Plabrain DB

2011/03/02

HTTPS Site: https://dbarchive.biosciencedbc.jp/data/plabrain-db/

Plabrain DB is a database for planarian nervous system analysis, including results of the gene expression profiling of single cells, the gene expression analysis by whole-mount in situ hybridization and the analysis by Immunohistochemical staining. This is the first case to release the result of gene expression analysis at the single-cell resolution by semi-quantitative single-cell RT-PCR (FBSC-PCR) method using FACS (Fluorescence Activated Cell Sorting) .

README Content

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

1. Database Component

  1. README
  2. FACS-based single-cell PCR data
  3. Image files of PCR data plotted on the FACS profiles
  4. A list of image files of planarians analyzed by in situ hybridication and immunohistochemical staining
  5. Image files of planarians analyzed by in situ hybridication and immunohistochemical staining
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "Plabrain DB" data.
File README_e.html(English)
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2.2 FACS-based single-cell PCR data

Data name FACS-based single-cell PCR data
Description of data contents Gene expression patterns at the single-neuron (cell) resolution using FACS-based single cell PCR. "+" indicates a cell co-expressing each gene and a neural-specific marker gene EF1. Although all genes in this table are known to be expressed in the nervous system, the patterns of "+" indicate that these genes have different expression pattern in single neurons. Image file names of plotting the gene expression on the FACS profile are also included. A set of the image files is downloadble from "Image files of PCR data plotted on the FACS profiles".
File planaria_fbsc_pcr.zip (110MB)
Data items are the following:
Data item Description
Gene name (Link to Image list) Gene name (Link to "Image list" in simple search.)
Single-cell PCR data (+ describes cells expressing the gene.) "+" indicates a cell co-expressing each gene and a neural-specific marker gene EF1.
Mapping on FACS profile PCR data plotting onto the FACS profile, in which cells are sorted by DNA content (Hoechst33342) and cell size (CalceinAM). Blue dots indicate the "+"cells. The FACS profile image is displayed when you click "FACS Profile" in simple search. In the downloaded data, its file name is shown.

2.3  Image files of PCR data plotted on the FACS profiles

Data name Image files of PCR data plotted on the FACS profiles
Description of data contents FACS-based single-cell PCR data was plotted on the FACS profile, in which cells are sorted by DNA content (Hoechst33342) and cell size (CalceinAM). Blue dots indicate the "+"cells. Individual FACS profile images are displayed when you click "FACS Profile" in "FACS-based single-cell PCR data" simple search.
File planaria_facs_profile.zip (107KB)

2.4 A list of image files of planarians analyzed by in situ hybridication and immunohistochemical staining

Data name A list of image files of planarians analyzed by in situ hybridication and immunohistochemical staining
Description of data contents This list includes file names of images of gene expression pattern by whole-mount in situ hybridication and also protein distribution by immunohistochemical staining in intact planarians or planarian head regions in the regeneration process. A set of the image files is downloadable from "Image files of planarians analyzed by In situ hybridication and immunohistochemical staining".
File planaria_image_list.zip (1KB)
Data items are the following:
Data item Description
Gene name (Link to Image list) Gene name (Link to a image list in simple search.)
Accession GenBank accession number (Link to NCBI in simple search.)
Adult (ISH) Image of in situ hybridization of adult planarians. (The image is displayed in simple search. In the downloaded data, its file name is shown.)
Adult (Ab) Image of whole-mount immunostaining of intact planarians. (The image is displayed in simple search. In the downloaded data, its file name is shown.)
Regeneration 1 day (Ab) Image of immunostaining at 1 day after decapitation. (The image is displayed in simple search. In the downloaded data, its file name is shown.)
Regeneration 3 days (Ab) Image of immunostaining at 3 days after decapitation. (The image is displayed in simple search. In the downloaded data, its file name is shown.)
Regeneration 5 days (Ab) Image of immunostaining at 5 days after decapitation. (The image is displayed in simple search. In the downloaded data, its file name is shown.)
Regeneration 7 days (Ab) Image of immunostaining at 7 days after decapitation. (The image is displayed in simple search. In the downloaded data, its file name is shown.)

