Bovine granulosa cells and oocytes cultured on plastic plate or Xanthan and Locust Bean Gum gel

Oocyte maturation is a crucial step determining oocyte quality. Polysaccharide gel made of Xanthan and Locust Bean Gum (each 0.1%/volume) is a useful culture substrate which significantly improves oocyte developmental competence. This data is RNAseq of the granulosa cells and oocytes cultured for 24 hours on plastic plate or gels. Oocyte and granulosa cells complexes (COCs) were collected from bovine antral follicles (3-5 mm in diameter) of Japanese Black Cows. Ovaries were collected at a slaughterhouse and transported to the laboratory within 4 hours. At the end of culture period (24 h), Seventy COCs were cultured on plate or gel for 24 hours and then oocytes and granulosa cells were used for RNA extraction. Three samples were created for each experimental group using differential ovary series. RNA extraction was conducted using RNAqueous-Micro (Thermo Fisher), For RNAseq, the quality and concentration of total RNA were determined using a 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). RNA quality index (RIN) was 7.7±1.1. A cDNA library of the RNA from oocytes was prepared using the SMART Seq v4 Ultra Low Input RNA Kit for Sequencing (Clontech). Concentration of the cDNA libraries were determined using Agilent high sensitivity DNA kit and Bioanalyzer 2100 (Agilent Technology). cDNA libraries of the RNA of granulosa cells were prepared using NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs). The concentration of the cDNA libraries was reassessed using Kapa library quantification kit (Kapa Biosystem). The multiplexed sample was sequenced in single-read 75 cycles on the NextSeq 500 (Illumina). Raw data were generated using bcl2fastq2 (Illumina) software, according to the manufacturer's instructions. The sequence data were filtered to discard adapter sequences, ambiguous nucleotides, and low-quality sequences.