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.

Keywords: RNA-Seq; biological rhythms; neurotranscriptomics; pineal; retina; transcriptome; webpage.

Figure 1

Home page and Search subpage. A, The Home page (https://snengs.nichd.nih.gov/home) opens subpages which are organized to search for genes specifically and to retrieve information relevant to the Experiments and datasets. In addition, the Methods page contains useful information about the Bioinformatics methods and the Help page has useful videos on use of the UCSC Genome Browser. B, The Search page (https://snengs.nichd.nih.gov/search). Entering an official gene symbol or an Ensemble ID symbol in the Search box retrieves data from all species. For aliases please refer to the Ensembl or NCBI Gene databases

Figure 2

Results subpage. The results of querying a gene symbol generates a listing of the experiments and species in which the gene was found (https://snengs.nichd.nih.gov/search). Depending on the size of the gene family, multiple gene symbols may be displayed. In this case, one has to use the data cautiously. From this page, highlighted links (View) direct the user to the Gene subpage, which lists results of a single species and experiment

Figure 3

Gene subpage. An example of the gene page (https://snengs.nichd.nih.gov/species/Rat/gene/ENSRNOG00000011182#Time_Series‐anchor) that displays information about a specific gene including relevant experimental details, the UCSC track hub (Open UCSC track hub for this gene) and a help page for use of the UCSC Genome Browser. General information about each gene is available by clicking on the gene id, for example, ENSRNOG00000011182. Experimental results are displayed below in a bar graph. In addition, accessing the results of a single experiment will open other experiments dependent on availability

Figure 4

Experiments subpage. The Experiments subpage (https://snengs.nichd.nih.gov/experiments) is accessed from the Home page. It is an index for all experiments, leading to several resources. The highlighted link retrieves the Search subpage, described above. The Data link (Download) returns the data for an entire experiment in an Excel file, which also contains the average expression values and variance. Selecting Details opens the page with experimental details (see Figure 5). The highlighted link to the UCSC Track Hub (Link) gives access to the mapped data on the UCSC Genome Browser

Figure 5

Details subpages. The Details subpages are accessed from the Experiments subpage (see Figure 4; https://snengs.nichd.nih.gov/experiments) by clicking on Details for a specific experiment. This yields information on sample preparation, RNA preparation, and data processing; and, the location of archived data. The search box is used to interrogate the table with identifiers (eg, SRX3229487) or fragments of identifiers (eg, _04h) in the table. The Samples section in this Figure is truncated for presentation purposes