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

Journal of Pineal Research
Eric ChangDavid C Klein

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 f...Continue Reading

References

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Jun 1, 2017·Proceedings of the National Academy of Sciences of the United States of America·Lue XiangZi-Bing Jin

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Methods Mentioned

BETA
Illumina sequencing

Software Mentioned

UCSC Genome Browser
trackhub Python
UCSC
deepTools
Flask
Salmon
HISAT2
FastQC
UCSC browser
Excel

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