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Characterization of technical variation in ChIP-on-chip studies

ABSTRACT: Analysis of technical variance of ChIP-on-Chip studies by characterization of Myc-binding in HL60 cells. Keywords: Chip-on-chip

ORGANISM(S): Homo sapiens

PROVIDER: GSE8448 | GEO | 2008/11/01

SECONDARY ACCESSION(S): PRJNA101523

REPOSITORIES: GEO

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Characterization of technical variation in ChIP-on-chip studies

Project description:Analysis of technical variance of ChIP-on-Chip studies by characterization of Myc-binding in HL60 cells. Keywords: Chip-on-chip Fully-blocked study of technical variance in Myc-binding in HL60 cells. Two different antibodies were used to generate 6 biologically independent replicates each. Each replicate was hybridized to arrays from two different batches in both dye-swap orientations, leading to 48 total arrays.

2008-10-31 | E-GEOD-8448 | biostudies-arrayexpress

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c-Myc binding in HL60 cells

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On the relevance of technical variation due to building pools in microarray experiments [Mouse]

Project description:The objective of the study was to assess the technical error due to blending of individual samples into pools in experimental data. The blending error variance component corresponds to random effects for inaccuracies, which were modeled on the logarithmic scale of normalized gene expression. It's estimation based on a linear mixed model, fitted for each transcript.

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BEARscc: robustness of single-cell clusters determined using simulated technical replicates

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Sox2 ChIP-chip on human neural stem cell line REN cells

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Technical controls MiCA

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RNA-seq: technical variability and sampling (female)

Project description:Background: RNA-seq is revolutionizing the way we study transcriptomes. mRNA can be surveyed without prior knowledge of gene transcripts. Alternative splicing of transcript isoforms and the identification of previously unknown exons are being reported. Initial reports of differences in exon usage, and splicing between samples as well as quantitative differences among samples are beginning to surface. Biological variation has been reported to be larger than technical variation. In addition, technical variation has been reported to be in line with expectations due to random sampling. However, strategies for dealing with technical variation will differ depending on the magnitude. The size of technical variance, and the role of sampling are examined in this manuscript. Results: Independent Solexa/Illumina experiments containing technical replicates are analyzed. When coverage is low, large disagreements between technical replicates are apparent. Exon detection between technical replicates is highly variable when the coverage is less than 5 reads per nucleotide and estimates of gene expression are more likely to disagree when coverage is low. Although large disagreements in the estimates of expression are observed at all levels of coverage. Conclusions: Technical variability is too high to ignore. Technical variability results in inconsistent detection of exons at low levels of coverage. Further, the estimate of the relative abundance of a transcript can substantially disagree, even when coverage levels are high. This may be due to the low sampling fraction and if so, it will persist as an issue needing to be addressed in experimental design even as the next wave of technology produces larger numbers of reads. We provide practical recommendations for dealing with the technical variability, without dramatic cost increases.

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