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

Eric Chang,Steven L Coon,Ryan Dale,Matthew Breymaier,Christopher E Mason,Caroline Esnault,Charles Wang,Adi Tovin,Jinhang Zhu,P Michael Iuvone,Margaret J Ochocinska,Pinxian Xu,Marjan Bozinoski,Samuel J Clokie,Shahar Alon,Yoav Gothilf,Diego M Bustos,Cong Fu,David C Klein

doi:10.1111/jpi.12673

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 nove gicus), 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.

Highlights

The pineal transcriptome has been studied for over 30 years, starting with Northern blot detection of single transcripts encoding proteins involved in melatonin synthesis, including those encoding Tph[1] and Asmt (Hiomt) 1-4
Genome browsers such as the UCSC Genome Browser 17 allow just this. This browser supports track hubs that allow for the configuration, coloration and organization of collections of many tracks using a web interface 18. This allows researchers to generate highly customized views tailored to their research interest, viewing pineal gland data from this study directly alongside a wealth of publicly available data prepared and made available by the UCSC team
Mixed tissue RNA samples were used in conjunction with the pineal gland and retina to estimate the enrichment of a transcript

Summary

Introduction

The pineal transcriptome has been studied for over 30 years, starting with Northern blot detection of single transcripts encoding proteins involved in melatonin synthesis, including those encoding Tph[1] and Asmt (Hiomt) 1-4. Data from earlier studies cannot be meaningfully compared with data from later studies that used different methods without completely re-processing all data uniformly using updated methods, assemblies, and annotations This has been recognized for example in the recount[2] project 16, which has re-processed tens of thousands of human RNA-Seq samples from public repositories uniformly. This browser supports track hubs that allow for the configuration, coloration and organization of collections of many tracks using a web interface 18 This allows researchers to generate highly customized views tailored to their research interest, viewing pineal gland data from this study directly alongside a wealth of publicly available data prepared and made available by the UCSC team

Methods

Results

Conclusion