Pooling mRNA in microarray experiments and its effect on power

Zhang, Wuyan; Carriquiry, Alicia L.; Nettleton, Dan; Dekkers, Jack C. M.

doi:10.1093/bioinformatics/btm081

Cited by 49 publications

(52 citation statements)

References 9 publications

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“…Peripheral blood and kidney samples were harvested at 8 hours after CM/NS administration. The plasma or renal RNA samples extracted from rats in same subgroup were pooled and then measured with a single microarray 20. The Agilent microarray platform was adapted to profile the miRNA spectra.…”

Section: Resultsmentioning

confidence: 99%

Circulating MicroRNA‐188, ‐30a, and ‐30e as Early Biomarkers for Contrast‐Induced Acute Kidney Injury

Sun

Zhang

Ding

et al. 2016

JAHA

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BackgroundContrast‐induced acute kidney injury (CI‐AKI) is typically defined by an increase in serum creatinine after intravascular administration of contrast medium. Because creatinine is an unreliable indicator of acute changes in kidney function, we assessed whether circulating microRNAs (miRNAs) could serve as biomarkers for early detection of CI‐AKI.Methods and ResultsUsing a rat model of CI‐AKI, we first evaluated the miRNA profile of rat plasma and kidney. Three miRNA species with >1.5‐fold increase in plasma samples of CI‐AKI rats, including miRNA‐188, miRNA‐30a, and miRNA‐30e, were selected as candidate miRNAs. Quantitative real‐time polymerase chain reaction showed that these candidate miRNAs peaked in concentration around 4 hours after contrast medium exposure and were relatively renal‐specific. We compared the plasma levels of these candidate miRNAs in 71 patients who underwent coronary angiography or percutaneous coronary intervention and developed CI‐AKI with those of 71 matched controls. The plasma levels of the 3 candidate miRNAs were significantly elevated in the CI‐AKI group as compared to the control group. Receiver operating characteristic analysis showed that these miRNAs significantly distinguished patients with CI‐AKI from those without CI‐AKI. MiRNA composites were highly accurate for CI‐AKI prediction, as shown in maximized specificity by treble‐positive miRNA composite or maximized Youden index by any‐positive miRNA composite. Moreover, the selected miRNAs changes were associated with Mehran Risk Scores.ConclusionsPlasma levels of candidate miRNAs significantly distinguished patients with CI‐AKI from those without CI‐AKI. Thus, miRNAs are potential biomarkers for early detection of CI‐AKI.

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Section: Resultsmentioning

confidence: 99%

Circulating MicroRNA‐188, ‐30a, and ‐30e as Early Biomarkers for Contrast‐Induced Acute Kidney Injury

Sun

Zhang

Ding

et al. 2016

JAHA

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“…Experiments were designed to comply with MIAME guidelines [30]. In an effort to reduce variability, target synthesis using pooled RNA (of equal quantity and comparable quality from 5 females per treatment group) [31][32][33], biotin-labeling, hybridizations, and staining were performed using standard Affymetrix reagents and methods (http://www.affymetrix.com/index.affx). Pooled samples were run in duplicate such that a total of eight arrays were used.…”

Section: Microarray Hybridization and Analysismentioning

confidence: 99%

Molecular targets of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) within the zebrafish ovary: Insights into TCDD-induced endocrine disruption and reproductive toxicity

Heiden

Struble

Rise

et al. 2008

Reproductive Toxicology

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TCDD is a reproductive toxicant and endocrine disruptor, yet the mechanisms by which it causes these reproductive alterations are not fully understood. In order to provide additional insight into the molecular mechanisms that underlie TCDD's reproductive toxicity, we assessed TCDD-induced transcriptional changes in the ovary as they relate to previously described impacts on serum estradiol concentrations and altered follicular development in zebrafish. In-silico computational approaches were used to correlate candidate regulatory motifs with observed changes in gene expression. Our data suggest that TCDD inhibits follicle maturation via attenuated gonadotropin responsiveness and/ or depressed estradiol biosynthesis, and that interference of estrogen-regulated signal transduction may also contribute to TCDD's impacts on follicular development. TCDD may also alter ovarian function by disrupting various signaling pathways such as glucose and lipid metabolism, and regulation of transcription. Furthermore, events downstream from initial TCDD molecular-targets likely contribute to ovarian toxicity following chronic exposure to TCDD. Data presented here provide further insight into the mechanisms by which TCDD disrupts follicular development and reproduction in fish, and can be used to formulate new hypotheses regarding previously documented ovarian toxicity.

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“…The same amount of tissue for each subject was used in the different experimental procedures and arranged in three different pools for each area: 12 12 samples belonging to proximal and medial ureter were respectively pooled for each area as follows: pool #1: 4 samples, pool #2: 4 samples, pool #3: 4 samples; 22 samples from distal ureter, detrusor muscle, trigone, neck and prostatic urethra, respectively pooled for each area as follows: pool #1: 8 samples, pool #2: 7 samples, pool #3: 7 samples.…”

Section: Tissue Collectingmentioning

confidence: 99%

Molecular and pharmacological detection of dopaminergic receptors in the human male urinary tract

Arrighi¹,

Bodei²,

Zani³

et al. 2008

Neurourology and Urodynamics

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DA receptors were expressed throughout the human male urinary tract, from the ureter to the prostatic urethra. In particular, we observed a distinctive DA receptor subtype distribution, with evidence of the presence of mRNA encoding both subtypes of the D(1)-like DA receptor family (D(1) and D(5)), while the D(4) receptors were the only expressed subtype of the D(2)-like family. These results suggested that DAergic drugs used for the treatment of a number of diseases may influence the micturition physiology not only in the CNS, but at the peripheral level as well.

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Pooling mRNA in microarray experiments and its effect on power

Cited by 49 publications

References 9 publications

Circulating MicroRNA‐188, ‐30a, and ‐30e as Early Biomarkers for Contrast‐Induced Acute Kidney Injury

Circulating MicroRNA‐188, ‐30a, and ‐30e as Early Biomarkers for Contrast‐Induced Acute Kidney Injury

Molecular targets of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) within the zebrafish ovary: Insights into TCDD-induced endocrine disruption and reproductive toxicity

Molecular and pharmacological detection of dopaminergic receptors in the human male urinary tract

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