GETDB

2014/05/09

WebSite: http://kyotofly.kit.jp/stocks/GETDB/getdb.html
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/getdb

About 4,600 insertion lines of enhancer trap lines based on the Gal4-UAS method were generated in Drosophila, and all of these insertion lines were tested for enhancer activity in embryo and larva by NP consortium. Moreover, the insertion position was mapped in the genome sequence form, and the correspondence relationship with gene was identified for 2,157 independent sites. This database is available to the public as the database that has compiled the insertion position and enhancer activity of Gal4 enhancer trap lines.

README Content

  1. Database Component
  2. Data Description
  3. License
  4. Update History
  5. Literature
  6. Contact address

1. Database Component

  1. README
  2. Expression information data table (Strain List) of Drosophila GAL4 enhancer trap lines
  3. Genome mapping data table of Drosophila GAL4 enhancer trap lines (Clone List)
  4. Clustering Table of the genome insert site of Drosophila GAL4 enhancer trap lines (Cluster List)
  5. Expression image data of Drosophila GAL4 enhancer trap lines
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "GETDB" data.
File README_e.html(English)
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2.2 Expression information data table (Strain List) of Drosophila GAL4 enhancer trap lines

Data name Expression information data table (Strain List) of Drosophila GAL4 enhancer trap lines
Description of data contents

Line-related information on Drosophila GAL4 enhancer trap lines, and the text information and expression image data concerning expression of enhancer activity 4,250 lines.

File getdb.zip (331KB)
Data items are the following:
Data item Primary key Foreign key Description
Line information
DGRC Number * Line number of DGRC (Drosophila Genetic Resource Center) (Link to DGRC in TogoDB)
Genotype Genotype
Insertion Site Insert site(s) on the physical map. For two or more insert sites, use semicolon to delimit each site (see http://www.dgrc.kit.jp/~jdd/chromosome/index.html). (Link to the DGRC genome viewer is created, and the download file has link tag.)
Map Viewer DGRC Number (TogoDB has link to the DGRC genome viewer.)
Related Genes Name of related gene
Original Number Line number in GETDB
Chr. Chromosome number
Comments Comment
Balancer Name of balancer chromosome
Link to Clone Table Link to clone list (Empty column in downloaded file)
Num of clones Number of clones
Cluster id Cluster ID (two or more)
Link to Cluster Table Cluster ID. Two or more IDs will be delimited by %7C ("|" decoded by UTF8). (Link to cluster table is available in TogoDB.)
Num of clusters Number of clusters
Stock Request Link to placing an order for the stock (Empty column in the downloaded file.)
Expression information
Embryonic Expression Information on expression in embryo
Larval GFP Information on expression of GFP in larva
Larval X-gal Information on expression of X-gal in larva
Adult GFP Information on expression of GFP in adult
Lethality Lethality
Also known as Genotype alias
Original Comments Original Comment (Comment by GETDB)
Fluorescence expression image
Disc(Image) Expression image in imaginal disc
Disc (Number) Number of expression images in imaginal disc
Embryo(Image) Expression image in embryo
Embryo (Number) Number of expression images in embryo
Larval GFP(Image) Fluorescence expression image in GFP-dyed larva
Larval GFP (Number) Number of fluorescence expression images in GFP-dyed larva
Adult(Image) Expression image in adult
Adult (Number) Number of expression images in adult

2.3 Genome mapping data table of Drosophila GAL4 enhancer trap lines (Clone List)

Data name Genome mapping data table of Drosophila GAL4 enhancer trap lines (Clone List)
Description of data contents

A table showing the insert position of the Drosophila GAL4 enhancer trap element and the data on the adjacent downstream sequence for each clone. 5,555 clones.

File getdb_clone.zip (1.4MB)
Data items are the following:
Data item Primary key Foreign key Description
Clone Name * Name of the clone of the genome sequence adjacent to the 5'-end of the Drosophila GAL4 enhancer trap element
DGRC Number * Line number (Link to Strain Table in TogoDB)
Cluster Id * Cluster ID of genome insert coordinate (Link to Cluster Table in TogoDB)
Strand Insert direction to genome sequence (*)
Insertion Point Insert position on genome sequence (*)
Chr. Band Chromosome band
Flanking Sequence Adjacent sequence downstream of the insert point.

*1: Obtained by the BLAST search of the sequence identified by the Berkeley Drosophila Genome Project (BDGP)/Celera (Release 3.1) and Flanking Sequence.

