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The presence and type (HPV type 18) was confirmed by automated sequencing of the PCR products shown in Figure 3. Having established the method and demonstrated the presence of HPV in breast cancer cell lines, we screened a series of fixed breast cancer and normal breast tissue specimens using in situ PCR.
We further verified miR-133a expression in fresh breast tissue specimens using qRT-PCR and the data confirmed our in situ hybridization data, i.e., miR-133a expression level was significantly lower in breast cancer compared with benign breast disease (P < 0.01; Figure 1D).
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In this study, we first determined the expression profile of miRNAs using miRNA arrays in different breast cancer cells with diverse invasive ability and then chose one of them, miR-339-5p, furtherther study of its expression in breast cancer tissue specimens using in situ hybridization.
The breast cancer tissue specimens used in the present study came from two independent patient cohorts as described below.
The breast cancer tissue specimens used for isolation of stromal fibroblasts were diagnosed as invasive ductal carcinoma with histological grade II and classified as luminal A subtype with oestrogen receptor-positive/progesterone receptor-positive/human epidermal growth factor receptor 2-negative.
Parallel data of 12 normal breast organoids RNA samples and 7 bulk normal breast tissue specimens were used as normal control.
Tissue specimens used in qRT-PCR were obtained retrospectively from the surgical specimens.
Total RNA was extracted from breast tissue specimens or cells using the Trizol reagent (Invitrogen) following manufacturer's instructions.
Normal breast tissue specimen was used as negative and human palatine tonsil tissue specimen as positive control for cyclin B1.
BORIS and CTCF mRNA levels were measured in breast tissue specimens and cell lines using the Platinum® Quantitative PCR Supermix (Invitrogen).
Ultrasonic pulse-echo and through-transmission data were acquired from breast tissue specimens with the use of two immersion transducers (Olympus NDT, V358-SU, 50 MHz, 0.635-cm diameter active element), a HF square-wave pulser/receiver (UTEX, UT340), and a digital storage oscilloscope (Hewlett-Packard, HP-54522A, 500 MHz, 1Gs/s).
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