Gene Expression Nebulas
基于标准化流程分析的转录图谱综合数据库

Gene Expression Nebulas

多物种转录图谱整合数据库

PRJNA610586: Genome-wide profiling of age-dependent changes in gene expression between L4 larvae and Day 6 adult Caenorhabditis elegans

来源: NCBI / GSE146443
提交时间: Mar 05 2020
释放时间: Mar 06 2020
最后更新时间: May 18 2020

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

GEN 数据集:
GEND000162
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方案
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
测序信息
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
样本
基本信息:
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数据来源 GEN样本编号 GEN数据集编号 系列编号 项目编号 样本编号 样本名称 生物样本编号 样本访问号 实验访问号 释放时间 提交时间 最后更新时间 物种 种族 族裔 年龄 年龄单位 性别 来源名称 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
文章
DAF-16 and SMK-1 Contribute to Innate Immunity During Adulthood in Caenorhabditis elegans.
G3 (Bethesda, Md.) . 2020-05-04 [PMID: 32161087]