Additional file 3 of Effects of caloric restriction on the gut microbiome are linked with immune senescence

Additional file 2. The three supplementary Excel files, for colon (colon_cca_xlsx), spleen (spleen_cca_xlsx), and liver(liver_cca_xlsx), comprise each four spreadsheets: The sheets “corr.matrix” and “corr.fdr” contain estimated coefficients of the latent cross-correlation matrix (as shown in Fig. 6 and Supplementary Figure 5 heatmaps) and corresponding FDR-adjusted P-values, respectively. The sheet “asv.cca” contains for all ASVs (with the same order as in the correlation matrix) FDR-adjusted P-values and log-fold change values (columns C, D) from DESeq2 differential abundance testing (as shown in heatmap Fig. 1 C), the corresponding taxonomy table including seven taxonomic ranks (columns E-K), taxa labels used for heatmaps (column L) and two columns indicating the top (upper and lower) ASVs that were highlighted in correlation heatmap and circular chord diagrams (column M) and that were selected by sparse canonical correlation analysis using the Bayesian information criterion (column N), with sparse coefficients’ weights provided in column O. The sheet “imm.cca” contains for all immunological parameters (with the same order as in the correlation matrix) that were assessed in a given organ, FDR-adjusted P-values from GLMM and non-parametric (Wilcoxon-Mann-Whitney) differential abundance testing (columns C, D) between AdLib and CalRes groups. Columns E indicates type of parameter, i.e., whether absolute cell counts, or cell frequencies were determined. Column F denotes which cell population served as input for cluster-based analyses or was manually gated. Columns G – I provide cell subset IDs including prepended cluster numbers, manually annotated population names, and differentiation state. Columns J – L contain labels as displayed in correlation heatmap and circular chord diagrams for subset name, differentiation/antigen-experience, and lineage membership, respectively. Columns M – O indicate the top left and right immune parameters in the correlation heatmap, those selected by sparse canonical correlation analysis using the Bayesian information criterion, and sparse coefficients’ weights, respectively.

补充文件2。本数据集包含3份补充Excel文件，分别对应结肠（colon_cca_xlsx）、脾脏（spleen_cca_xlsx）与肝脏（liver_cca_xlsx），每份文件均包含4张工作表：
工作表"corr.matrix"与"corr.fdr"分别包含潜在互相关矩阵的估计系数（对应图6及补充图5的热图），以及经错误发现率（False Discovery Rate, FDR）校正后的P值。
工作表"asv.cca"针对所有扩增子序列变体（Amplicon Sequence Variants, ASVs，其排序与相关矩阵一致）提供如下内容：列C、D为基于DESeq2差异丰度分析得到的经FDR校正的P值与对数倍变化值（对应热图见图1C）；列E-K为包含7个分类层级的分类学注释表；列L为热图所用的分类群标签；列M为标注于相关热图与环形和弦图中的上下排名靠前的ASVs；列N为通过贝叶斯信息准则（Bayesian Information Criterion, BIC）进行稀疏典型相关分析筛选得到的ASVs；列O为稀疏系数权重。
工作表"imm.cca"针对对应器官中检测的所有免疫学参数（其排序与相关矩阵一致）提供如下内容：列C、D为自由采食（AdLib）组与热量限制（CalRes）组间经广义线性混合模型（Generalized Linear Mixed Model, GLMM）及非参数威尔科克森-曼-惠特尼（Wilcoxon-Mann-Whitney）检验得到的FDR校正P值；列E标注参数类型，即测定的是绝对细胞计数还是细胞频率；列F标明用于基于聚类分析或人工门控的细胞群；列G-I分别为带前置聚类编号的细胞亚群ID、人工注释的亚群名称及分化状态；列J-L分别为亚群名称、分化/抗原经历及谱系归属在相关热图与环形和弦图中所用的标签；列M-O分别为相关热图中的左上与右侧免疫参数、通过贝叶斯信息准则进行稀疏典型相关分析筛选得到的参数，以及稀疏系数权重。