Decode-seq: a practical approach to improve differential gene expression analysis
Abstract Many differential gene expression analyses are conducted with an inadequate number of biological replicates. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling of a large number of replicates simultaneously. This approach significantly improves...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
BMC
2020-03-01
|
| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-020-01966-9 |
| _version_ | 1819028417538949120 |
|---|---|
| author | Yingshu Li Hang Yang Hujun Zhang Yongjie Liu Hanqiao Shang Herong Zhao Ting Zhang Qiang Tu |
| author_facet | Yingshu Li Hang Yang Hujun Zhang Yongjie Liu Hanqiao Shang Herong Zhao Ting Zhang Qiang Tu |
| author_sort | Yingshu Li |
| collection | DOAJ |
| description | Abstract Many differential gene expression analyses are conducted with an inadequate number of biological replicates. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling of a large number of replicates simultaneously. This approach significantly improves the performance of differential gene expression analysis. Using this approach in medaka (Oryzias latipes), we discover novel genes with sexually dimorphic expression and genes necessary for germ cell development. Our results also demonstrate why the common practice of using only three replicates in differential gene expression analysis should be abandoned. |
| first_indexed | 2024-12-21T05:58:02Z |
| format | Article |
| id | doaj.art-3f3de81434f246bf9af626c7755a8658 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-21T05:58:02Z |
| publishDate | 2020-03-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-3f3de81434f246bf9af626c7755a86582022-12-21T19:13:49ZengBMCGenome Biology1474-760X2020-03-012111710.1186/s13059-020-01966-9Decode-seq: a practical approach to improve differential gene expression analysisYingshu Li0Hang Yang1Hujun Zhang2Yongjie Liu3Hanqiao Shang4Herong Zhao5Ting Zhang6Qiang Tu7State Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of SciencesState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of SciencesState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of SciencesState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of SciencesState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of SciencesState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of SciencesState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of SciencesState Key Laboratory of Molecular Developmental Biology, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of SciencesAbstract Many differential gene expression analyses are conducted with an inadequate number of biological replicates. We describe an easy and effective RNA-seq approach using molecular barcoding to enable profiling of a large number of replicates simultaneously. This approach significantly improves the performance of differential gene expression analysis. Using this approach in medaka (Oryzias latipes), we discover novel genes with sexually dimorphic expression and genes necessary for germ cell development. Our results also demonstrate why the common practice of using only three replicates in differential gene expression analysis should be abandoned.http://link.springer.com/article/10.1186/s13059-020-01966-9Differential expressionRNA-seqReplicationMedakaGerm cell |
| spellingShingle | Yingshu Li Hang Yang Hujun Zhang Yongjie Liu Hanqiao Shang Herong Zhao Ting Zhang Qiang Tu Decode-seq: a practical approach to improve differential gene expression analysis Genome Biology Differential expression RNA-seq Replication Medaka Germ cell |
| title | Decode-seq: a practical approach to improve differential gene expression analysis |
| title_full | Decode-seq: a practical approach to improve differential gene expression analysis |
| title_fullStr | Decode-seq: a practical approach to improve differential gene expression analysis |
| title_full_unstemmed | Decode-seq: a practical approach to improve differential gene expression analysis |
| title_short | Decode-seq: a practical approach to improve differential gene expression analysis |
| title_sort | decode seq a practical approach to improve differential gene expression analysis |
| topic | Differential expression RNA-seq Replication Medaka Germ cell |
| url | http://link.springer.com/article/10.1186/s13059-020-01966-9 |
| work_keys_str_mv | AT yingshuli decodeseqapracticalapproachtoimprovedifferentialgeneexpressionanalysis AT hangyang decodeseqapracticalapproachtoimprovedifferentialgeneexpressionanalysis AT hujunzhang decodeseqapracticalapproachtoimprovedifferentialgeneexpressionanalysis AT yongjieliu decodeseqapracticalapproachtoimprovedifferentialgeneexpressionanalysis AT hanqiaoshang decodeseqapracticalapproachtoimprovedifferentialgeneexpressionanalysis AT herongzhao decodeseqapracticalapproachtoimprovedifferentialgeneexpressionanalysis AT tingzhang decodeseqapracticalapproachtoimprovedifferentialgeneexpressionanalysis AT qiangtu decodeseqapracticalapproachtoimprovedifferentialgeneexpressionanalysis |