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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Evaluation of multiple displacement amplification in a 5 cM STR genome-wide scan.
PMID 16055919 · PMC1182175 · Nucleic acids research · 2005 · 7 claims · 5 setups
MDA genotyping call rates and accuracy are only marginally lower than for genomic DNA
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MLGA--a rapid and cost-efficient assay for gene copy-number analysis.
PMID 17823203 · PMC2034490 · Nucleic acids research · 2007 · 8 claims · 4 setups
MLGA is a novel selector-based technique using multiplex ligation-dependent circularization of genomic DNA fragments for copy-number analysis
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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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Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.
PMID 18842124 · PMC2569949 · BMC genomics · 2008 · 7 claims · 7 setups
GS-FLX pyrosequencing of pooled amplicons detects sequence variants with high specificity (99.95%) and no false negatives at ≥30× coverage
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Has reproduction · 65
High-throughput sequencing SELEX for the determination of DNA-binding protein specificities in vitro.
PMID 35776646 · PMC9243297 · STAR protocols · 2022 · 8 claims · 8 setups
HT-SELEX enables unbiased, in vitro determination of preferred DNA target motifs for DNA-binding proteins by iterative selection and PCR amplification of bound oligonucleotides
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Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.
PMID 15673711 · PMC548376 · Nucleic acids research · 2005 · 8 claims · 6 setups
A new technique combining whole-genome selective PCR amplification and subtractive hybridization can experimentally identify polymorphic retroelement insertions without prior knowledge of RE evolutionary history or sequence
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Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.
PMID 16221972 · PMC1253841 · Nucleic acids research · 2005 · 8 claims · 6 setups
Reducing array complexity by pooling five BACs per spot (covering a chromosome arm) increases robustness to amplification-related ratio variation compared with single-BAC spotting
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A genome annotation-driven approach to cloning the human ORFeome.
PMID 15461802 · PMC545604 · Genome biology · 2004 · 8 claims · 8 setups
Existing human cDNA clone collections together provide only 60% coverage of full-length chromosome 22 ORFs, with the best single collection (MGC) providing 48%
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Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.
PMID 19759830 · PMC2736399 · PloS one · 2009 · 8 claims · 7 setups
Statistical evidence of genetic compartmentalization between lung and blood HIV-1 env sequences was found in 10 of 18 subjects.
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PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.
PMID 16199750 · PMC1240117 · Nucleic acids research · 2005 · 7 claims · 6 setups
The PPC algorithm, which applies a probe-pair-specific second-degree polynomial correction, increases the accuracy of allele frequency estimates from pooled DNA compared with previously described algorithms
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Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.
PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups
Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs
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Has reproduction · 74
Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.
PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups
Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.
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Has reproduction · 50
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.
PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups
330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.
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Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.
PMID 17855397 · PMC2094090 · Nucleic acids research · 2007 · 8 claims · 5 setups
A new weighted formula that accounts for the number of methylated CpG sites per fragment removes the bias of the original MassCLEAVE™ formula toward higher apparent methylation in fragments with more CpG sites.