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

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

Bibliographical note

Publisher Copyright:
© 2020 The Authors. Journal of Pineal Research published by John Wiley & Sons Ltd

Funding

The authors wish to express their appreciation for discussion and testing services provided by Apratim Mitra and Sydney Hertafeld of the Bioinformatics and Scientific Programming Core, Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). The authors also want to acknowledge the contributions of the following: David “Dr J.” Jacobowitz, Collaborative Health Initiative Research Program, Uniformed Services University of the Health Sciences; Stephen W. Hartley and James C. Mullikin, National Human Genome Research Institute, National Institutes of Health; Leming Shi, United States Food and Drug Administrations, National Center for Toxicological Research and the School of Basic Medical Sciences, Anhui Medical University, Hefei; and, Artem Zykovich, NICHD. This work utilized the computational resources of the NIH HPC Biowulf cluster (http://hpc.nih.gov).

Funders	Funder number
Anhui Medical University, Hefei
Artem Zykovich
National Institutes of Health
National Human Genome Research Institute
National Institute of Child Health and Human Development	ZICHD008986
Uniformed Services University of the Health Sciences
Eunice Kennedy Shriver National Institute of Child Health and Human Development

Keywords

RNA-Seq
biological rhythms
neurotranscriptomics
pineal
retina
transcriptome
webpage

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10.1111/jpi.12673

Cite this

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

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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",

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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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AU - Clokie, Samuel J.

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AU - Esnault, Caroline

AU - Michael Iuvone, P.

AU - Mason, Christopher E.

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

Abstract

Bibliographical note

Funding

Keywords

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