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) .
Data name | README |
Description of data contents | HTML file to describe "Plabrain DB" data. |
File | README_e.html(English) |
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 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. |
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) |
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 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.) |
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) |
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:
"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:
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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
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
You can freely provide links to all contents in this database. But, contents might be changed without notice.
Date | Update contents |
2011/03/02 | Plabrain DB english archive site is opened. |
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