Identification of novel transcripts and peptides in developing murine lens

Shahid Khan, Muhammad Ali, Firoz Kabir, Ruiqiang Chen, Chan-Hyun Na, Mei Chong W. Lee, Nader Pourmand, Sean F. Hackett, Sheikh Amer Riazuddin

Research output: Contribution to journalArticle

Abstract

We previously investigated the transcriptome and proteome profiles of the murine ocular lens at six developmental time points including two embryonic (E15 and E18) and four postnatal time points (P0, P3, P6, and P9). Here, we extend our analyses to identify novel transcripts and peptides in developing mouse lens. We identified a total of 9,707 novel transcripts and 325 novel fusion genes in developing mouse lens. Additionally, we identified 13,281 novel alternative splicing (AS) events in mouse lens including 6,990 exon skipping (ES), 2,447 alternative 3′ splice site (A3SS), 1,900 alternative 5′ splice site (A5SS), 1,771 mutually exclusive exons (MXE), and 173 intron retention (IR). Finally, we integrated our OMIC (Transcriptome and Proteome) datasets identifying 20 novel peptides in mouse lens. All 20 peptides were validated through matching MS/MS spectra of synthetic peptides. To the best of our knowledge, this is the first report integrating OMIC datasets to identify novel peptides in developing murine lens.

Original languageEnglish (US)
Article number11162
JournalScientific Reports
Volume8
Issue number1
DOIs
StatePublished - Dec 1 2018

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Lenses
RNA Splice Sites
Peptides
Proteome
Transcriptome
Exons
Gene Fusion
Alternative Splicing
Introns
Datasets

ASJC Scopus subject areas

  • General

Cite this

Identification of novel transcripts and peptides in developing murine lens. / Khan, Shahid; Ali, Muhammad; Kabir, Firoz; Chen, Ruiqiang; Na, Chan-Hyun; Lee, Mei Chong W.; Pourmand, Nader; Hackett, Sean F.; Riazuddin, Sheikh Amer.

In: Scientific Reports, Vol. 8, No. 1, 11162, 01.12.2018.

Research output: Contribution to journalArticle

Khan, Shahid ; Ali, Muhammad ; Kabir, Firoz ; Chen, Ruiqiang ; Na, Chan-Hyun ; Lee, Mei Chong W. ; Pourmand, Nader ; Hackett, Sean F. ; Riazuddin, Sheikh Amer. / Identification of novel transcripts and peptides in developing murine lens. In: Scientific Reports. 2018 ; Vol. 8, No. 1.
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