Mouse Basement Membrane Bodymap

2018/04/17

Web Site: http://dbarchive.biosciencedbc.jp/archive/matrixome/bm/home.html
HTTPS Site: https://dbarchive.biosciencedbc.jp/data/matrixome/

This is a database of body-wide localizations of basement membrane proteins in developing mouse embryos.

README Content

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

1. Database Component

  1. README
  2. Protein List
  3. AntiBody
  4. Bodymap
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2. Data Description

2.1 README

Data name README
Description of data contents HTML file to describe "Mouse Basement Membrane Bodymap" data.
File README_e.html (English)
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2.2 Protein List

Data name Protein List
Description of data contents

It is the list of basement membrane proteins shown in images.
File matrixome_protein.zip (2.1 KB)

Data items are the following:
Data itemDescription
Protein Category Protein Category
Protein Name Protein Name
Mouse Genomic Loci Chromosome region of the mouse gene locus
Human Genomic Loci Chromosome region of the human gene locus
Genbank Accession # Genbank Accession Number of the coding region in the mRNA
MGI MGI ID of the gene
Mouse Embryo Age in days of mouse embryo (In simple search, it shows the link to mouse embryo image page)
Antibody Antibody to stain the target protein
Validation Validation result (medium or high)
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2.3 AntiBody

Data name AntiBody
Description of data contents

It is the list of antibodies to stain the target proteins.
File matrixome_antibody.zip (1.3 KB)

Data items are the following:
Data itemDescription
Protein Name Protein Name
Antibody Name Antibody Name
Producer / Vender Producer / Vender
Catalog # Catalog #
Immunization Species Immunization Species
Clonality Clonality(monoclonal or polyclonal)
Fixative Fixative
Hyaluronidase / Chondroitinase Treatment Hyaluronidase / Chondroitinase Treatment
Acid Treatment Acid Treatment
Validation Score Validation result (medium or high)
Validation Detail of validation result
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2.4 Bodymap

Data name Bodymap
Description of data contents

It is the collection of high resolution virtual slides created from gigapixel digital images of mouse embryo.

Simple search has two interfaces, "protein-based" and "tissue-based".

Protein-based search: http://togodb.biosciencedbc.jp/togodb/view/matrixome_bodymap_protein_based

Tissue-based search: http://togodb.biosciencedbc.jp/togodb/view/matrixome_bodymap_tissue_based

To view or download original images of virtual slides, see the following page.
https://togodb.biosciencedbc.jp/togodb/view/matrixome_bodymap_imagelist#en
File images (278.6 GB)
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3. License

License to Use This Database

Last updated : 2018/04/17

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 4.0 International.
If you use data from this database, please be sure attribute this database as follows: "Mouse Basement Membrane Bodymap © Kiyotoshi Sekiguchi (Osaka Univ.) licensed under CC Attribution-Share Alike 4.0 International".

The summary of the Creative Commons Attribution-Share Alike 4.0 International 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 adapted materials 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 adapted material.
  2. You must distribute any adapted material based on part or whole of the data from this database under CC Attribution-Share Alike 4.0 (or later), or CC Attribution-Share Alike Compatible License (the list is here).
  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.

E-mail: matrixome[at]protein[dot]osaka-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

DateUpdate contents
2018/04/17 Mouse Basement Membrane Bodymap English archive site is opened.
2008/08/18 Mouse Basement Membrane Bodymap (http://dbarchive.biosciencedbc.jp/archive/matrixome/bm/home.html) is opened.
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5. Literature

Manabe R, Tsutsui K, Yamada T, Kimura M, Nakano I, Shimono C, Sanzen N, Furutani Y, Fukuda T, Oguri Y, Shimamoto K, Kiyozumi D, Sato Y, Sado Y, Senoo H, Yamashina S, Fukuda S, Kawai J, Sugiura N, Kimata K, Hayashizaki Y, Sekiguchi K.
Transcriptome-based systematic identification of extracellular matrix proteins.
Proc Natl Acad Sci U S A. 2008 Sep 2;105(35):12849-54. doi: 10.1073/pnas.0803640105. Epub 2008 Aug 29.
PMID: 18757743

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6. Contact address

When you have any question about "Mouse Basement Membrane Bodymap", contact the following:

matrixome[at]protein[dot]osaka-u[dot]ac[dot]jp

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