Additional file 2 of Ionizing radiation responses appear incidental to desiccation responses in the bdelloid rotifer Adineta vaga

Additional file 2: Supplementary Table S1. Genes within Adineta vaga genome. The columns give the gene ids from the gene assembly in Simion et al. (2020), the correspondence gene ids in the genome published by Simion et al. (2021), if the gene is annotated as HGT, the BLAST hits, the KEGG ids, GO ids, pfam domains, the results for all analyses with DESeq2 and EdgeR, and the TPM values for all the different analyzed conditions. The columns with the results from DESeq2 and EdgeR are explained in the second table sheet. Supplementary Table S2. GO analysis of Under-Expressed genes in the core radiation response. Supplementary Table S3. Genes found over-expressed in the core common response to radiation and desiccation. The columns give the gene ids, if the gene is annotated as HGT, its hypothesized function, its function acronym, pfam domains, best BLAST hits, the results for all analyses with DESeq2 and EdgeR, and the TPM values for all the different analyzed conditions. The columns with the results from DESeq2 and EdgeR are explained in the second table sheet of Supplementary Table S1. Supplementary Table S4. Genes found over-expressed in the core rehydration response. The columns give the gene ids, if the gene is annotated as HGT, its hypothesized function, its function acronym, pfam domains, best BLAST hits, the results for all analyses with DESeq2 and EdgeR, and the TPM values for all the different analyzed conditions. The columns with the results from DESeq2 and EdgeR are explained in the second table sheet of Supplementary Table S1. Supplementary Table S5. Genes found over-expressed in the core irradiation response. The columns give the gene ids, if the gene is annotated as HGT, its hypothesized function, its function acronym, pfam domains, best BLAST hits, the results for all analyses with DESeq2 and EdgeR, and the TPM values for all the different analyzed conditions. The columns with the results from DESeq2 and EdgeR are explained in the second table sheet of Supplementary Table S1. Supplementary Table S6. List of genes coding for the defined antioxidant gene families. The columns give the gene ids, the antioxidant family, if the gene is annotated as HGT, the BLAST hits, the KEGG ids, GO ids, pfam domains, the results for all analyses with DESeq2 and EdgeR, and the TPM values for all the different analyzed conditions. The columns with the results from DESeq2 and EdgeR are explained in the second table sheet of Supplementary Table S1. Supplementary Table S7. 34 Genes coding for antioxidants exclusively significantly over-expressed in A. vaga individuals 1.5 h post rehydration after 14 days of desiccation. The columns give the gene ids, if the gene is annotated as HGT, the antioxidant family, the pfam domains, the results for all analyses with DESeq2 and EdgeR for all the different analyzed conditions. The columns with the results from DESeq2 and EdgeR are explained in the second table sheet of Supplementary Table S1. Supplementary Table S8. List of genes coding for proteins involved in DNA repair. The columns give the gene ids, if the gene is annotated as HGT, the DNA repair pathway in which the gene is involved, its hypothesized functions (acronym and description) based on BLAST hits, on the KEGG ids, GO ids, and on pfam domains, the results for all analyses with DESeq2 and EdgeR, and the TPM values for all the different analyzed conditions. The columns with the results from DESeq2 and EdgeR are explained in the second table sheet of Supplementary Table S1. Supplementary Table S9. List of genes with unknown functions but high log2foldchange and TPMs post radiation and/or desiccation. The columns give the gene ids, if the gene is annotated as HGT, its hypothesized function, its function acronym, pfam domains, best BLAST hits, the results for all analyses with DESeq2 and EdgeR, and the TPM values for all the different analyzed conditions. The columns with the results from DESeq2 and EdgeR are explained in the second table sheet of Supplementary Table S1.

附加文件2：补充表S1。光滑阿德兰轮虫（Adineta vaga）基因组内的基因。各列依次包含Simion等人2020年基因组装中的基因ID、Simion等人2021年发布的基因组中的对应基因ID、该基因是否被注释为水平基因转移（Horizontal Gene Transfer, HGT）、BLAST比对结果、KEGG编号、GO编号、pfam结构域、所有基于DESeq2与EdgeR的分析结果，以及所有不同分析条件下的转录本每百万reads（Transcripts Per Million, TPM）值。含DESeq2与EdgeR分析结果的列的说明见补充表S1的第二个工作表页签。

补充表S2：核心辐射响应中低表达基因的GO富集分析。

补充表S3：辐射与干燥核心共同响应中上调表达的基因。各列依次包含基因ID、该基因是否被注释为水平基因转移（Horizontal Gene Transfer, HGT）、推测功能、功能缩写、pfam结构域、最佳BLAST比对结果、所有基于DESeq2与EdgeR的分析结果，以及所有不同分析条件下的TPM值。含DESeq2与EdgeR分析结果的列的说明见补充表S1的第二个工作表页签。

补充表S4：核心复水响应中上调表达的基因。各列依次包含基因ID、该基因是否被注释为水平基因转移（Horizontal Gene Transfer, HGT）、推测功能、功能缩写、pfam结构域、最佳BLAST比对结果、所有基于DESeq2与EdgeR的分析结果，以及所有不同分析条件下的TPM值。含DESeq2与EdgeR分析结果的列的说明见补充表S1的第二个工作表页签。

补充表S5：核心辐照响应中上调表达的基因。各列依次包含基因ID、该基因是否被注释为水平基因转移（Horizontal Gene Transfer, HGT）、推测功能、功能缩写、pfam结构域、最佳BLAST比对结果、所有基于DESeq2与EdgeR的分析结果，以及所有不同分析条件下的TPM值。含DESeq2与EdgeR分析结果的列的说明见补充表S1的第二个工作表页签。

补充表S6：编码已定义抗氧化基因家族的基因列表。各列依次包含基因ID、抗氧化家族、该基因是否被注释为水平基因转移（Horizontal Gene Transfer, HGT）、BLAST比对结果、KEGG编号、GO编号、pfam结构域、所有基于DESeq2与EdgeR的分析结果，以及所有不同分析条件下的TPM值。含DESeq2与EdgeR分析结果的列的说明见补充表S1的第二个工作表页签。

补充表S7：34个仅在干燥14天后复水1.5小时的A. vaga个体中显著上调表达的抗氧化编码基因。各列依次包含基因ID、该基因是否被注释为水平基因转移（Horizontal Gene Transfer, HGT）、抗氧化家族、pfam结构域、所有不同分析条件下基于DESeq2与EdgeR的分析结果。含DESeq2与EdgeR分析结果的列的说明见补充表S1的第二个工作表页签。

补充表S8：编码参与DNA修复的蛋白质的基因列表。各列依次包含基因ID、该基因是否被注释为水平基因转移（Horizontal Gene Transfer, HGT）、该基因参与的DNA修复通路、基于BLAST比对结果、KEGG编号、GO编号及pfam结构域推测的功能（缩写及描述）、所有基于DESeq2与EdgeR的分析结果，以及所有不同分析条件下的TPM值。含DESeq2与EdgeR分析结果的列的说明见补充表S1的第二个工作表页签。

补充表S9：功能未知但辐射和/或干燥处理后log₂倍数变化及TPM值较高的基因列表。各列依次包含基因ID、该基因是否被注释为水平基因转移（Horizontal Gene Transfer, HGT）、推测功能、功能缩写、pfam结构域、最佳BLAST比对结果、所有基于DESeq2与EdgeR的分析结果，以及所有不同分析条件下的TPM值。含DESeq2与EdgeR分析结果的列的说明见补充表S1的第二个工作表页签。