2.5  Image files of planarians analyzed by in situ hybridication and immunohistochemical staining

Data name Image files of planarians analyzed by in situ hybridication and immunohistochemical staining
Description of data contents mage files of gene expression patterns by whole-mount in situ hybridication and also protein distribution by immunohistochemical staining of intact planarians or planarian head regions in the regeneration process. Images are displayed in "A list of image files of planarians analyzed by in situ hybridication and immunohistochemical staining" simple search. The file name is created by the following rule.
<In situ hybridization>
[gene name]-insitu.jpg
<Immunohistochemical staining>
For planarian adult, [gene name]-Ab.jpg
For planarian brain regeneration, [gene name]regeneration[days after decapitation ].jpg
File planaria_image.zip (2.74MB)
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3. License

Last updated : 2010/12/16

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.


Creative Commons License

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: "Plabrain DB © 2010 Kiyokazu Agata(Kyoto Univ.) 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.

Kiyokazu Agata
Laboratory for Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University
Kitashirakawa-Oiwake, Sakyo, Kyoto 606-8502
Email: agata[at]mdb[dot]biophys[dot]kyoto-u[dot]ac[dot]jp

Requests to the Users

  1. You are requested that when you conduct research by using this database and describe the research results in an article or paper, you always cite this database, and specify the name and URL of this database (http://dbarchive.lifesciencedb.jp/english/en/plabrain-db/desc.html) in the article or paper.
  2. You are requested to contact the licensor shown below when you
    - redistribute part or whole of the data from this database; and
    - distribute database and other derivative works based on part or whole of the data from this database.
    It is for our tracking usage of this database.

Kiyokazu Agata
Laboratory for Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University
Kitashirakawa-Oiwake, Sakyo, Kyoto 606-8502
Email: agata[at]mdb[dot]biophys[dot]kyoto-u[dot]ac[dot]jp

About Providing Links to This Database

You can freely provide links to all contents in this database. But, contents might be changed without notice.

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4. Update History

Date Update contents
2011/03/02 Plabrain DB english archive site is opened.
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5. Literature

Tetsutaro Hayashi, Norito Shibata, Ryo Okumura, Tomomi Kudome, Osamu Nishimura, Hiroshi Tarui and Kiyokazu Agata
Single-cell gene profiling utilizing FACS and its “index sorting” function for stem cell research
Dev Growth Differ., 52, 131-144 (2010)
PMID: 20078655

Kaneyasu Nishimura, Yoshihisa Kitamura, Takashi Taniguchi and Kiyokazu Agata
Analysis of motor function modulated by cholinergic neurons in planarian Dugesia japonica
Neuroscience, 168, 18-30 (2010)
PMID: 20338223

Hiroyuki Takeda, Kaneyasu Nishimura and Kiyokazu Agata
Planarians change their body size by maintaining a constant ratio of different cell types using stem cell system
Zoolog. Sci., 26, 805-813.
PMID: 19968467

Kaneyasu Nishimura, Yoshihisa Kitamura, Takeshi Inoue, Yoshihiko Umesono, Kanji Yoshimoto, Takashi Taniguchi and Kiyokazu Agata
Characterization of tyramine beta-hydroxylase in planarian Dugesia japonica: Cloning and expression
Dev Growth Differ., 52, 131-144 (2010)
PMID: 20078655

Kaneyasu Nishimura, Yoshihisa Kitamura, Takeshi Inoue, Yoshihiko Umesono, Kanji Yoshimoto, Kosei Takeuchi, Takashi Taniguchi and Kiyokazu Agata
Identification and distribution of tryptophan hydroxylase (TPH)-positive neurons in the planarian Dugesia japonica
Neurosci. Res., 59, 101-106 (2007)
PMID: 17624455

Kaneyasu Nishimura, Yoshihisa Kitamura, Takeshi Inoue, Yoshihiko Umesono, Shozo Sano, Kanji Yoshimoto, Masatoshi Inden, Kazuyuki Takata, Takashi Taniguchi, Shun Shimohama and Kiyokazu Agata
Reconstruction of dopaminergic neural network and recovery of behavioral function in planarian regenerates
Dev. Neurobiol., 67, 1059-1078 (2007)
PMID: 17565705

6. Contact address

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

Kiyokazu Agata
Laboratory for Molecular Developmental Biology, Department of Biophysics, Division of Biological Sciences, Graduate School of Science, Kyoto University
Kitashirakawa-Oiwake, Sakyo, Kyoto 606-8502
Email: agata[at]mdb[dot]biophys[dot]kyoto-u[dot]ac[dot]jp

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