ArticleBMC biotechnology2007
Characterization of the effect of sample quality on high density oligonucleotide microarray data using progressively degraded rat liver RNA.
Article in BMC biotechnology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 88 citations in OpenAlex.
- Pervasive effects of RNA degradation on Nanopore direct RNA sequencing.NAR genomics and bioinformatics · 2023Article
- Transcriptomic Responses to Polymyxin B and Analogues in Human Kidney Tubular Cells.Antibiotics (Basel, Switzerland) · 2023Article
- Performance and Metabolic, Inflammatory, and Oxidative Stress-Related Parameters in Early Lactating Dairy Cows with High and Low Hepatic FGF21 Expression.Animals : an open access journal from MDPI · 2022Article
- Multiple freeze-thaw cycles lead to a loss of consistency in poly(A)-enriched RNA sequencing.BMC genomics · 2021Article
- Compared DNA and RNA quality of breast cancer biobanking samples after long-term storage protocols in - 80 °C and liquid nitrogen.Scientific reports · 2020Article
- Controlling technical variation amongst 6693 patient microarrays of the randomized MINDACT trial.Communications biology · 2020Article
- Article
- In search of an evidence-based strategy for quality assessment of human tissue samples: report of the tissue Biospecimen Research Working Group of the Spanish Biobank Network.Journal of translational medicine · 2019Review
- Cold Ischemia Score: An mRNA Assay for the Detection of Extended Cold Ischemia in Formalin-Fixed, Paraffin-Embedded Tissue.The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society · 2019Article
- Tissue alkalosis in cold-ischemia time.Scientific reports · 2017Article
- RNA isolation from precision-cut lung slices (PCLS) from different species.BMC research notes · 2017Article
- The effect of long-term -80°C storage of thyroid biospecimens on RNA quality and ensuring fitness for purpose.Journal of clinical pathology · 2016Article
- A method for isolation of cone photoreceptors from adult zebrafish retinae.BMC neuroscience · 2016Article
- Simultaneous purification of DNA and RNA from microbiota in a single colonic mucosal biopsy.BMC research notes · 2016Article
- Molecular mechanisms of D-cycloserine in facilitating fear extinction: insights from RNAseq.Metabolic brain disease · 2016Article
- Preservation of Multiple Mammalian Tissues to Maximize Science Return from Ground Based and Spaceflight Experiments.PloS one · 2016Article
- The use of exome capture RNA-seq for highly degraded RNA with application to clinical cancer sequencing.Genome research · 2015Article
- RNA Sequencing and Analysis.Cold Spring Harbor protocols · 2015Article
- Long-term stability of total RNA in RNAstable® as evaluated by expression microarray.Biopreservation and biobanking · 2015Article
- Pre-Analytical Determination of the Effect of Extended Warm or Cold Ischaemia on RNA Stability in the Human Ileum Mucosa.PloS one · 2015Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe interpretability of microarray data can be affected by sample quality. To systematically explore how RNA quality affects microarray assay performance, a set of rat liver RNA samples with a progressive change in RNA integrity was generated by thawing frozen tissue or by ex vivo incubation of fresh tissue over a time course.
resultsIncubation of tissue at 37 degrees C for several hours had little effect on RNA integrity, but did induce changes in the transcript levels of stress response genes and immune cell markers. In contrast, thawing of tissue led to a rapid loss of RNA integrity. Probe sets identified as most sensitive to RNA degradation tended to be located more than 1000 nucleotides upstream of their transcription termini, similar to the positioning of control probe sets used to assess sample quality on Affymetrix GeneChip(R) arrays. Samples with RNA integrity numbers less than or equal to 7 showed a significant increase in false positives relative to undegraded liver RNA and a reduction in the detection of true positives among probe sets most sensitive to sample integrity for in silico modeled changes of 1.5-, 2-, and 4-fold.
conclusionAlthough moderate levels of RNA degradation are tolerated by microarrays with 3'-biased probe selection designs, in this study we identify a threshold beyond which decreased specificity and sensitivity can be observed that closely correlates with average target length. These results highlight the value of annotating microarray data with metrics that capture important aspects of sample quality.
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