Computational protocol: MicroRNA-708-5p acts as a therapeutic agent against metastatic lung cancer

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Protocol publication

[…] Total RNA was evaluated the integrity and concentration using Agilent Technologies 2100 bioanalyzer. For each sample, 2 ug of total RNA with a RIN value more than 8.0, was imputed into the procedure of RNA-seq library preparation as per Illumina TruSeq RNA Sample Preparation protocol. RNA-seq libraries were sequenced using the Illumina HiSeq 2000 instrument as per manufacturer's instructions. Sequencing of libraries was performed up to 2 × 101 cycles. Image analysis and base calling were performed with the standard Illumina pipeline version RTA 2.8.0.The sequencing reads containing either N over 3% or low quality bases (< 18) over 50% of the full length in each end were removed. All the clean reads were then aligned to the UCSC (the University of California Santa) Homo sapiens reference genome using TopHat v1.3.3 with default parameters []. The expression levels of the transcripts were quantified by Mapped Fragments per Kilobase of Exon model per Million mapped reads (FPKM) using Cufflinks []. Differential expression gene was identified with the output q ≥ 0.8 using non-parameter test provided by NOISeq []. The panel of differential expression genes was performed functional clustering and enrichment analyses using the Database for Annotation, Visualization and Integrated Discovery (DAVID) []. […]

Pipeline specifications

Software tools TopHat, Cufflinks, NOISeq, DAVID
Application RNA-seq analysis
Organisms Mus musculus
Diseases Carcinoma, Non-Small-Cell Lung, Lung Neoplasms, Neoplasms, Drug-Related Side Effects and Adverse Reactions
Chemicals Polyethyleneimine