kallisto quantifications of Frahm et al., 2017

The analysis was performed in Yi et al., 2017, which used p-value aggregation on transcript differential analysis to make gene-level determinations. For more details, see https://doi.org/10.1186/s13059-018-1419-z<br><br>We analyzed a dataset (GEO Series GSE95363) consisting of reads derived from RNA-seq on primary mouse neural progenitor cells extracted from two regions of the brain, from female and male embryonic mice, and with and without dexamethasone treatment. Three replicates were performed for each of the eight combinatorial conditions, resulting in a total of 24 single-end RNA-seq samples. Samples were quantified with kallisto v0.43.1 (default kmer length 31, with 30 bootstraps per sample), using an index constructed from Ensembl <em>Mus musculus</em> GRCm38 cDNA release 88. <br>RNA-Seq performed by:Frahm KA, Waldman JK, Luthra S, Rudine AC, Monaghan-Nichols AP, Chandran UR. A comparison of the sexually dimorphic dexamethasone transcriptome in mouse cerebral cortical and hypothalamic embryonic neural stem cells. Mol Cell Endocrinol. 2017; https://doi.org/10.1016/j.mce.2017.05.026.

本分析基于Yi等人2017年的研究，该研究在转录本差异分析中采用p值聚集法完成基因水平的判定。如需获取更多细节，请参阅https://doi.org/10.1186/s13059-018-1419-z。

本研究分析的数据集为基因表达综合数据库（Gene Expression Omnibus，GEO）系列GSE95363，其数据来源于对提取自雌雄胚胎小鼠大脑两个区域的原代神经前体细胞开展的RNA-seq测序，实验设置了地塞米松处理与未处理两种条件。针对8种组合实验条件各进行3次生物学重复，最终获得24个单端RNA-seq样本。本研究采用基于Ensembl小鼠（*Mus musculus*）GRCm38 cDNA 88版构建的索引，使用kallisto v0.43.1工具对样本进行定量分析（默认k-mer长度为31，每个样本执行30次自举采样）。

该RNA-seq实验由以下研究者完成：Frahm KA、Waldman JK、Luthra S、Rudine AC、Monaghan-Nichols AP、Chandran UR。相关研究论文题为《小鼠大脑皮层与下丘脑胚胎神经干细胞中性别二态性地塞米松转录组比较》，发表于《分子与细胞内分泌学》（*Mol Cell Endocrinol*）2017年；DOI链接：https://doi.org/10.1016/j.mce.2017.05.026。