Additional file 7: Figure S3. of Guanylate-binding protein-1 is a potential new therapeutic target for triple-negative breast cancer

Quality assessment of RNA-Seq data. (A) FastQC [30] plot of the Phred scores of each nucleotide position of all reads before and after Skewer [31] trimming for BT549, MCF7, MDAMB436 and MDAMB468, sequenced at LaCTAD-UNICAMP, and MDAMB231 and SKBR3, sequenced at HTSF-UNC. (B) RNA-Seq data from in-house-sequenced cell lines were evaluated for reproducibility by comparing the log2 RSEM +1 values of 48 genes with the obtained qPCR 1/ΔCT values. Density of raw log2-transformed RSEM values for the in-house-sequenced and Varley et al. [25] and Daemen et al. [26] datasets (C, left) and the normalized RSEMs (C, right), showing success in the harmonization of all data, despite variations in sample preparation and sequencing (XLS 4164 kb)

RNA测序（RNA-Seq）数据的质量评估。(A) 针对BT549、MCF7、MDAMB436及MDAMB468细胞系（于LaCTAD-UNICAMP完成测序），以及MDAMB231、SKBR3细胞系（于HTSF-UNC完成测序），展示了经Skewer[31]修剪过滤前后所有测序读段各核苷酸位置的Phred质量值的FastQC[30]绘图结果。(B) 将内部测序细胞系的RNA-Seq数据中48个基因的log₂(RSEM + 1)值与qPCR检测得到的1/ΔCT值进行比对，以此评估数据的可重现性。(C) 分别展示内部测序数据集以及Varley等[25]、Daemen等[26]数据集的原始log₂转换后RSEM值密度分布（左图）与标准化RSEM值密度分布（右图），结果表明尽管样本制备与测序流程存在差异，但所有数据已成功实现整合标准化（附件：4164 KB的XLS格式文件）