A 3-μm–thick FFPE breast tissue was stained with hematoxylin and eosin to confirm the presence of invasive tumor cells and determine the tumor area by an expert pathologist (L. Comerma). For RNA isolation (RNeasy FFPE Kit, Qiagen), 1–6 ten-micron–thick FFPE slides were used for each tumor specimen and, if needed, tumor area was macrodissected to avoid contamination of normal breast tissue. After sample quality control using the 2200 TapeStation Software (Agilent Technologies), a minimum of approximately 150 ng of total RNA was used to measure the expression of 50 breast cancer–related genes plus 5 housekeeping genes using the nCounter platform (NanoString Technologies; ref. 27 (link)). Data were log2 transformed and normalized using the housekeeping genes. Intrinsic subtyping (luminal A, luminal B, HER2-enriched, basal-like, and normal-like) was performed according to the research-based PAM50 intrinsic subtype predictor (27 (link)).
2200 tapestation software
Manufactured by Agilent Technologies
Sourced in Sweden
The 2200 TapeStation Software is a data analysis software designed for use with the Agilent 2200 TapeStation System. It provides automated analysis of DNA and RNA samples, delivering key quality metrics such as sample concentration and integrity. The software streamlines the sample analysis process, enabling efficient and consistent data interpretation.
Automatically generated - may contain errors
2 protocols using 2200 tapestation software
1
Profiling Breast Cancer Gene Expression
2
RNA Extraction and Microarray Analysis
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Total RNA from tumors, prostate TINT, and LNs were extracted using Allprep DNA/RNA/Protein mini kit (Qiagen). The RNA samples (n = 8/group) were sent to the core facility for Bioinformatics and Expression Analysis at Karolinska Institutet (BEA, Novum, KI, Stockholm, Sweden) for RNA integrity evaluation using RNA ScreenTape® and 2200 TapeStation Software (Agilent Technologies), sample preparation and subsequent cDNA microarray analysis on Affymetrix® GeneTitan Gene 1.1 ST Rat array (Affymetrix). Two of the samples from AT1-TINT were excluded due to poor RNA quality.
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