![bio-rad cfx manager 3.1 normalize bio-rad cfx manager 3.1 normalize](https://storage.googleapis.com/bioz_article_images/PMC4931339/fig-2.jpg)
#BIO RAD CFX MANAGER 3.1 NORMALIZE SOFTWARE#
Over 90% of the mRNA, reads were mapped on the Rattus norvegicus reference genome (rn5) using Lifescope v2.5.1 software (ThermoFisher, Grand Island, NY) with two-mismatch settings. Exploring such phenotypic mechanisms in rats could help improve our understanding of abnormal lung development in human CDH.Ī total of 5,045,279 single-end (50bp) MiSeq miRNA sequence reads were generated and 153,253,385 pair-end (50 × 35) SOLiD sequence mRNA reads were generated from nitrofen-treated and control lung samples. We hypothesize that transcriptome changes contribute to abnormal lung development in the nitrofen rat model of CDH. In this study, we used next-generation sequencing (NGS) technology to characterize transcriptome differences between control lungs and nitrofen-induced hypoplastic lungs in embryonic lung tissues prior to the development of the diaphragmatic defect. Thus far, the transcriptomic changes associated with nitrofen-modulated developmental signaling have not been characterized in the lung. Some hypotheses suggest that nitrofen influences diaphragm and lung development in rodent embryos similar to the human condition ( 6, 7, 8). Whether the nitrofen-rat model shares the same pathogenesis with human CDH remains to be determined. In rodents, nitrofen induces CDH and lung hypoplasia similar to the phenotype observed in humans ( 5). CDH constitutes about 8% of major congenital anomalies and has the highest mortality rate ( 4). Deregulation of miRNAs, and consequently, loss of fine adjustments to target genes can lead to lung diseases ( 3).īabies with congenital diaphragmatic hernia (CDH) have a hole in their diaphragm and abnormal lung development resulting in lung hypoplasia and persistent pulmonary hypertension. The role of miRNAs in lung development is currently poorly defined. MicroRNAs (miRNAs) are small (17–24 bp), noncoding RNAs that regulate different biological functions by modulating expression and stability of target genes posttranscriptionally ( 1, 2). Nitrofen-induced hypoplastic lungs have an abnormal transcriptome that may lead to impaired development. Potential miRNA pathways relevant to nitrofen-induced lung hypoplasia include PI3K, TGF-β, and cell cycle kinases. A subset of these genes may promote lung hypoplasia in rat and/or human, and we discuss their associations. Sixty-four rat miRNAs homologous to known human miRNAs were identified. Our study identified 186 known mRNA and 100 miRNAs which were differentially expressed in nitrofen-induced hypoplastic lungs. Once the dataset was validated by both RT-qPCR and digital-PCR, we conducted gene ontology, miRNA target analysis, and orthologous miRNA sequence matching for the deregulated miRNAs in silico.
![bio-rad cfx manager 3.1 normalize bio-rad cfx manager 3.1 normalize](https://storage.googleapis.com/bioz_article_images/PMC7661706/41598_2020_76612_Fig4_HTML.jpg)
Using next-generation sequencing technology, we identified the expression profile of microRNA (miRNA) and mRNA genes.
![bio-rad cfx manager 3.1 normalize bio-rad cfx manager 3.1 normalize](https://media.springernature.com/full/springer-static/image/art%3A10.1038%2Fs41388-021-02018-7/MediaObjects/41388_2021_2018_Fig1_HTML.png)
Our aim was to compare the differentially expressed transcriptome of nitrofen-induced hypoplastic lungs to control lungs in embryonic day 13 rat embryos before the development of embryonic diaphragmatic defects. We currently do not know how the herbicide nitrofen induces lung hypoplasia and congenital diaphragmatic hernia in rats.