README: ErythronDB Database

https://doi.org/10.5061/dryad.2bvq83bwq

The Erythron Database (ErythronDB) was a resource dedicated to facilitating better understanding of the cellular and molecular underpinnings of mammalian erythropoiesis. For more information about this project, please visit https://cstoeckert.github.io/past-projects/ErythronDB.html.

The project has been retired, but users can deploy the website and paired-database on their own systems using Docker and the ErythronDB-docker build, available freely on GitHub.

Description of the data and file structure

This dataset is the database that powers the ErythrondDB website, which is required to deploy the containerized website:

• erythrondb.sql.gz - a gzipped PostgreSQL database dump

Also included are the following files:

• md5sums.txt - md5sum file for the database dump file
• web-db-creds.txt - credentials required for the website to access the database. If planning to deploy publicly\, these should be changed.

Sharing/Access information

Any publications referencing ErythronDB records/reports, search results or analysis tools should cite the following publication:

Kinglsey et al. 2013. Ontogeny of erythroid gene expression.
E-blood: https://doi.org/10.1182/blood-2012-04-422394

The following citations should be used to acknowledge specific datasets in ErythronDB:

Mouse Transcriptomics

• Ontogeny of erythroid gene expression Kinglsey et al. 2013. Ontogeny of erythroid gene expression. E-blood: https://doi.org/10.1182/blood-2012-04-422394 ArrayExpress Accession: E-MTAB-1035
• EPO-regulated targets in murine erythroid progenitors Wojchowski, D. et al. 2017. ArrayExpress Accession: E-MTAB-5373
• EPO-regulated targets in murine E1 cells with a truncated erthropoietin receptor (EpoR) Wojchowski, D. et al. EPO-regulated targets in murine E1 cells with a truncated erthropoietin receptor (EpoR). ErythronDB Website

Human Proteomics

• EPO phosphorylation PTM targets in UT-7epo-E cells Held MA et al. 2020. Phospho-proteomic discovery of novel signal transducers including thioredoxin-interacting protein as mediators of erythropoietin-dependent human erythropoiesis. Experimental hematology: https://doi.org/10.1016/j.exphem.2020.03.003 Held MA et al. 2020. Phospho-PTM proteomic discovery of novel EPO-modulated kinases and phosphatases, including PTPN18 as a positive regulator of EPOR/JAK2 Signaling. Cellular signalling: https://doi.org/10.1016/j.cellsig.2020.109554

Code/Software

A detailed README about building the ErythronDB website to access the data is available on GitHub: https://github.com/ErythronDB/erythrondb-docker.