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 49

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

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

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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

normal aneuploid same genomiphi-amplified array-cgh
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

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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.

inhbb cloned same fresh-frozen rnase masscleave clonal
MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

PMID 17823203 · PMC2034490 · Nucleic acids research · 2007 · 8 claims · 4 setups

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MLGA is a novel selector-based technique using multiplex ligation-dependent circularization of genomic DNA fragments for copy-number analysis

pooled genomic aneuploid dog mlga
Increased DNA microarray hybridization specificity using sscDNA targets.

PMID 15847692 · PMC1090574 · BMC genomics · 2005 · 7 claims · 5 setups

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A single round of ribo-SPIA amplification produces sufficient sscDNA for microarray hybridization from as little as 5 ng of starting total RNA

cuhr k562 input sscdna microarray quantitative capillary
Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

PMID 16480507 · PMC1382214 · BMC genomics · 2006 · 7 claims · 4 setups

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Pooled genotyping on Affymetrix 10K arrays estimates allele frequency differences between pools with accuracy comparable to lower-throughput pooling platforms.

pools individual same parental pooled individual test-retest
Allelotyping of pooled DNA with 250 K SNP microarrays.

PMID 17367522 · PMC1839100 · BMC genomics · 2007 · 8 claims · 5 setups

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The polynomial based probe specific correction (PPC) algorithm is the most accurate method for estimating allele frequency from pooled DNA.

pool nspi individual snp individual call
PDA: Pooled DNA analyzer.

PMID 16643673 · PMC1539032 · BMC bioinformatics · 2006 · 8 claims · 4 setups

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No software existed prior to PDA for complete pooled-DNA analysis including data standardization, allele frequency estimation, and single/multipoint association tests

heterozygous pools ordered peak pooled single-point
TEMP: a computational method for analyzing transposable element polymorphism in populations.

PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

Has reproduction · 61

TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

drosophila five four melanogaster simulated comparative whole-genome
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
Proteomic analysis of human aqueous humor using multidimensional protein identification technology.

PMID 20019884 · PMC2793904 · Molecular vision · 2009 · 8 claims · 4 setups

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Albumin/IgG depletion combined with MudPIT (2D-LC-MS/MS) enables high-confidence, extensive characterization of the human AH proteome

pooled albumin-bound analysis mudpit immunoaffinity bca
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
An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

PMID 16872505 · PMC1550395 · BMC medical genetics · 2006 · 7 claims · 7 setups

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Marginally significant (uncorrected) transmission distortion was found for four SNPs after stratification by HLA-DRB1*1501 status, disease course, or gender.

pooled australian independent trio pool snapshot snplex
Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

PMID 17344319 · PMC1874664 · Nucleic acids research · 2007 · 7 claims · 7 setups

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aPRIMES is a novel array-based method that detects direct (absolute) methylation status of CGIs via competitive hybridization of McrBC-digested (methylated) versus HpaII/BstUI-digested (unmethylated) DNA from the same genome, avoiding reference-tissue and copy-number biases

pediatric tumor eight desmoplastic aprimes bisulfite quantitative
A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

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SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

teds diagnosed ceph snp individual transmission
A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva.

PMID 19813771 · PMC2789208 · Journal of proteome research · 2009 · 7 claims · 7 setups

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Coupling DRC (hexapeptide libraries) with 3D peptide fractionation (IEF + SCX + µLC-MS/MS) substantially increases the number of proteins identified in whole saliva

saliva offgel-fractionated identified sds-page trypsin strong
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

Has reproduction · 83

MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

pooled hc227 contig sets shotgun novo alignment-free
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
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

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GS-FLX pyrosequencing of pooled amplicons detects sequence variants with high specificity (99.95%) and no false negatives at ≥30× coverage

pools pcr genomic gs-flx massively sanger pcr
Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps.

PMID 36828829 · PMC9958023 · Nature communications · 2023 · 8 claims · 7 setups

Has reproduction · 52

A shared genetic toolkit of caste-associated genes exists across vespid wasp species spanning different levels of social complexity

vespid single-copy brain caste-biased bulk orthology principal
Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.

PMID 17303479 · PMC7105233 · Journal of chromatography. B, Analytical technologies in the biomedical and life sciences · 2007 · 5 claims · 5 setups

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Pre-fractionation of plasma with immuno-affinity depletion and anion-exchange chromatography prior to 2D-DIGE substantially increases the number of detectable protein spots compared with unfractionated plasma.

plasma excised fractionated 2d-dige multi-dimensional lc-ms

Experiments

Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

Genomic profiling of CpG methylation and allelic specificity using quantitative high-throughput mass spectrometry: critical evaluation and improvements.

MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

Increased DNA microarray hybridization specificity using sscDNA targets.

Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

Allelotyping of pooled DNA with 250 K SNP microarrays.

PDA: Pooled DNA analyzer.

TEMP: a computational method for analyzing transposable element polymorphism in populations.

Of mice and men: comparative proteomics of bronchoalveolar fluid.

Proteomic analysis of human aqueous humor using multidimensional protein identification technology.

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

An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma.

A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

A dynamic range compression and three-dimensional peptide fractionation analysis platform expands proteome coverage and the diagnostic potential of whole saliva.

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

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

Evaluation of human gene variant detection in amplicon pools by the GS-FLX parallel Pyrosequencer.

Social complexity, life-history and lineage influence the molecular basis of castes in vespid wasps.

Plasma proteomics of pancreatic cancer patients by multi-dimensional liquid chromatography and two-dimensional difference gel electrophoresis (2D-DIGE): up-regulation of leucine-rich alpha-2-glycoprotein in pancreatic cancer.