Dataset of HOXB7, HOXB8 and HOXB9 basal RNA expression in breast cancer cell lines

Published: 31 March 2020| Version 3 | DOI: 10.17632/v77kmkzj88.3
Contributors:
Simone Aparecida de Bessa-Garcia,
Mafalda Araújo,
Renata Freitas

Description

The HOXB7, HOXB8 and HOXB9 gene expression profiles in breast cancer are contradictory due to disease complexity and technical issues. The data presented here cover these two points by analyzing the expression of these genes in breast cancer cell lines representative of distinct molecular subtypes using a very sensitive quantification technique, the qPCR. The cell lines analyzed were MCF7, BT474, SKBR3, MDA231, MDA468 and MCF10A representative of Luminal A, Luminal B, HER2+, triple-negative claudin low, triple-negative basal and normal model, respectively. The raw data was accessed by CFX Manager 3.1 software (Bio-Rad) and a threshold line was put into the exponential phase of the amplification curve generating a Cycle Threshold (CT) number for each sample. The CT numbers were transferred to an Excel file, provided in the Raw data folder, to be analyzed using the formula: RATIO= E target^ – (CT sample for the target gene) / E reference^ – (CT sample for the reference gene), in which “E” refers to primer efficiencies previously calculated and GAPDH is the reference gene. The statistical analyses were made with Prism 8 using the unpaired T test with Welch’s correction using the MCF10A cells as reference sample. P-values were considered statistically significant when P≤0.05. The obtained values are provided in Analyzed data folder. Data are presented as the mean ± SD of at least three independent experiments. When more than three experiments are available, we used all replicates to do the analysis or excluded discrepant results but always keeping at least three replicates. The analyzed results showed that HOXB7 tends to be upregulated in all breast cancer cell lines when compared to the normal cell model, while HOXB8 and HOXB9 are significantly upregulated in MCF7, BT474 and MDA231 cells with no significant differences in SKBR3 and MDA468 cells. All genes presented expression levels highly subtype-dependent among different breast cancer cell lines.

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