概要: We report the application of paired-end RNA sequencing for high throughput profiling of the Xenopus transcriptome in 23 distinct developmental stages. In total, we obtained over 900 million reads and the deep coverage allowed us to examine the transcriptome in detail. First, we found that ~150 genes are transcribed before embryonic genome activation when transcription is generally thought to be repressed. Second, we discovered thousands of novel splice junctions, the majority of which modify existing gene structures. Third, we curated a confident set of 6686 non-coding transcripts in 3859 genomic loci. Many of these non-coding RNAs are also developmentally regulated, which suggests that they may play important roles during embryogenesis. Finally, we found hundreds of contigs that cannot be aligned to the reference genome, which indicates that the current genome (XenTro3) is still unfinished. Our results will aid in the full assembly and annotation of the Xenopus tropicalis genome.
项目整体设计: Examination of the transcriptome of Xenopus tropicalis from a 2-cell fertilized embryo to a stage 45 feeding tapole
The general Illumina mRNA-Seq library preparation workflow was followed with some modifications. First, polyA-containing RNAs were selected. The RNAs were then fragmented in 5X First-Strand Buffer (Invitrogen) at 85oC for 7-8 minutes. Random hexamers and SuperScript III (Invitrogen) were used to synthesize the first strand cDNA. Second strand cDNA synthesis was performed with dUTP in place of dTTP to mark the second strand. After end repair and addition of adenosine to the 3'ends, standard Illumina adapters were ligated. DNA fragments in the size range of 300 to 600bp were gel extracted and treated with UDG before each library was amplified using Phusion (Finnzymes).
测序信息
分子类型:
poly(A)+ RNA
库的片段类型:
PAIRED
库的链类型:
Forward
测序平台:
ILLUMINA
测序仪型号:
Illumina HiSeq 2000
链特异性:
Specific
样本
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样本描述:
生物条件:
实验变量:
方案:
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质量评估:
数据来源
GEN样本编号
GEN数据集编号
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物种
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组织
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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）
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平均测序片段长度_1
平均测序片段长度_2
唯一比对率
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覆盖度
文章
RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development.
