Transcriptome profiling of developing murine lens through RNA sequencing

Shahid Y. Khan, Sean F. Hackett, Mei Chong W. Lee, Nader Pourmand, C. Conover Talbot, S. Amer Riazuddin

Research output: Contribution to journalArticlepeer-review

34 Scopus citations


PURPOSE. Transcriptome is the entire repertoire of transcripts present in a cell at any particular time. We undertook a next-generation whole transcriptome sequencing approach to gain insight into the transcriptional landscape of the developing mouse lens. METHODS. We ascertained mouse lenses at six developmental time points including two embryonic (E15 and E18) and four postnatal stages (P0, P3, P6, and P9). The ocular tissue at each time point was maintained as two distinct pools serving as biological replicates for each developmental stage. The mRNA and small RNA libraries were paired-end sequenced on Illumina HiSeq 2000 and subsequently analyzed using bioinformatics tools. RESULTS. Mapping of mRNA and small RNA libraries generated 187 56 and 154 22 million paired-end reads, respectively. We detected a total of 14,465 genes in the mouse ocular lens at the above-mentioned six developmental stages. Of these, 46 genes exhibited a 40-fold differential (higher or lower) expression at one the five developmental stages (E18, P0, P3, P6, and P9) compared with their expression level at E15. Likewise, small RNA profiling identified 379 microRNAs (miRNAs) expressed in mouse lens at six developmental time points. Of these, 49 miRNAs manifested an 8-fold differential (higher or lower) expression at one the five developmental stages, as mentioned above compared with their expression level at E15. CONCLUSIONS. We report a comprehensive profile of developing murine lens transcriptome including both mRNA and miRNA through next-generation RNA sequencing. A complete repository of the lens transcriptome of six developmental time points will be monumental in elucidating processes essential for the development of the ocular lens and maintenance of its transparency.

Original languageEnglish (US)
Pages (from-to)4919-4926
Number of pages8
JournalInvestigative Ophthalmology and Visual Science
Issue number8
StatePublished - 2015


  • Lens development
  • Next-generation sequencing
  • Transcriptome
  • mRNA
  • miRNA

ASJC Scopus subject areas

  • Ophthalmology
  • Sensory Systems
  • Cellular and Molecular Neuroscience


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