Expression data from C. elegans during L3 and L3-lethargus. Caenorhabditis elegans

To identify genes differentially expressed during L3 lethargus, we collected RNA during the third larval stage (L3) lethargus period, 37 hours after feeding developmentally-arrested L1 animals. Animals in lethargus were identified based on quiescence of locomotion and feeding. Additional time point for RNA collection was in the mid-L3 stage, 32 hours after feeding developmentally-arrested L1 animals. These samples were interrogated with the Affymetrix C. elegans Genome Array. A total of 153 gene transcripts were up regulated, and 48 gene transcripts were down regulated, during the L3 lethargus period compared to the L3 stage (false discovery rate (FDR) < 0.05). Overall design: There were 2 groups and 3x replication for each group, for 6 total samples. The groups were (1) L3 and (2) L3-lethargus. We compared L3-lethargus vs L3 using R/maanova. The permutation based p-values for each test were significant for FDR≤5%.

为鉴定L3眠期（L3 lethargus）期间的差异表达基因，我们在喂食发育停滞的L1期线虫幼虫后37小时，于第三幼虫期（L3）眠期时段采集了RNA样本。研究人员通过运动与摄食静止状态鉴定处于眠期的线虫个体。另一RNA采集时间点为L3中期，即喂食发育停滞的L1期线虫幼虫后32小时。本研究采用Affymetrix秀丽隐杆线虫基因组芯片（Affymetrix C. elegans Genome Array）对上述样本进行表达谱检测。相较于L3期样本，L3眠期样本中共鉴定出153个上调基因转录本、48个下调基因转录本（错误发现率（False Discovery Rate，FDR）<0.05）。
实验设计概况：共设置2组样本，每组设置3次生物学重复，总计6个样本。两组分别为（1）L3期组与（2）L3眠期组。我们采用R/maanova软件包对L3眠期组与L3期组进行差异表达分析。基于置换检验得到的各检验P值均满足错误发现率（FDR）≤5%的显著性要求。