2.4 Clustering Table of the genome insert site of Drosophila GAL4 enhancer trap lines (Cluster List)

Data name Clustering Table of the genome insert site of Drosophila GAL4 enhancer trap lines (Cluster List)
Description of data contents

Cluster data in which the insert positions of the Drosophila GAL4 enhancer trap element are clustered by the closeness of their positions from each other. 2,099 clusters.

File getdb_cluster.zip (56KB)
Data items are the following:
Data item Primary key Foreign key Description
ClusterId * Cluster ID of genome insert coordinate
Cluster Member(Clone Name : Cluster Id) Clone name corresponding to each of the insert point sequences belonging to the cluster
Cluster Size Number of insert coordinates belonging to the cluster.
Link to Clone Table Cluster ID. (Link to CloneTable in TogoDB.)
Link to Strain Table Cluster ID. (Link to Strain Table in TogoDB)
Chr. Band Chromosome band
Insertion Point (Min) Minimum value in the cluster of insert positions on genome sequence
Insertion Point (Max) Maximum value in the cluster of insert positions on genome sequence
Max-Min Maximum value minus minimum value of insert positions on genome sequence

2.5 Expression image data of Drosophila GAL4 enhancer trap lines

Data name Expression image data of Drosophila GAL4 enhancer trap lines
Description of data contents

3,075 expression image data by developmental stages of Drosophila
Images are classified into the following four developmental stages.
- Expression image in imaginal disc
- Expression image in embryo
- Fluorescence expression image in GFP-dyed larva
- Expression image in adult
The image file is provided in the JPEG format. The file name is composed of
"the number corresponding to the line"_"a single alphabet denoting the developmental phase (imaginal disc (d), embryo (e), larva (g), adult (a))""serial number of the images classified by developmental stages in the line".jpg.
(Example: 4310_d1.jpg) Correspondence between "the number corresponding to the line" and the DGRC Number is shown in "dgrcnum_imagenum.csv" in the ZIP file.

File getdb_images.zip (247MB)
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3. License

You may use this database in compliance with the terms and conditions of the license described below. The license specifies the license terms regarding the use of this database and the requirements you must follow in using this database.

The license for this database is specified in the Creative Commons Attribution-Share Alike 2.1 Japan.
If you use data from this database, please be sure attribute this database as follows: "GETDB, Copyright© 2010 Shigeo Hayashi(RIKEN) licensed under CC Attribution-Share Alike 2.1 Japan".

The summary of the Creative Commons Attribution-Share Alike 2.1 Japan is found here.

With regard to this database, you are licensed to:

  1. freely access part or whole of this database, and acquire data;
  2. freely redistribute part or whole of the data from this database; and
  3. freely create and distribute database and other derivative works based on part or whole of the data from this database,

under the license, as long as you comply with the following conditions:

  1. You must attribute this database in the manner specified by the author or licensor when distributing part or whole of this database or any derivative work.
  2. You must distribute any derivative work based on part or whole of the data from this database under the license.
  3. You need to contact the Licensor shown below to request a license for use of this database or any part thereof not licensed under the license.

Shigeo Hayashi
Laboratory for Morphogenetic Signaling, RIKEN Center for Developmental Biology
2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe
650-0047
Tel: +81-78-306-3185
FAX: +81-78-306-3183
E-mail: shayashi[at]cdb[dot]riken[dot]jp

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4. Update History

Date Update contents
2014/05/09 "URL of the portal site" is changed.
2010/03/29 GETDB English archive site is opened.
2003/8/1 GETDB(http://kyotofly.kit.jp/stocks/GETDB/getdb.html) is released.
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5. Literature

Hayashi S, Ito K, Sado Y, Taniguchi M, Akimoto A, Takeuchi H, Aigaki T, Matsuzaki F, Nakagoshi H, Tanimura T, Ueda R, Uemura T, Yoshihara M, Goto S.
GETDB, a database compiling expression patterns and molecular locations of a collection of Gal4 enhancer traps.
Genesis. 2002 Sep-Oct;34(1-2):58-61.
PMID: 12324948

6. Contact address

When you have any question about "GETDB", contact the following:

Shigeo Hayashi
Laboratory for Morphogenetic Signaling, RIKEN Center for Developmental Biology
2-2-3 Minatojima-Minamimachi, Chuo-ku, Kobe
650-0047
Tel: +81-78-306-3185
FAX: +81-78-306-3183
E-mail: shayashi[at]cdb[dot]riken[dot]jp

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