Tag Archive Gene expression

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MAGEST

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General information

Homepage

http://magest.hgc.jp

 

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 

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Ghost

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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

 

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CiAID

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General information

Homepage

http://bioinfo.s.chiba-u.jp/ciaid/

 

Description

CiAID (Ciona intestinalis Adult In situ hybridization Database) is a gene expression database with body atlas of the ascidian Ciona juvenile.

 

Developed in Japan

Created in 2009

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ANISEED

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General information

Homepage

https://www.aniseed.fr/

 

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

 

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 

 

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