title: Transcriptome Profiling of Developing Murine Lens Through RNA Sequencing.
abstract: OBJECTIVE
  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.
authors.affiliation: The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.
authors.forename: Shahid Y
authors.initials: SY
authors.lastname: Khan
authors.affiliation: The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.
authors.forename: Sean F
authors.initials: SF
authors.lastname: Hackett
authors.affiliation: Departpart of Biomolecular Engineering, University of California, Santa Cruz, California, United States.
authors.forename: Mei-Chong W
authors.initials: MC
authors.lastname: Lee
authors.affiliation: Departpart of Biomolecular Engineering, University of California, Santa Cruz, California, United States.
authors.forename: Nader
authors.initials: N
authors.lastname: Pourmand
authors.affiliation: Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.
authors.forename: C Conover
authors.initials: CC
authors.lastname: Talbot
authors.affiliation: The Wilmer Eye Institute, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States.
authors.forename: S Amer
authors.initials: SA
authors.lastname: Riazuddin
mesh_terms: D000818:Animals; D000831:Animals, Newborn; D002386:Cataract / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D019295:Computational Biology / Q000379:methods*; D004195:Disease Models, Animal; D005260:Female; D020869:Gene Expression Profiling / Q000379:methods*; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D007908:Lens, Crystalline / Q000378:metabolism* / Q000473:pathology; D051379:Mice; D038081:Organogenesis / Q000235:genetics*; D011247:Pregnancy; D011270:Pregnancy, Animal; D012333:RNA, Messenger / Q000235:genetics* / Q000378:metabolism
chemical_list: D012333:RNA, Messenger