Tags

Type your tag names separated by a space and hit enter

SmedGD 2.0: The Schmidtea mediterranea genome database.
Genesis. 2015 Aug; 53(8):535-46.G

Abstract

Planarians have emerged as excellent models for the study of key biological processes such as stem cell function and regulation, axial polarity specification, regeneration, and tissue homeostasis among others. The most widely used organism for these studies is the free-living flatworm Schmidtea mediterranea. In 2007, the Schmidtea mediterranea Genome Database (SmedGD) was first released to provide a much needed resource for the small, but growing planarian community. SmedGD 1.0 has been a depository for genome sequence, a draft assembly, and related experimental data (e.g., RNAi phenotypes, in situ hybridization images, and differential gene expression results). We report here a comprehensive update to SmedGD (SmedGD 2.0) that aims to expand its role as an interactive community resource. The new database includes more recent, and up-to-date transcription data, provides tools that enhance interconnectivity between different genome assemblies and transcriptomes, including next-generation assemblies for both the sexual and asexual biotypes of S. mediterranea. SmedGD 2.0 (http://smedgd.stowers.org) not only provides significantly improved gene annotations, but also tools for data sharing, attributes that will help both the planarian and biomedical communities to more efficiently mine the genomics and transcriptomics of S. mediterranea.

Authors+Show Affiliations

Stowers Institute for Medical Research, Howard Hughes Medical Institute, Kansas City, Missouri, 64110.Stowers Institute for Medical Research, Howard Hughes Medical Institute, Kansas City, Missouri, 64110.Stowers Institute for Medical Research, Howard Hughes Medical Institute, Kansas City, Missouri, 64110.Stowers Institute for Medical Research, Howard Hughes Medical Institute, Kansas City, Missouri, 64110.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

26138588

Citation

Robb, Sofia M C., et al. "SmedGD 2.0: the Schmidtea Mediterranea Genome Database." Genesis (New York, N.Y. : 2000), vol. 53, no. 8, 2015, pp. 535-46.
Robb SM, Gotting K, Ross E, et al. SmedGD 2.0: The Schmidtea mediterranea genome database. Genesis. 2015;53(8):535-46.
Robb, S. M., Gotting, K., Ross, E., & Sánchez Alvarado, A. (2015). SmedGD 2.0: The Schmidtea mediterranea genome database. Genesis (New York, N.Y. : 2000), 53(8), 535-46. https://doi.org/10.1002/dvg.22872
Robb SM, et al. SmedGD 2.0: the Schmidtea Mediterranea Genome Database. Genesis. 2015;53(8):535-46. PubMed PMID: 26138588.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - SmedGD 2.0: The Schmidtea mediterranea genome database. AU - Robb,Sofia M C, AU - Gotting,Kirsten, AU - Ross,Eric, AU - Sánchez Alvarado,Alejandro, Y1 - 2015/07/17/ PY - 2015/05/22/received PY - 2015/06/29/revised PY - 2015/06/30/accepted PY - 2015/7/4/entrez PY - 2015/7/4/pubmed PY - 2016/6/4/medline KW - GBrowse KW - GMOD KW - Schmidtea mediterranea KW - planaria genome SP - 535 EP - 46 JF - Genesis (New York, N.Y. : 2000) JO - Genesis VL - 53 IS - 8 N2 - Planarians have emerged as excellent models for the study of key biological processes such as stem cell function and regulation, axial polarity specification, regeneration, and tissue homeostasis among others. The most widely used organism for these studies is the free-living flatworm Schmidtea mediterranea. In 2007, the Schmidtea mediterranea Genome Database (SmedGD) was first released to provide a much needed resource for the small, but growing planarian community. SmedGD 1.0 has been a depository for genome sequence, a draft assembly, and related experimental data (e.g., RNAi phenotypes, in situ hybridization images, and differential gene expression results). We report here a comprehensive update to SmedGD (SmedGD 2.0) that aims to expand its role as an interactive community resource. The new database includes more recent, and up-to-date transcription data, provides tools that enhance interconnectivity between different genome assemblies and transcriptomes, including next-generation assemblies for both the sexual and asexual biotypes of S. mediterranea. SmedGD 2.0 (http://smedgd.stowers.org) not only provides significantly improved gene annotations, but also tools for data sharing, attributes that will help both the planarian and biomedical communities to more efficiently mine the genomics and transcriptomics of S. mediterranea. SN - 1526-968X UR - https://www.unboundmedicine.com/medline/citation/26138588/SmedGD_2_0:_The_Schmidtea_mediterranea_genome_database_ L2 - https://doi.org/10.1002/dvg.22872 DB - PRIME DP - Unbound Medicine ER -