Evaluating the impact of sequencing depth on transcriptome profiling in human adipose.
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2013-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3691247?pdf=render |
| _version_ | 1830416093277061120 |
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| author | Yichuan Liu Jane F Ferguson Chenyi Xue Ian M Silverman Brian Gregory Muredach P Reilly Mingyao Li |
| author_facet | Yichuan Liu Jane F Ferguson Chenyi Xue Ian M Silverman Brian Gregory Muredach P Reilly Mingyao Li |
| author_sort | Yichuan Liu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-20T21:18:52Z |
| format | Article |
| id | doaj.art-c457a83470c743ebbe85503fd7e6e51e |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-20T21:18:52Z |
| publishDate | 2013-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-c457a83470c743ebbe85503fd7e6e51e2022-12-21T19:26:21ZengPublic Library of Science (PLoS)PLoS ONE1932-62032013-01-0186e6688310.1371/journal.pone.0066883Evaluating the impact of sequencing depth on transcriptome profiling in human adipose.Yichuan LiuJane F FergusonChenyi XueIan M SilvermanBrian GregoryMuredach P ReillyMingyao LiRecent 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.http://europepmc.org/articles/PMC3691247?pdf=render |
| spellingShingle | Yichuan Liu Jane F Ferguson Chenyi Xue Ian M Silverman Brian Gregory Muredach P Reilly Mingyao Li Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. PLoS ONE |
| title | Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. |
| title_full | Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. |
| title_fullStr | Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. |
| title_full_unstemmed | Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. |
| title_short | Evaluating the impact of sequencing depth on transcriptome profiling in human adipose. |
| title_sort | evaluating the impact of sequencing depth on transcriptome profiling in human adipose |
| url | http://europepmc.org/articles/PMC3691247?pdf=render |
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