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TranscriptomicsDye Bias Array Set
Spot intensity serves as a proxy for gene expression in dual-label microarray experiments. Dye bias is defined as an intensity difference between samples labeled with different dyes attributable to the dyes instead of the gene expression in the samples. Dye bias that is not removed by array normaliz...
ORGANISM(S): Homo sapiens 
2006-06-06 | E-GEOD-4982 | biostudies-arrayexpress
TranscriptomicsCodon usage bias is correlated with gene expression levels in the fission yeast Schizosaccharomyces pombe.
Usage of synonymous codons represents a characteristic pattern of preference in each organism. It has been inferred that such bias of codon usage has evolved as a result of adaptation for efficient synthesis of proteins. Here we examined synonymous codon usage in genes of the fission yeast Schizosac...
ORGANISM(S): Schizosaccharomyces pombe 
2010-06-20 | E-GEOD-13554 | biostudies-arrayexpress
ProteomicsAddressing the Protease Bias in Quantitative Proteomics
Protein quantification strategies using multiple proteases have been shown to deliver poor inter-protease accuracy in label-free mass spectrometry experiments. By utilizing six different proteases with different cleavage sites, this study explores the protease bias and its effect on accuracy and pre...
ORGANISM(S): Homo Sapiens 
PXD033574 | panorama
TranscriptomicsSystematic Bias in Genomic Classification Due to Contaminating Normal Tissue in Breast Tumor Samples
Results: Normal tissue contamination caused misclassification of tumors in all predictors, but different breast cancer predictors showed different susceptibility to normal tissue bias. Sensitivity and negative predictive value (NPV) of the PAM50 assay was improved by accounting for normal tissue. C...
ORGANISM(S): Homo sapiens 
2011-07-18 | E-GEOD-22384 | biostudies-arrayexpress
TranscriptomicsBias in ligation-based small RNA sequencing library construction is determined by adaptor and RNA structure
High-throughput sequencing (HTS) has become a powerful tool for the detection of and sequence characterization of microRNAs (miRNA) and other small RNAs (sRNA). Unfortunately, the use of HTS data to determine the relative quantity of different miRNAs in a sample has been shown to be inconsistent wi...
ORGANISM(S): synthetic construct 
2015-05-15 | E-GEOD-67053 | biostudies-arrayexpress
GenomicsBias musicus
Bias musicus
PRJNA920250 | ENA
TranscriptomicsGenotyping of human cell lines with amplification of single cell vs. non amplied products to examime the effect of allele bias during amplification
Single-cell human genome analysis using whole-genome amplified product is hampered by allele bias during amplification. Using an oligonucleotide SNP array, we examined the nature of the allele bias and its effect on the chromosomal copy number analysis. Experiment Overall Design: TB106, lymphoblasto...
ORGANISM(S): Homo sapiens 
2008-06-16 | E-GEOD-8567 | biostudies-arrayexpress
TranscriptomicsDigital RNA Sequencing Minimizes Sequence-Dependent Bias and Amplification Noise with Optimized Single Molecule Barcodes
RNA-Seq is a powerful tool for transcriptome profiling, but is hampered by sequence-dependent bias and inaccuracy at low copy numbers intrinsic to exponential PCR amplification. We developed a simple strategy for mitigating these complications, allowing truly digital RNA-Seq. Following reverse tra...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2012-01-07 | E-GEOD-34449 | biostudies-arrayexpress
TranscriptomicsExon and junction microarrays detect widespread mouse strain- and sex-bias expression differences
71 liver RNA samples from three mouse strains - DBA/2J, C57BL/6J and C3H/HeJ - were profiled using a custom-designed microarray monitoring exon and exon-junction expression of 1,020 genes representing 9,406 exons. Gene expression was calculated via two different methods, using the 3'-most exon prob...
ORGANISM(S): Mus musculus 
2010-05-25 | E-GEOD-10736 | biostudies-arrayexpress
TranscriptomicsEvaluating bias-reducing protocols for RNA sequencing library preparation
The ligation step in RNA sequencing library generation is a known source of bias. We present the first comparison of the standard duplex adaptor protocol supplied by Life Technologies for use on the Ion Torrent PGM with an alternate single adaptor approach involving CircLigase (CircLig). We also...
ORGANISM(S): synthetic construct 
2014-06-24 | E-MTAB-2566 | biostudies-arrayexpress
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