SMART-Seq of untreated and auxin-treated blastocysts for OGT degradation

Zygotes were recovered from crosses of OgtAID/WT females with OsTIR-homozygous males and cultured ex vivo for 72 hours in standard culture conditions, then the morulae were divided in two groups and one was treated with 250 ?M auxin for 24 hours. After that, all blastocysts were collected for single embryo mRNA-Seq. The 119 blastocysts in the sequencing library come from five replicates of breeding-treatment-collection. Then, cDNA library was prepared from all of them at the same time and they were all pooled in the same run of a NextSeq500 (75 bp SE mode). Sex and genotype of the embryos was identified in silico from the sequencing data (see paper Methods).