Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina

• Type of Material: Article
• Authors: Eric Chang, Eunice Kennedy Shriver National Institute of Child Health and Human Development; Cong Fu, Eunice Kennedy Shriver National Institute of Child Health and Human Development; Steven L. Coon, Eunice Kennedy Shriver National Institute of Child Health and Human Development; Shahar Alon, Tel Aviv University; Marjan Bozinoski, Weill Cornell Medical College; Matthew Breymaier, Eunice Kennedy Shriver National Institute of Child Health and Human Development; Diego M. Bustos, Eunice Kennedy Shriver National Institute of Child Health and Human Development; Samuel J. Clokie, Eunice Kennedy Shriver National Institute of Child Health and Human Development; Yoav Gothilf, Tel Aviv University; Caroline Esnault, Eunice Kennedy Shriver National Institute of Child Health and Human Development; P Michael Iuvone, Emory University; Christopher E. Mason, Weill Cornell Medical College; Margaret J. Ochocinska, Eunice Kennedy Shriver National Institute of Child Health and Human Development; Adi Tovin, Tel Aviv University; Charles Wang, Loma Linda University; Pinxian Xu, Mount Sinai School of Medicine; Jinhang Zhu, Federal Drug Administration; Ryan Dale, Eunice Kennedy Shriver National Institute of Child Health and Human Development; David C. Klein, Eunice Kennedy Shriver National Institute of Child Health and Human Development
• Language: English
• Date: 2020-07-08
• Publisher: WILEY
• Publication Version: Final Published Version
• Copyright Statement: © 2020 The Authors. Journal of Pineal Research published by John Wiley & Sons Ltd
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1111/jpi.12673
• Title of Journal or Parent Work: JOURNAL OF PINEAL RESEARCH
• Volume: 69
• Issue: 3
• Start Page: e12673
• End Page: e12673
• Keywords: pineal; biological rhythms; Physiology; SEQUENCE; TRYPTOPHAN-HYDROXYLASE; Neurosciences; transcriptome; RNAS; Science & Technology; retina; EVOLUTION; RNA-Seq; AANAT; GENE; Endocrinology & Metabolism; MELATONIN SYNTHESIS; Life Sciences & Biomedicine; Neurosciences & Neurology; neurotranscriptomics; CDNA; webpage; ARYLALKYLAMINE N-ACETYLTRANSFERASE
• Research Categories: Biology, Physiology; Biology, Genetics; Biology, Neuroscience

Abstract

The website and database https://snengs.nichd.nih.gov provides RNA sequencing data from multi-species analysis of the pineal glands from zebrafish (Danio rerio), chicken (White Leghorn), rat (Rattus novegicus), mouse (Mus musculus), rhesus macaque (Macaca mulatta), and human (Homo sapiens); in most cases, retinal data are also included along with results of the analysis of a mixture of RNA from tissues. Studies cover day and night conditions; in addition, a time series over multiple hours, a developmental time series and pharmacological experiments on rats are included. The data have been uniformly re-processed using the latest methods and assemblies to allow for comparisons between experiments and to reduce processing differences. The website presents search functionality, graphical representations, Excel tables, and track hubs of all data for detailed visualization in the UCSC Genome Browser. As more data are collected from investigators and improved genomes become available in the future, the website will be updated. This database is in the public domain and elements can be reproduced by citing the URL and this report. This effort makes the results of 21st century transcriptome profiling widely available in a user-friendly format that is expected to broadly influence pineal research.