Transcriptomic Profiling of Hamster Gonads

The RNA-seq library in oocytes was prepared using the SMART-Seq® Stranded Kit (TaKaRa, 634442). Total RNAs obtained using NucleoSpin® RNA Plus XS (TaKaRa, 740990) from approximately 100 oocytes were fragmented at 85°C for 6 min. Sheared RNAs were processed under the ‘Low input category.’ PCR1 was performed with 5 cycles, followed by PCR2 with 13 cycles, and the final cleanup was performed once. RNA-seq libraries in the ovary and testis were prepared using the TruSeq Stranded mRNA Sample Prep kit. The libraries were sequenced using HiSeq2000 (Illumina) and the obtained reads were combined, resulting in a total of 79 152 300 pair-end reads for hamster testis and 81 979 150 pair-end reads for hamster ovary, respectively. Reads with trimming adaptors and quality filtering were mapped to the hamster reference genome (hamster.sequel.draft-20200302.arrow.fasta) using hisat2 version 2.2.0 (67 (link)) with the strandness option (–strandness FR). To calculate transcripts per kilobase million mapped (TPM) as expression levels of genes, we used StringTie version 2.1.3 (68 (link)).