Transcriptomic analyses of a Cyberlindnera jadinii strain (NBRC0988) grown in glucose and xylose

Strand-specific RNA-seq libraries were constructed for two samples, including (I) wild-type strain NBRC0988 grown in YEP medium containing 2% w/v glucose;(II) wild-type strain NBRC0988 grown in YEP medium containing 2% w/v xylose. For preparation of RNA samples, NBRC0988 cells grown overnight were inoculated into 100 ml liquid Yeast Extract Peptone Dextrose (YEPD) medium with the initial inoculation amount of OD600= 0.1, and cultured for 15 hours at 30℃ and 250 rpm. The cells were collected by centrifugation at 6,000g for 5 minutes. After washing twice with phosphate buffer saline (PBS), they were inoculated into new 100 mL YEP medium containing 2% w/v glucose or xylose.After flask culturing at 30°C and 250 rpm for an additional 5 hours, the yeast cells were collected by centrifugation for total RNA isolation and Illumina RNA-seq library construction. Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The 150-nt paired-end strand-specific RNA-seq libraries (SS_lib_type RF) were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s novaseq 6000 platform (Illumina, San Diego, USA). RNA profiles of C. jadinii wild-type strain NBRC0988 grown in YEP medium containing 2% w/v glucose or xylose were generated by deep sequencing, using Illumina’s novaseq 6000 platform

本研究针对两组样本构建了链特异性RNA测序（strand-specific RNA-seq）文库，两组样本具体为：(I) 于含2%质量体积比葡萄糖的YEP培养基中培养的野生型菌株NBRC0988；(II) 于含2%质量体积比木糖的YEP培养基中培养的野生型菌株NBRC0988。
样本RNA制备流程如下：将过夜培养的NBRC0988菌株接种至100 mL液体酵母提取物蛋白胨葡萄糖（Yeast Extract Peptone Dextrose, YEPD）培养基中，初始接种浊度OD₆₀₀为0.1，于30℃、250 rpm条件下培养15小时。以6000g离心5分钟收集菌体，经磷酸盐缓冲液（Phosphate Buffered Saline, PBS）洗涤两次后，转接至含2%质量体积比葡萄糖或木糖的新鲜100 mL YEP培养基中。于30℃、250 rpm条件下继续振荡培养5小时后，离心收集酵母菌体，用于总RNA提取及Illumina RNA测序文库构建。
样本总RNA采用TRIzol试剂（美国Grand Island Invitrogen公司）提取，随后用于高通量RNA测序。本研究委托中国天津诺禾致源生物科技有限公司，基于Illumina NovaSeq 6000测序平台（美国San Diego Illumina公司），商业化构建了长度为150 nt的双端链特异性RNA测序文库（SS_lib_type RF）。本研究通过Illumina NovaSeq 6000平台开展深度测序，获得了在含2%质量体积比葡萄糖或木糖的YEP培养基中培养的雅罗假丝酵母（C. jadinii）野生型菌株NBRC0988的转录组图谱。