Profiling of microRNA Expression in HER2-Positive Breast Cancer Tumors among Filipino Patients Using Next-Generation Sequencing

Raw sequencing reads were assessed using FastQC and MultiQC, followed by adapter trimming with Trim Galore. Mature human miRNA expression was quantified against miRBase release 22.1 using the miRDeep2 quantifier implemented in Galaxy. Differential miRNA expression was assessed using DESeq2 with an unpaired design and edgeR with a paired design. miRNAs identified as statistically significant in both analyses were retained as differentially expressed.

Two miRNAs, hsa-miR-7-5p and hsa-miR-99a-5p, were subsequently validated by RT-qPCR using the same tissue specimens. Paired comparisons were evaluated using the Wilcoxon signed-rank test. Three samples were excluded from the RT-qPCR analysis because of insufficient RNA.

The shared data files comprise: (1) raw miRNA count matrices for all 21 sequencing libraries; (2) differential miRNA expression results; (3) RT-qPCR results for the two validated miRNAs; and (4) de-identified clinical data for the 11 patients, including age group, disease stage, and tumor, nodal, and metastasis categories.