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 39

System / cell line: probe ✕ Assay: signal ✕ Clear

Free energy of DNA duplex formation on short oligonucleotide microarrays.

PMID 17169993 · PMC1807971 · Nucleic acids research · 2007 · 8 claims · 6 setups

Full-text index only

The PDNN model, originally built for DNA/RNA hybridization, can be applied to model DNA/DNA duplex formation on SNP and genome tiling arrays

mapping50k_xba240 dgcr hg-u133a pdnn free correlation
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

Full-text index only

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
SNP identification in unamplified human genomic DNA with gold nanoparticle probes.

PMID 15659576 · PMC548375 · Nucleic acids research · 2005 · 8 claims · 5 setups

Full-text index only

A microarray-based method allows multiplex SNP genotyping in total human genomic DNA without target amplification or complexity reduction

unamplified genomic fragmented factor multiplex sequencing poly
MLGA--a rapid and cost-efficient assay for gene copy-number analysis.

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

Full-text index only

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
Detecting transcriptionally active regions using genomic tiling arrays.

PMID 16859498 · PMC1779562 · Genome biology · 2006 · 8 claims · 4 setups

Full-text index only

A non-parametric method (TranscriptionDetector) integrates single-channel p-values from multiple replicate arrays into a multi-channel p-value (MCPV) to identify transcribed probed loci without assumptions about intensity distributions.

anopheles chromosomes simulated genomic high-density sequence-based
Detection of YMDD motif mutants by oligonucleotide chips in lamivudine-untreated patients with chronic hepatitis B virus infection.

PMID 15308845 · PMC2816888 · Journal of Korean medical science · 2004 · 6 claims · 5 setups

Full-text index only

An oligonucleotide chip was developed using probes for wild-type YMDD, M552V, and three M552I probe variants to detect HBV polymerase YMDD motif mutations

serum hbv nested pcr oligonucleotide pcr restriction
Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

PMID 18818683 · PMC2756756 · Kidney international · 2008 · 8 claims · 8 setups

Full-text index only

Developed an MLPA assay with PKD1 exon 1-33 probes designed at single base-pair mismatches with the six PKD1 pseudogenes to achieve locus specificity

blood-derived blood crisp father mlpa long-range field
Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

PMID 16319823 · PMC1477589 · European journal of human genetics : EJHG · 2006 · 7 claims · 8 setups

Full-text index only

ALX4 and MSX2 mutations contribute approximately equally to PFM/CB and cause skull defects that are usually clinically indistinguishable

pfm selected point-mutation-negative family dhplc bidirectional multiplex
Lineage-specific gene duplication and loss in human and great ape evolution.

PMID 15252450 · PMC449870 · PLoS biology · 2004 · 8 claims · 7 setups

Full-text index only

Genome-wide interspecies cDNA aCGH can identify lineage-specific gene copy number changes across five hominoid species

bonobo chimpanzee gorilla orangutan cdna fluorescence literature-based
The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

PMID 20025771 · PMC2803494 · BMC microbiology · 2009 · 7 claims · 5 setups

Full-text index only

The daaC probe cross-hybridizes with a specific subset of EAEC strains, namely those carrying the aafA gene (AAF/II fimbriae)

coli hep-2 pslm862 eaec colony hep-2 pcr
In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

PMID 15871745 · PMC1156887 · BMC genomics · 2005 · 7 claims · 6 setups

Full-text index only

Only 14±2% of canine transcripts were detected by U133A probe sets versus 49±6% of human transcripts when hybridized to the same chip

canine tissues hg-u133a probes microarray sequence ortholog
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

Full-text index only

A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

maqc hepatocytes japanese illeum microarray dasl sequence
Increased DNA microarray hybridization specificity using sscDNA targets.

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

Full-text index only

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
Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

PMID 15722479 · PMC549431 · Nucleic acids research · 2005 · 7 claims · 4 setups

Full-text index only

Two base deletion probes display the highest average hybridization specificity, followed by single base substitution, single base deletion, and single base insertion probes.

atm hybridized probe oligonucleotide transcription microarray
A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

Full-text index only

Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

serum plasmids coli pcr oligonucleotide chip
Differential analysis for high density tiling microarray data.

PMID 17892592 · PMC2231405 · BMC bioinformatics · 2007 · 8 claims · 6 setups

Full-text index only

gSAM, a generalized extension of Significance Analysis of Microarrays (SAM), uses a piece-wise function to segment genome-wide differential response by protein-coding vs non-coding regions and by 5' vs 3' vs intra-genic bias within genes, rather than treating a gene as an atomic unit.

hl60 profiling chip-on-chip
Headloop suppression PCR and its application to selective amplification of methylated DNA sequences.

PMID 16091627 · PMC1184225 · Nucleic acids research · 2005 · 8 claims · 5 setups

Full-text index only

Headloop PCR: a 5' primer extension homologous to internal amplicon sequence causes hairpin formation after incorporation, suppressing further amplification of the matching sequence while unaffected sequences amplify normally

plasmid genomic bacterial real-time methylation-specific
Sequence polymorphisms cause many false cis eQTLs.

PMID 17637838 · PMC1906859 · PloS one · 2007 · 8 claims · 7 setups

Full-text index only

Many reported local/cis eQTLs are false positives caused by probe-region sequence polymorphisms affecting hybridization rather than true cis-regulatory expression differences.

lymphoblastoid hematopoietic caenorhabditis genome anova-based sanger eqtl
Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

PMID 18545673 · PMC2409220 · PloS one · 2008 · 8 claims · 6 setups

Full-text index only

An integrative ad-hoc functional GO analysis combining threshold-based (Fisher exact/hypergeometric) and threshold-free (Kolmogorov-Smirnov) statistics, plus term-to-parent comparisons, detects disease-relevant splicing events from exon array data.

mg-thymoma colon exon fluorescent reverse
Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing.

PMID 19682357 · PMC2782262 · BMC microbiology · 2009 · 8 claims · 5 setups

Full-text index only

The RCA assay correctly identified all ERG11 mutations in eight 'reference' azole-resistant C. albicans isolates with known mutations.

clinical pcr template padlock sequencing antifungal

Experiments

Free energy of DNA duplex formation on short oligonucleotide microarrays.

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

SNP identification in unamplified human genomic DNA with gold nanoparticle probes.

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

Detecting transcriptionally active regions using genomic tiling arrays.

Detection of YMDD motif mutants by oligonucleotide chips in lamivudine-untreated patients with chronic hepatitis B virus infection.

Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome.

Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

Lineage-specific gene duplication and loss in human and great ape evolution.

The commonly-used DNA probe for diffusely-adherent Escherichia coli cross-reacts with a subset of enteroaggregative E. coli.

In vitro identification and in silico utilization of interspecies sequence similarities using GeneChip technology.

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

Increased DNA microarray hybridization specificity using sscDNA targets.

Comparisons of substitution, insertion and deletion probes for resequencing and mutational analysis using oligonucleotide microarrays.

A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

Differential analysis for high density tiling microarray data.

Headloop suppression PCR and its application to selective amplification of methylated DNA sequences.

Sequence polymorphisms cause many false cis eQTLs.

Identifying alternative hyper-splicing signatures in MG-thymoma by exon arrays.

Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing.