MOESM2 of Non-coding RNAs underlie genetic predisposition to breast cancer

Additional file 2: Table S1. Breast derived samples on which RNA CaptureSeq was performed. Table S2. Expression (FPKM) of the mencRNAs across all RNA CaptureSeq samples. Table S3. Breast cancer risk signals and surrounding regions captured by RNA CaptureSeq. Table S4. Control sequences captured by RNA CaptureSeq. Table S5. MencRNAs with FPKM ≥0.5 identified by RNA CaptureSeq. Table S6. Novel mencRNAs with FPKM ≥0.5. Those overlapping with GENCODE, FANTOM-CAT, or NONCODE lncRNAs have been excluded. Table S7. Coding potential of the transcripts from mencRNAs with FPKM ≥0.5 assessed by coding potential calculator (CPC2). Table S8. MencRNAs differentially expressed between MCF7 estrogen-treated and control samples (FDR < 0.01). Table S9. MencRNAs expressed in TCGA with FPKM ≥1 in at least one sample. Table S10. Count of CCVs overlapping transcript features. Table S11. Breast cancer CCVs linked to genomic features. Table S12. MencRNA eQTLs. Table S13. Colocalized mencRNA eQTLs. Table S14. MencRNAs targeted by breast cancer risk signals. Table S15. Primers used for mencRNA validation. Table S16. Publically available genomic data and software.附加文件2：表S1：开展了RNA捕获测序（RNA CaptureSeq）的乳腺来源样本 表S2：所有RNA捕获测序样本中膜富集非编码RNA（mencRNAs）的表达量（FPKM值） 表S3：RNA捕获测序捕获的乳腺癌风险信号及其侧翼区域 表S4：RNA捕获测序捕获的对照序列 表S5：经RNA捕获测序鉴定得到的FPKM≥0.5的mencRNAs 表S6：FPKM≥0.5的新型mencRNAs，已剔除与GENCODE、FANTOM-CAT或NONCODE长链非编码RNA（long non-coding RNAs, lncRNAs）存在序列重叠的条目 表S7：由编码潜能计算器（CPC2）评估的FPKM≥0.5的mencRNAs转录本的编码潜能 表S8：经雌激素处理与对照的MCF7样本之间差异表达的mencRNAs（错误发现率FDR<0.01，False Discovery Rate） 表S9：在癌症基因组图谱（The Cancer Genome Atlas, TCGA）至少一个样本中FPKM≥1的表达mencRNAs 表S10：与转录本特征存在序列重叠的CCVs的数量 表S11：与基因组特征相关联的乳腺癌CCVs 表S12：mencRNA表达数量性状位点（expression quantitative trait loci, eQTLs） 表S13：共定位的mencRNA eQTLs 表S14：受乳腺癌风险信号靶向调控的mencRNAs 表S15：用于mencRNAs验证的引物序列 表S16：公开可用的基因组数据与软件工具