The polyadenylation landscape after in vivo long-term potentiation in the rat brain

Supplementary Table 1. Summary of dentate gyri DRS data per gene. (A) Differential expression and differential adenylation data for 10 min timepoint. (B) Differential expression and differential adenylation data for 60 min timepoint. (C) GO-terms for genes with significantly elongated poly(A) tails in 10 min timepoint. (D) GO-terms for genes with significantly elongated poly(A) tails in 60 min timepoint. (E) GO-terms for upregulated genes in 10 min timepoint. (F) GO-terms for upregulated genes in 60 min timepoint. (G) GO-terms for upregulated genes with CPEB-binding motifs in 10 min timepoint. (H) GO-terms for upregulated genes with CPEB-binding motifs in 60 min timepoint. Supplementary Table 2. Summary of dentate gyri cDNA data per gene. (A) Differential expression and differential adenylation data for 10 min timepoint. (B) Differential expression and differential adenylation data for 60 min timepoint. (C) GO-terms for genes with significantly elongated poly(A) tails in 10 min timepoint. (D) GO-terms for genes with significantly elongated poly(A) tails in 60 min timepoint. (E) GO-terms for upregulated genes in 10 min timepoint. (F) GO-terms for upregulated genes in 60 min timepoint. (G) GO-terms for upregulated genes with CPEB-binding motifs in 10 min timepoint. (H) GO-terms for upregulated genes with CPEB-binding motifs in 60 min timepoint. Supplementary Table 3. High-confidence PASs. (A) PASs predicted for datasets obtained 10 min after LTP induction by TAPAS. (B) High confidence poly(A) clusters predicted by LAPA for datasets obtained 10 min after LTP induction. (C) PASs predicted for datasets obtained 60 min after LTP induction. (D) High confidence poly(A) clusters predicted by LAPA for datasets obtained 60 min after LTP induction. Supplementary Table 4. Nonadenosine profiling upon LTP induction. (A) Summary of Ninetails pipeline for dentate gyrus. (B) List of genes containing semi-templated poly(A) tails with their 3′UTR coordinates. Supplementary Table 5. Summary of synaptoneurosomal DRS data per gene. Differential expression and differential adenylation data. Supplementary Table 6. Characteristics of analyzed material. Detailed information with sequencing depth, accession numbers, software used for analyses, and additional data characteristics. Supplementary Resource High-confidence poly(A) clusters annotation in bed format.补充表1. 各基因齿状回直接RNA测序（Direct RNA Sequencing, DRS）数据汇总。(A) 10分钟时间点的差异表达与差异腺苷酸化数据。(B) 60分钟时间点的差异表达与差异腺苷酸化数据。(C) 10分钟时间点中多聚腺苷酸（poly(A)）尾显著延长的基因对应的基因本体（Gene Ontology, GO）术语。(D) 60分钟时间点中多聚腺苷酸尾显著延长的基因对应的基因本体术语。(E) 10分钟时间点中上调基因对应的基因本体术语。(F) 60分钟时间点中上调基因对应的基因本体术语。(G) 10分钟时间点中带有胞质多聚腺苷酸化元件结合蛋白（Cytoplasmic Polyadenylation Element Binding Protein, CPEB）结合基序的上调基因对应的基因本体术语。(H) 60分钟时间点中带有CPEB结合基序的上调基因对应的基因本体术语。 补充表2. 各基因齿状回互补DNA（complementary DNA, cDNA）数据汇总。(A) 10分钟时间点的差异表达与差异腺苷酸化数据。(B) 60分钟时间点的差异表达与差异腺苷酸化数据。(C) 10分钟时间点中多聚腺苷酸尾显著延长的基因对应的基因本体术语。(D) 60分钟时间点中多聚腺苷酸尾显著延长的基因对应的基因本体术语。(E) 10分钟时间点中上调基因对应的基因本体术语。(F) 60分钟时间点中上调基因对应的基因本体术语。(G) 10分钟时间点中带有CPEB结合基序的上调基因对应的基因本体术语。(H) 60分钟时间点中带有CPEB结合基序的上调基因对应的基因本体术语。 补充表3. 高置信度多聚腺苷酸化信号位点（Polyadenylation Signal Sites, PASs）汇总。(A) 由TAPAS预测的长时程增强（Long-Term Potentiation, LTP）诱导10分钟后获得的数据集对应的PASs。(B) 由LAPA预测的长时程增强诱导10分钟后获得的数据集对应的高置信度多聚腺苷酸簇。(C) 长时程增强诱导60分钟后获得的数据集对应的PASs。(D) 由LAPA预测的长时程增强诱导60分钟后获得的数据集对应的高置信度多聚腺苷酸簇。 补充表4. 长时程增强诱导后的非腺苷酸修饰分析。(A) 齿状回Ninetails分析流程汇总。(B) 含有半模板型多聚腺苷酸尾的基因列表及其3'非翻译区（3' Untranslated Region, 3'UTR）坐标信息。 补充表5. 各基因突触体DRS数据汇总，包含差异表达与差异腺苷酸化数据。 补充表6. 分析样本的特征信息，包含测序深度、登录号、分析所用软件及其他数据特征的详细信息。 补充资源：BED格式（Browser Extensible Data format）的高置信度多聚腺苷酸簇注释文件。