Additional file 1 of Age-related gene expression signatures from limb skeletal muscles and the diaphragm in mice and rats reveal common and species-specific changes

Additional file 1: Table S1. Number of samples for individual muscles in male rats and male and female mice. Number of samples corresponds to the number of animals. E.g. 12 muscles are collected from 12 animals. Table S2. Fold change and adjusted p values of age-related genes in skeletal muscles of rats and mice. Table S3. Probe and primer sequences used for RT-qPCR in mice. Highlighted genes were used as reference genes. Table S4. Probe and primer sequences used for RT-qPCR in rats. Highlighted genes were used as reference genes. Figure S1. Numbers of age-related genes under a stringent cutoff. Figure S2. Gastrocnemius, tibialis anterior and soleus muscle weights in male and female C57Bl6J mice (A, B) and male Sprague Dawley rats (C). Figure S3. Numbers of age-related genes in rat muscles, using lower animal numbers. Figure S4. Numbers of linear and logistic age-related genes in diaphragm, gastrocnemius, soleus and tibialis anterior muscles from female mice. Figure S5. Under stricter examination, rat muscles still enrich for more age-related up-regulated pathways. Figure S6. Age-related genes in male rats and male mice that are associated with immune (A) and mitochondrial (B) pathways. Figure S7. Pathways enriched by age-related genes that were shared between male and female mice. Figure S8. Under stricter examination, rat muscles still enrich for more age-related down-regulated pathways. Figure S9. Transcription factors (TFs) associated with pathways enriched by age-related genes. Figure S10. RT-qPCR validation of top five up- and down-regulated genes in skeletal muscles from male (A and B) and female (C and D) mice. Figure S11. RT-qPCR validation of top five up- and down-regulated genes in skeletal muscles from rats. Figure S12. RT-qPCR validation of transcription factors identified in mice (selected from Figure S9A). Figure S13. RT-qPCR validation of transcription factors identified in rats (selected from Figure S9B).

附加文件1：表S1：雄性大鼠、雄性与雌性小鼠的单块肌肉样本量。样本量即所用动物个体的数量，例如从12只动物中采集12块肌肉。
表S2：大鼠与小鼠骨骼肌中年龄相关基因的倍数变化及校正后p值。
表S3：小鼠实时定量聚合酶链反应（Real-Time Quantitative Polymerase Chain Reaction, RT-qPCR）所用探针与引物序列，标亮基因为内参基因。
表S4：大鼠实时定量聚合酶链反应（RT-qPCR）所用探针与引物序列，标亮基因为内参基因。
图S1：严格筛选阈值下的年龄相关基因数量。
图S2：雄性与雌性C57Bl6J小鼠（A、B）及雄性斯普拉格-道利（Sprague Dawley）大鼠（C）的腓肠肌、胫骨前肌与比目鱼肌重量。
图S3：使用较低动物样本量时大鼠肌肉中的年龄相关基因数量。
图S4：雌性小鼠膈肌、腓肠肌、比目鱼肌与胫骨前肌中线性与逻辑回归型年龄相关基因的数量。
图S5：经更严格验证后，大鼠肌肉仍富集更多年龄相关上调通路。
图S6：雄性大鼠与雄性小鼠中与免疫通路（A）及线粒体通路（B）相关的年龄相关基因。
图S7：雌雄小鼠共享的年龄相关基因所富集的通路。
图S8：经更严格验证后，大鼠肌肉仍富集更多年龄相关下调通路。
图S9：与年龄相关基因富集通路相关的转录因子（Transcription Factors, TFs）。
图S10：雄性（A、B）与雌性（C、D）小鼠骨骼肌中前5个上调及下调基因的实时定量聚合酶链反应验证结果。
图S11：大鼠骨骼肌中前5个上调及下调基因的实时定量聚合酶链反应验证结果。
图S12：小鼠中鉴定出的转录因子（源自图S9A）的实时定量聚合酶链反应验证结果。
图S13：大鼠中鉴定出的转录因子（源自图S9B）的实时定量聚合酶链反应验证结果。