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 31

System / cell line: pooled ✕ Assay: mapping ✕ Clear

Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs.

PMID 15811185 · PMC1079828 · BMC genomics · 2005 · 8 claims · 4 setups

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Relative Allele Signal (RAS) values from SNP microarrays provide a quantitative index of allele frequencies in pooled DNA

pooled pool snps snp snapshot individual
Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

PMID 16197552 · PMC1262713 · BMC genomics · 2005 · 8 claims · 5 setups

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Pooling genomic DNA and genotyping on SNP microarrays accurately predicts allelic frequencies relative to individual genotyping

genomic pools training siddt individual pooled k-correction
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

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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

individually reference equimolar independently snp reference pooled
Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

PMID 19724645 · PMC2731166 · PloS one · 2009 · 7 claims · 5 setups

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159 novel miRNAs and 116 novel miRNA*s were identified from ALL patient and normal donor small RNA libraries

pooled sequenced analysis predicted small bioinformatic qrt-pcr
Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

PMID 19011008 · PMC2719557 · Investigative ophthalmology & visual science · 2009 · 6 claims · 5 setups

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TGFBIp (multiple molecular weight forms) is significantly overexpressed in FECD HCEC-DM complex compared to normal endothelium

pooled hcec-dm corneal 2-d western real-time
Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups

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Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window

pooled computational identified additional label-free lspad pathway-associated
Paired-end mapping reveals extensive structural variation in the human genome.

PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

genomic na15510 stretched reference paired-end pcr array
High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.

PMID 17702760 · PMC2018616 · Nucleic acids research · 2007 · 7 claims · 4 setups

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An integrated strategy combining en masse pentapeptide insertion mutagenesis, yeast two-hybrid screening, and parallel genetic footprinting can map protein-protein interfaces at amino acid precision and is generally applicable to any interacting protein pair.

saccharomyces plasmid pooled individual yeast pcr-based restriction
Of mice and men: comparative proteomics of bronchoalveolar fluid.

PMID 20032019 · PMC3049194 · The European respiratory journal · 2010 · 8 claims · 8 setups

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Comparative shotgun proteomics of human and mouse BALF identifies conserved pathways (immunity, defence response, protease activity) alongside species-specific divergent pathways.

pooled oxidative unpooled balf shotgun functional protein-protein
Back to basics.

PMID 12186643 · PMC139395 · Genome biology · 2002 · 8 claims · 8 setups

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Human PDS (Pendrin) gene mutations damage ear structures and are linked to hereditary deafness and goiter

chromosome pendrin yeast carbonic genome gene mudpit
Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.

PMID 35983322 · PMC9378778 · Frontiers in microbiology · 2022 · 6 claims · 7 setups

Has reproduction · 75

RPL29 (60S ribosomal protein L29) is highly/consistently expressed across all COVID-19 infected groups regardless of severity, suggesting it as a novel host therapeutic target for mRNA-based nanomedicines.

pbmcs pbmc aligned bulk read transcript
Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

PMID 17598913 · PMC1929078 · BMC genomics · 2007 · 8 claims · 4 setups

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Standard Affymetrix expression GeneChips (MOE430, HG-U133) contain probe sets that detect natural antisense transcripts (NATs)

moe430 pooled organs probe strand-specific microarray
Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.

PMID 25943316 · PMC4422317 · BMC genomics · 2015 · 7 claims · 6 setups

Has reproduction · 73

De novo assembly of the S. fruticosa transcriptome (Velvet/Oases k-45, CDHIT-EST) produced 54,526 high-quality unigenes with N50 of 957 bp

suaeda rna-seq novo blastx
Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

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MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical
Genomics--from Neanderthals to high-throughput sequencing.

PMID 16934106 · PMC1779599 · Genome biology · 2006 · 8 claims · 8 setups

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Next-generation sequencing platforms (GS20/454 and Solexa) can deliver the throughput and cost reductions needed for population-scale and medical resequencing.

bacterial ion-channel drosophila arrays next-generation pooled multiplex
Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.

PMID 29335641 · PMC5864184 · The ISME journal · 2018 · 7 claims · 6 setups

Has reproduction

Increasing salinity to >=43 ppt inhibits Trichodesmium growth/increases mortality while stimulating growth of associated Alteromonas, shifting community dominance to the heterotroph

alteromonas co-culture trichodesmium differential bulk whole-genome
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

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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

genomic driver coli individual whole-genome subtractive cloning
Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

PMID 17000641 · PMC1636412 · Nucleic acids research · 2006 · 8 claims · 6 setups

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An anonymous SHyP oligonucleotide microarray can capture genomic signatures of DNA sequence variation from any organism, including a previously unsequenced species

genomic gonystylus subset restriction-digested custom self-self blast
Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.

PMID 24400075 · PMC3882208 · PloS one · 2014 · 8 claims · 5 setups

Has reproduction · 74

RNA-seq-based bulked segregant analysis of russet- vs green-pericarp F1 pools identified 29,100 unigenes, 206 of which were significantly differentially expressed (|log2 fold change| > 1).

pericarp green cuiguan illumina bulk qrt-pcr light
Prostate cancer genomics: towards a new understanding.

PMID 19104501 · PMC2721916 · Nature reviews. Genetics · 2009 · 8 claims · 8 setups

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Multiple GWAS have identified over a dozen replicated germline SNPs each associated with a modest increase in prostate cancer risk

germline families african-american combined genome-wide linkage admixture

Experiments

Genotyping DNA pools on microarrays: tackling the QTL problem of large samples and large numbers of SNPs.

Identification of disease causing loci using an array-based genotyping approach on pooled DNA.

PPC: an algorithm for accurate estimation of SNP allele frequencies in small equimolar pools of DNA using data from high density microarrays.

Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach.

Colocalization of increased transforming growth factor-beta-induced protein (TGFBIp) and Clusterin in Fuchs endothelial corneal dystrophy.

Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

Paired-end mapping reveals extensive structural variation in the human genome.

High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform.

Of mice and men: comparative proteomics of bronchoalveolar fluid.

Back to basics.

Identification of Novel Therapeutic Candidates Against SARS-CoV-2 Infections: An Application of RNA Sequencing Toward mRNA Based Nanotherapeutics.

Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

Transcriptome assembly, profiling and differential gene expression analysis of the halophyte Suaeda fruticosa provides insights into salt tolerance.

Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

Genomics--from Neanderthals to high-throughput sequencing.

Benefit from decline: the primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise.

Whole-genome experimental identification of insertion/deletion polymorphisms of interspersed repeats by a new general approach.

Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

Exploring candidate genes for pericarp russet pigmentation of sand pear (Pyrus pyrifolia) via RNA-Seq data in two genotypes contrasting for pericarp color.

Prostate cancer genomics: towards a new understanding.