PRJNA610586: Genome-wide profiling of age-dependent changes in gene expression between L4 larvae and Day 6 adult Caenorhabditis elegans
概要: The objective of this study was to identify genes whose expression changes significantly between the L4 larval stage (Day 0 of adulthood) and the sixth day of adulthood (Day 6) in C. elegans.
项目整体设计: Transcriptomic analysis of age-related changes in gene expression were identified by isolating RNA from L4 and Day 6 adult wild type N2 Caenorhabditis elegans. After rRNA depletion, RNA was sequenced on the Illumina HiSeq platform and changes in expression identified by DESeq2 analysis
| 生长方案: |
Wild type N2 animals were synchronized by sodium hypochlorite treatment and dropped as L1 larvae to NGM RNAi plates containing 2mM IPTG, 100 mg/mL carbenicillin and seeded with E. coli strain HT115 harboring the L4440 plasmid (vector only control for feeding-based RNAi experiments). Animals were maintained on these plates at 20˚C until the L4 larval stage when half of the cohort was harvested for total RNA (brief description to follow). The other half of the cohort was transferred to new NGM RNAi plates containing 2mM IPTG, 100 mg/mL carbenicillin, 25ug/mL FUDR and seeded with E. coli strain HT115 harboring the L4440 plasmid. C. elegans were maintained on these plates at 20˚C until they reached the sixth day of adulthood when they were harvested for total RNA |
| 处理方案: |
- |
| 提取方案: |
Worms were harvested from plates in M9 buffer, pelleted, then resuspended in Trizol. After a phenol-chloroform extraction, total RNA was precipitated in isopropanol, washed with ethanol, and resuspended in H2O. RNA was then treated with DNase, cleaned up using a Qiagen RNeasy column, and eluted in H2O. |
| 建库方案: |
RNA libraries were prepared for sequencing using standard Illumina protocols |
| 分子类型: |
rRNA- RNA |
| 库的片段类型: |
SINGLE |
| 库的链类型: |
Forward |
| 测序平台: |
ILLUMINA |
| 测序仪型号: |
Illumina HiSeq 2500 |
| 链特异性: |
Specific |
| 数据来源 |
GEN样本编号 |
GEN数据集编号 |
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样本名称 |
生物样本编号 |
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物种 |
种族 |
族裔 |
年龄 |
年龄单位 |
性别 |
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组织 |
细胞类型 |
细胞亚型 |
细胞系 |
疾病 |
疾病状态 |
发育阶段 |
突变/变异 |
表型 |
Condition Detail |
生长方案 |
处理方案 |
提取方案 |
建库方案 |
分子类型 |
库的片段类型 |
链特异性 |
库的链类型 |
加标(Spike-In) |
测序方法 |
测序平台 |
测序仪型号 |
细胞数 |
测序片段数 |
碱基数 |
平均测序片段长度_1 |
平均测序片段长度_2 |
唯一比对率 |
多重比对率 |
覆盖度 |
DAF-16 and SMK-1 Contribute to Innate Immunity During Adulthood in Caenorhabditis elegans.
G3 (Bethesda, Md.) . 2020-05-04 [PMID:
32161087]