, pathology, and phenotype data.
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Has reproduction · 50
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.
PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups
A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.