Computational protocol: Core Needle Biopsy of Breast Cancer Tumors Increases Distant Metastases in a Mouse Model12

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Protocol publication

[…] Immediately after blood collection for analysis, mice from biopsy (n = 5) and non-biopsy (n = 5) groups were sacrificed for the 0-, 3-, 12-, and 24-hour post biopsy time points (n = 40). Sections of tumor and lung were harvested and snap frozen in TRIzol and RNAlater (Qiagen Inc). Frozen tissue samples were later thawed, the tissue was crushed, and the RNA extracted using Purelink RNA Kit (Invitrogen Inc). Generation of cDNA was performed using Superscript II (Invitrogen Inc). For qPCR analysis of relative expression of genes of interest, specific primers for neomycin resistance gene (Neo), S100A8, Ly-6G (Gr-1), CXCL2 (MIP-2), CCL3 (MIP-1a), FOXP3, transforming growth factor–β (TGF-β), SOX-4, Ezh2, SNAI2, ZEB2, CDH2 (N cadherin), IL-1β, IL-10, TNF-α, matrix metalloproteinase 9, and urokinase plasminogen activator were designed on the basis of RefSeq data for Mus musculus using the NCBI Primer-BLAST online primer designing tool ().Using the Bio-Rad CFX-96 system, qPCR assay was performed and analysis of results was done using the CFX manager software applying ΔΔCt analysis with relative normalization calculations based on the murine glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and β-actin housekeeping genes. […]

Pipeline specifications

Software tools Primer-BLAST, CFX Manager
Application qPCR
Organisms Mus musculus, Homo sapiens
Diseases Breast Neoplasms, Neoplasms