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

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

doi:10.1111/jpi.12673

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

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

^*Corresponding author for this work

Department of Neurobiology

Research output: Contribution to journal › Article › peer-review

13 Scopus citations

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.

Original language	English
Article number	e12673
Journal	Journal of Pineal Research
Volume	69
Issue number	3
DOIs	https://doi.org/10.1111/jpi.12673
State	Published - 1 Oct 2020

Keywords

RNA-Seq
biological rhythms
neurotranscriptomics
pineal
retina
transcriptome
webpage

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10.1111/jpi.12673

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Chang, E., Fu, C., Coon, S. L., Alon, S., Bozinoski, M., Breymaier, M., Bustos, D. M., Clokie, S. J., Gothilf, Y., Esnault, C., Michael Iuvone, P., Mason, C. E., Ochocinska, M. J., Tovin, A., Wang, C., Xu, P., Zhu, J., Dale, R., & Klein, D. C. (2020). Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina. Journal of Pineal Research, 69(3), Article e12673. https://doi.org/10.1111/jpi.12673

@article{417dfaa206a34685bc1bc27f3277c580,

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

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.",

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

note = "Publisher Copyright: {\textcopyright} 2020 The Authors. Journal of Pineal Research published by John Wiley & Sons Ltd",

year = "2020",

month = oct,

day = "1",

doi = "10.1111/jpi.12673",

language = "אנגלית",

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Chang, E, Fu, C, Coon, SL, Alon, S, Bozinoski, M, Breymaier, M, Bustos, DM, Clokie, SJ, Gothilf, Y, Esnault, C, Michael Iuvone, P, Mason, CE, Ochocinska, MJ, Tovin, A, Wang, C, Xu, P, Zhu, J, Dale, R & Klein, DC 2020, 'Resource: A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina', Journal of Pineal Research, vol. 69, no. 3, e12673. https://doi.org/10.1111/jpi.12673

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T2 - A multi-species multi-timepoint transcriptome database and webpage for the pineal gland and retina

AU - Chang, Eric

AU - Fu, Cong

AU - Coon, Steven L.

AU - Alon, Shahar

AU - Bozinoski, Marjan

AU - Breymaier, Matthew

AU - Bustos, Diego M.

AU - Clokie, Samuel J.

AU - Gothilf, Yoav

AU - Esnault, Caroline

AU - Michael Iuvone, P.

AU - Mason, Christopher E.

AU - Ochocinska, Margaret J.

AU - Tovin, Adi

AU - Wang, Charles

AU - Xu, Pinxian

AU - Zhu, Jinhang

AU - Dale, Ryan

AU - Klein, David C.

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KW - biological rhythms

KW - neurotranscriptomics

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KW - retina

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

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