JGI
JGI
Tag Archive EST
The Tunicate Web Portal, a collaborative tool for the Tunicate Community
- Home /
- Page
Ensembl
General information
Homepage
Contact information
Tools
| Ciona robusta browser | https://www.ensembl.org/Ciona_intestinalis/Info/Index |
| Ciona savignyi browser | https://www.ensembl.org/Ciona_savignyi/Info/Index |
Standards used
Publications
Social networks
MAGEST
General information
Homepage
Description
MAGEST (MAboya Gene Expression patterns and Sequence Tags) is a database dealing with ESTs and gene expression of Halocynthia roretzi.
Developed in Japan
Created in
How to cite this resource :
Contact information
Tools
| Search | http://magest.hgc.jp/ |
| Download | http://magest.hgc.jp/files/download.html |
Standards used
Publications
Social networks
Ghost
General information
Homepage
http://ghost.zool.kyoto-u.ac.jp/cgi-bin/gb2/gbrowse/kh/
Description
The Ghost database is providing nearly 30,000 in situ hybridization photographs for 4700 genes of Ciona intestinalis. Up-to-date lists of genes for transcription factors, zinc finger proteins and signaling molecules are linked to their expression data.
Developed in Japan
Created in 2005
How to cite this resource :
An integrated database of the ascidian, Ciona intestinalis: towards functional genomics.
Satou Y, Kawashima T, Shoguchi E, Nakayama A, Satoh N.
Zoolog Sci. 2005 Aug;22(8):837-843
Contact information
Yutaka Satou, yutaka@ascidian.zool.kyoto-u.ac.jp
Tools
| Blast | http://ghost.zool.kyoto-u.ac.jp/blast_kh.html |
| Search | http://ghost.zool.kyoto-u.ac.jp/SearchGenomekh.html |
| Browse expression profiles | http://ghost.zool.kyoto-u.ac.jp/otherfr_kh.html |
| Genome browser | http://ghost.zool.kyoto-u.ac.jp/cgi-bin/gb2/gbrowse/kh/ |
| Download | http://ghost.zool.kyoto-u.ac.jp/download_kh.html |
Standards used
Publications
Social networks
ANISEED
Comments Off on ANISEED
Databases, Resources
Anatomy, EST, Gene expression, Genome browser, Regulatory regions
General information
Homepage
Description
Aniseed database provides high throughput data and in situ experiment data from literature for ascidian species.
Developed in France
Created in 2007
How to cite this resource
The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. Tassy et al. Genome Res 2010.
Contact information
Delphine Dauga, contact@bioself-communication.com
Tools
Standards used
- Article Minimum Information Standard
- Minimum Information Specification For In Situ Hybridization and Immunohistochemistry Experiments
- Evidence codes
- Gene Ontology
- Ascidian developmental and anatomical ontologies
Publications
- ANISEED 2017: extending the integrated ascidian database to the exploration and evolutionary comparison of genome-scale datasets. Brozovic et al. Nucleic Acids Res. 2018
- ANISEED 2015: a digital framework for the comparative developmental biology of ascidians. Brozovic et al. Nucleic Acids Res 2015.
- Biocuration: a new challenge for the tunicate community. Dauga. 2015
- Guidelines for the nomenclature of genetic elements in tunicate genomes. Stolfi et al. 2015
- Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri. Manni et al. PLoS One. 2014
- The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program. Tassy et al. Genome Res 2010.
- Creating 3D digital replicas of ascidian embryos from stacks of confocal images. Robin et al. Cold Spring Harb Protoc. 2011.
- Imaging of fixed ciona embryos for creating 3D digital replicas. Robin et al. Cold Spring Harb Protoc. 2011
- Time-lapse imaging of live Phallusia embryos for creating 3D digital replicas. Robin et al. Cold Spring Harb Protoc. 2011
- Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE). Deutsch et al. Nat Biotechnol. 2008