Transcriptome landscape of human primary monocytes at different sequencing depth
Differential gene and transcript expression pattern of human primary monocytes from healthy young subjects were profiled under different sequencing depths (50M, 100M, and 200M reads). The raw data consisted of 1.3 billion reads generated from RNA sequencing (RNA-Seq) experiments. A total of 17,657 g...
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| Format: | Article |
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Elsevier
2017
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| _version_ | 1825721232713056256 |
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| author | Mirsafian, H. Ripen, A.M. Leong, W.M. Manaharan, T. Mohamad, S.B. Merican, A.F. |
| author_facet | Mirsafian, H. Ripen, A.M. Leong, W.M. Manaharan, T. Mohamad, S.B. Merican, A.F. |
| author_sort | Mirsafian, H. |
| collection | UM |
| description | Differential gene and transcript expression pattern of human primary monocytes from healthy young subjects were profiled under different sequencing depths (50M, 100M, and 200M reads). The raw data consisted of 1.3 billion reads generated from RNA sequencing (RNA-Seq) experiments. A total of 17,657 genes and 75,392 transcripts were obtained at sequencing depth of 200M. Total splice junction reads showed an even more significant increase. Comparative analysis of the expression patterns of immune-related genes revealed a total of 217 differentially expressed (DE) protein-coding genes and 50 DE novel transcripts, in which 40 DE protein-coding genes were related to the immune system. At higher sequencing depth, more genes, known and novel transcripts were identified and larger proportion of reads were allowed to map across splice junctions. The results also showed that increase in sequencing depth has no effect on the sequence alignment. |
| first_indexed | 2024-03-06T05:47:15Z |
| format | Article |
| id | um.eprints-19095 |
| institution | Universiti Malaya |
| last_indexed | 2024-03-06T05:47:15Z |
| publishDate | 2017 |
| publisher | Elsevier |
| record_format | dspace |
| spelling | um.eprints-190952018-09-05T01:07:03Z http://eprints.um.edu.my/19095/ Transcriptome landscape of human primary monocytes at different sequencing depth Mirsafian, H. Ripen, A.M. Leong, W.M. Manaharan, T. Mohamad, S.B. Merican, A.F. Q Science (General) QH Natural history Differential gene and transcript expression pattern of human primary monocytes from healthy young subjects were profiled under different sequencing depths (50M, 100M, and 200M reads). The raw data consisted of 1.3 billion reads generated from RNA sequencing (RNA-Seq) experiments. A total of 17,657 genes and 75,392 transcripts were obtained at sequencing depth of 200M. Total splice junction reads showed an even more significant increase. Comparative analysis of the expression patterns of immune-related genes revealed a total of 217 differentially expressed (DE) protein-coding genes and 50 DE novel transcripts, in which 40 DE protein-coding genes were related to the immune system. At higher sequencing depth, more genes, known and novel transcripts were identified and larger proportion of reads were allowed to map across splice junctions. The results also showed that increase in sequencing depth has no effect on the sequence alignment. Elsevier 2017 Article PeerReviewed Mirsafian, H. and Ripen, A.M. and Leong, W.M. and Manaharan, T. and Mohamad, S.B. and Merican, A.F. (2017) Transcriptome landscape of human primary monocytes at different sequencing depth. Genomics, 109 (5-6). pp. 463-470. ISSN 0888-7543, DOI https://doi.org/10.1016/j.ygeno.2017.07.003 <https://doi.org/10.1016/j.ygeno.2017.07.003>. http://dx.doi.org/10.1016/j.ygeno.2017.07.003 doi:10.1016/j.ygeno.2017.07.003 |
| spellingShingle | Q Science (General) QH Natural history Mirsafian, H. Ripen, A.M. Leong, W.M. Manaharan, T. Mohamad, S.B. Merican, A.F. Transcriptome landscape of human primary monocytes at different sequencing depth |
| title | Transcriptome landscape of human primary monocytes at different sequencing depth |
| title_full | Transcriptome landscape of human primary monocytes at different sequencing depth |
| title_fullStr | Transcriptome landscape of human primary monocytes at different sequencing depth |
| title_full_unstemmed | Transcriptome landscape of human primary monocytes at different sequencing depth |
| title_short | Transcriptome landscape of human primary monocytes at different sequencing depth |
| title_sort | transcriptome landscape of human primary monocytes at different sequencing depth |
| topic | Q Science (General) QH Natural history |
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