دورية أكاديمية
Evaluating the Impact of Sequencing Depth on Transcriptome Profiling in Human Adipose.
| العنوان: | Evaluating the Impact of Sequencing Depth on Transcriptome Profiling in Human Adipose. |
|---|---|
| المؤلفون: | Liu, Yichuan, Ferguson, Jane F., Xue, Chenyi, Silverman, Ian M., Gregory, Brian, Reilly, Muredach P., Li, Mingyao |
| المصدر: | PLoS ONE; Jun2013, Vol. 8 Issue 6, p1-10, 10p |
| مصطلحات موضوعية: | FAT cells, NUCLEOTIDE sequence, HEART metabolism disorders, COMPUTATIONAL biology, MOLECULAR genetics, CARDIOVASCULAR diseases, GENE expression |
| مستخلص: | Recent advances in RNA sequencing (RNA-Seq) have enabled the discovery of novel transcriptomic variations that are not possible with traditional microarray-based methods. Tissue and cell specific transcriptome changes during pathophysiological stress in disease cases versus controls and in response to therapies are of particular interest to investigators studying cardiometabolic diseases. Thus, knowledge on the relationships between sequencing depth and detection of transcriptomic variation is needed for designing RNA-Seq experiments and for interpreting results of analyses. Using deeply sequenced Illumina HiSeq 2000 101 bp paired-end RNA-Seq data derived from adipose of a healthy individual before and after systemic administration of endotoxin (LPS), we investigated the sequencing depths needed for studies of gene expression and alternative splicing (AS). In order to detect expressed genes and AS events, we found that ∼100 to 150 million (M) filtered reads were needed. However, the requirement on sequencing depth for the detection of LPS modulated differential expression (DE) and differential alternative splicing (DAS) was much higher. To detect 80% of events, ∼300 M filtered reads were needed for DE analysis whereas at least 400 M filtered reads were necessary for detecting DAS. Although the majority of expressed genes and AS events can be detected with modest sequencing depths (∼100 M filtered reads), the estimated gene expression levels and exon/intron inclusion levels were less accurate. We report the first study that evaluates the relationship between RNA-Seq depth and the ability to detect DE and DAS in human adipose. Our results suggest that a much higher sequencing depth is needed to reliably identify DAS events than for DE genes. [ABSTRACT FROM AUTHOR] |
| Copyright of PLoS ONE is the property of Public Library of Science and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| قاعدة البيانات: | Complementary Index |
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