Bovine granulosa cells cultured on plastic dish or Xanthan and Locust been gum gel

Granulosa cells are important for oocyte growth. When oocyte and granulosa cells (OGCs) derived from early antral follicles are cultured in vitro, they form antral like cavity and enclosed oocytes grow to the levels acquiring full developmental competence. Culture conditions of the OGCs profoundly affect this process such that using a polysaccharide gel made of Xanthan and Locust been gum as a culture substrate significantly stimulates growth of the oocytes and proliferation of the granulosa cells compared with those cultured on plastic substrate. This data is RNAseq of the granulosa cells of OGCs cultured for 14 days on plastic dish or gels. OGCs were collected form bovine early antral follicles (0.5-0.7 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 (16 days), the granulosa cells were collected from OGCs formed antrum and used for RNA seq. RNA in granulosa cells were extracted using RNAqueous (Invitrogen) and the RNA quality and concentration were examined using a Bioanalyzer (Agilent technologies, Palo Alto, CA, USA). Library quality and quantity were determined using the Agilent 2100 Bioanalyzer and the KAPA Library Quantification Kit (KAPA Biosystems, Wilmington, MA, USA), respectively. Clusters were generated on a cBot (Illumina), and one lane of the multiplied samples was sequenced as 75 bp reads (single read) on the NextSeq (Illumina). Image analysis, base calling and quality filtering were performed using the bcl2fastq2 v2.18.0.12 (Illumina) following the manufacturer's instructions. Sequence data were filtered to discard the adapter sequence, ambiguous nucleotides and low-quality sequences. The remaining sequence data were aligned to the Bos Taurus genome sequence (ARS-UCD1.2/bosTau9) to count sequence reads.

颗粒细胞（granulosa cells）对卵母细胞（oocyte）生长至关重要。当从早期窦状卵泡（early antral follicles）分离得到的卵母细胞与颗粒细胞（OGCs）进行体外培养时，会形成类似窦腔的结构，包裹其中的卵母细胞可生长至具备完全发育潜能的阶段。OGCs的培养条件对该过程影响显著：与塑料基质培养组相比，以黄原胶（Xanthan）和刺槐豆胶（Locust bean gum，原文笔误为been）配制的多糖凝胶作为培养底物，可显著促进卵母细胞生长与颗粒细胞增殖。本数据集为在塑料培养皿或多糖凝胶中培养14天后的OGCs颗粒细胞的RNA测序（RNA-seq）数据。OGCs取自日本和牛（Japanese Black Cows）直径为0.5~0.7 mm的早期窦状卵泡。实验用卵巢采集自屠宰场，并在4小时内运送至实验室。在培养周期（16天）结束时，从形成窦腔的OGCs中分离颗粒细胞用于RNA测序。采用RNAqueous试剂盒（Invitrogen）提取颗粒细胞总RNA，并使用生物分析仪（Agilent Technologies，美国加利福尼亚州帕洛阿尔托）检测RNA的质量与浓度。分别使用Agilent 2100生物分析仪与KAPA文库定量试剂盒（KAPA Biosystems，美国马萨诸塞州威尔明顿）评估文库的质量与浓度。在cBot系统（Illumina）上生成测序簇，随后在NextSeq测序平台（Illumina）上以单端75 bp读长对多重扩增后的样本进行单泳道测序。依照厂商操作指南，使用bcl2fastq2 v2.18.0.12（Illumina）完成图像分析、碱基识别与质量过滤流程。对测序数据进行过滤，去除接头序列、模糊碱基与低质量序列；将保留的序列比对至牛（Bos taurus）参考基因组序列（ARS-UCD1.2/bosTau9）以统计序列读段数目。