Supporting data for:"Integrated gene expression and alternative splicing analysis in human and mouse models of Rett Syndrome."

The folder "Homo_sapiens" contains 8 subfolders. Each of them is an individual input Bioproject downloaded from SRA and reanalized with the same transcriptomic pipeline in order to compute:1) Differentially Alternative spliced Genes (DAS) in .tsv format;2) Differentially expressed genes in csv format;3) Gene ontology analysis over DEGs results. When the analysis has produced statistically significant results for Gene Enrichment Ontology analysis, three .csv files have been added to each folder, one for BP=Biological Process results, one for CC=Cellular Component results and one for MF=Molecular Functions results.When a Bioprojects appears more than once, it means that DEGs have been computed over diffferent varibles (e.g. Rtt vs. wt) or treated as indipendent studies when multiple source materials are present. To distinguish the studies an "_0", "_1", "_2" progressive number has been added to the folder names (e.g. in PRJNA509687_0 the samples under study were iPSC derived neural cortical neurons RTT vs. Wt while in PRJNA509687_1 the samples were derived from iPSC derived neural progenitors RTT vs. Wt). To facilitate the folder navigation, a file named "parameters" has been added to each folder.4) DESeq2 inputs divided in:gene count matrices in csv formatassociated phenodata.csvThe same logic is applied to the main folder "Mus_musculus",which contains 13 subfolders with DAS and DEG results名为"Homo_sapiens（智人）"的文件夹包含8个子文件夹，每个子文件夹对应一个从SRA数据库下载的独立生物项目（Bioproject），并采用统一的转录组分析流程进行重分析，以计算以下四类结果： 1. 格式为.tsv的差异可变剪接基因（Differentially Alternative Spliced Genes, DAS）； 2. 格式为.csv的差异表达基因（Differentially Expressed Genes, DEGs）； 3. 基于DEGs结果的基因本体分析； 4. DESeq2分析输入文件，分为格式为.csv的基因计数矩阵与关联表型数据文件（phenodata.csv）。 若基因富集本体分析获得具有统计学显著性的结果，则每个子文件夹中会额外添加3个.csv文件，分别对应生物过程（Biological Process, BP）、细胞组分（Cellular Component, CC）和分子功能（Molecular Functions, MF）的富集分析结果。 当同一生物项目对应多个子文件夹时，表明针对不同变量（例如Rtt vs. wt）计算了DEGs，或当存在多种实验材料时将其视为独立研究。为区分此类研究，文件夹名称会追加递增数字后缀"_0"、"_1"、"_2"等（例如PRJNA509687_0的研究样本为诱导多能干细胞（induced Pluripotent Stem Cells, iPSC）分化而来的大脑皮层神经元，比较Rtt与野生型；而PRJNA509687_1的研究样本则为iPSC分化得到的神经前体细胞，同样比较Rtt与野生型）。 为方便文件夹导航，每个子文件夹中均添加了名为"parameters"的文件。 上述分析逻辑同样适用于主文件夹"Mus_musculus（小家鼠）"，该文件夹包含13个子文件夹，均存储有DAS与DEGs分析结果。