Computational protocol: Dysregulated miR-361-5p/VEGF Axis in the Plasma and Endothelial Progenitor Cells of Patients with Coronary Artery Disease

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Protocol publication

[…] Global miRNA profiles of cord blood (CB) and peripheral blood (PB) EPCs were from our previous study , and results were analyzed by a published bioinformatics pipeline constructed in our lab . Fastq raw sequences, which were without poly-A tracts, ambiguous nucleotides or a 5′ adapter, but contained the flanking 6–18 nt of the 3′ adapter sequence, had the adapter sequence trimmed and the identical sequences were then collapse to a series of unique sequences. As to miRNA quantification, all pre-processed datasets were mapped to the miRNA list based on miRBase R19 using Bowtie with options: -a -v 1 -S –f –norc, and then alignment results were produced in a BAM file format by SAMtools . The BAM files were processed by in-house JAVA software for miRNA quantification . Expression values of specific miRNAs were calculated as the RPM value (Reads Per mapped reads), namely RPM = C/MN×106, where C is "read numbers aligned to a given miRNA chromosomal region”, M is “multiple mapping numbers across all miRNA regions by one read (i.e., the number of different miRNA chromosome locations mapped by the same read)” and N is “total read numbers that map to human genome sequence”. To minimize the effect of cross mapping of sequences with uncertain genomic locations, the expression is divided by its number of cross-mapping events. […]

Pipeline specifications

Software tools Bowtie, SAMtools
Databases miRBase
Application sRNA-seq analysis
Organisms Mus musculus, Homo sapiens
Diseases Cardiovascular Diseases, Coronary Artery Disease, Neoplasms