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 13

System / cell line: pool ✕ Assay: microarray ✕ Clear

Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.

PMID 16204447 · PMC1243803 · Nucleic acids research · 2005 · 8 claims · 3 setups

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A Bayesian model incorporating experimental covariates (array, pen, probe, dye, scanning) can estimate absolute transcript concentrations from spotted microarray intensities without needing calibration of each sample or gene individually

cervix same spotted quantitative
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
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
Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

PMID 17610740 · PMC1925094 · BMC genomics · 2007 · 8 claims · 5 setups

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SNP-MaP can be effectively applied to the Affymetrix 500K GeneChip, providing a cost-effective, reliable and valid initial genomewide screen

independent ceph same unrelated snp individual simulated
Chemical genomics: what will it take and who gets to play?

PMID 11423004 · PMC138939 · Genome biology · 2001 · 8 claims · 8 setups

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Scaling chemical genetics to a genome-wide 'chemical genomics' requires large, well-funded, multidisciplinary centers that integrate compound libraries, protein resources, automation, and profiling technology, and freely distribute data and reagents.

iccb fluorescently yeast engineered cell-based small-molecule expression
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
Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans.

PMID 16478714 · PMC1368655 · Nucleic acids research · 2006 · 7 claims · 6 setups

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SNP-MaP allele frequency estimates from pooled DNA on the 100K microarray set correlate strongly with allele frequencies from individual genotyping

pooled single same caucasian snp individual quantification
An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention.

PMID 16351756 · PMC1866378 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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Meta-analysis of two independent BALB-neuT transcription profiling studies can identify new TAA candidates usable instead of or with Her2

balb-neut normal breast probe microarray statistical enrichment
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
Microarray-based DNA methylation profiling: technology and applications.

PMID 16428248 · PMC1345696 · Nucleic acids research · 2006 · 7 claims · 6 setups

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A microarray-based method enriching unmethylated and methylated DNA fractions via methylation-sensitive restriction enzymes followed by hybridization enables high-throughput DNA methylation profiling of large genomic regions.

genomic postmortem ligated custom cpg tiling
Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

PMID 18366677 · PMC2324081 · BMC medical genetics · 2008 · 8 claims · 7 setups

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Distinct sets of dysregulated genes are found in peripheral blood during the relapse phase versus the remission phase of RRMS

peripheral blood pooled trio gene quantitative promoter
Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

genomic normalized simulated tiling-resolution snp oligonucleotide
Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.

PMID 29157210 · PMC5697157 · BMC plant biology · 2017 · 7 claims · 8 setups

Has reproduction · 91

175 conserved and 83 novel miRNAs were identified mainly in one bud and two tender leaves of tea plant via small RNA sequencing combined with genome survey data

camellia sinensis small genome mirna

Experiments

Genome-wide estimation of transcript concentrations from spotted cDNA microarray data.

Allelotyping of pooled DNA with 250 K SNP microarrays.

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

Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

Chemical genomics: what will it take and who gets to play?

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

Genotyping pooled DNA using 100K SNP microarrays: a step towards genomewide association scans.

An integrated approach of immunogenomics and bioinformatics to identify new Tumor Associated Antigens (TAA) for mammary cancer immunological prevention.

Pooled DNA genotyping on Affymetrix SNP genotyping arrays.

Microarray-based DNA methylation profiling: technology and applications.

Genes implicated in multiple sclerosis pathogenesis from consilience of genotyping and expression profiles in relapse and remission.

Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

Genome-wide identification of conserved and novel microRNAs in one bud and two tender leaves of tea plant (Camellia sinensis) by small RNA sequencing, microarray-based hybridization and genome survey scaffold sequences.