Raw fragment counts of RNA sequencing from single oocytes

Pair end sequencing data were produced from five single oocytes following the procedures described in Biase (2021). Sequences were aligned with Hisat2 (Kim et al., 2015; Kim et al., 2019; Pertea et al., 2016), followed by filtering with samtools (Li et al., 2009) (remove unmapped reads, secondary alignments, failing of platform quality checks, PCR or optical duplicate) and removal of duplicates with the function ‘bammarkduplicates’ from biobambam (Tischler and Leonard, 2014). Sorting and indexing were done with Picard (http://broadinstitute.github.io/picard/). Finally, fragments were counted with ‘featurecounts’ (Liao et al., 2014) using the Ensembl (Flicek et al., 2014; Kinsella et al., 2011) bovine annotation as a guide.本研究遵循Biase（2021）所述的实验流程，对5枚单个卵母细胞获取了双端测序（Pair end sequencing）数据。测序序列首先经Hisat2（Kim等，2015；Kim等，2019；Pertea等，2016）完成比对，随后使用Samtools（Li等，2009）进行过滤，移除未比对读段、次级比对结果、未通过平台质量检测的序列以及PCR或光学重复序列；再借助biobambam工具包中的“bammarkduplicates”函数去除重复序列（Tischler和Leonard，2014）。后续使用Picard工具（http://broadinstitute.github.io/picard/）完成序列排序与索引构建。最后，采用featureCounts（Liao等，2014）工具，并以Ensembl（Flicek等，2014；Kinsella等，2011）数据库的牛基因组注释文件作为参考指南，完成片段计数。