Comprehensive miRNA profiling in IDC

A total of 48 IDC samples consisting of 8 biological replicates from each of the biological groups were taken for both array analyses (Grade 2 and 3 (24 from each grade) consisting of 8 samples each from stages I, II III of every grade) and were used for normalizing with pooled 10 adjacent normal samples. TLDA (ver2.0), which contains 667 human miRNAs covering Sanger miRBase (ver10.0), was performed as per the manufacturer’s protocols. The experiments were repeated with LNA arrays (ver11.0) containing 1372 miRNAs from hmr-miRBase 14.0 + miRPlus from Exiqon, Denmark, following the manufacturer’s instruction manual. Rodent array (Applied Biosystems version v 3.0) consisting of 641 mouse and 373 rat unique miRNAs along with appropriate controls were carried out in 5 biological replicates of Brca2/p53 double knock out mammary models along with 6 wild type controls to find out the common miRNAs between human and rodent systems.

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Verma V.K., Beevi S.S., Nair R.A., Kumar A., Kiran R., Alexander L.E, & Dinesh Kumar L. (2024). MicroRNA signatures differentiate types, grades, and stages of breast invasive ductal carcinoma (IDC): miRNA-target interacting signaling pathways. Cell Communication and Signaling : CCS, 22, 100.

Publication 2024

hmr-miRBase 14.0 + miRPlus

Corresponding Organization :

Other organizations : Centre for Cellular and Molecular Biology, Regional Cancer Center, Thiruvananthapuram

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Variable analysis

independent variables

Biological groups (Grade 2 and Grade 3)
Disease stages (Stage I, II, III)

dependent variables

Expression levels of 667 human miRNAs (TLDA ver2.0)
Expression levels of 1372 human miRNAs (LNA arrays ver11.0)
Expression levels of 641 mouse and 373 rat unique miRNAs (Rodent array)

control variables

Pooled 10 adjacent normal samples used for normalization

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

Annotations

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