> Links

<Image databases>

  RI ISH images and GFP expression of BAC transgenic mouse lines(linked to Entrez)
   ref)  Nature. (2003) 425:917-25.

Allen Brain Atlas
  ISH database of adult mouse brain by Allen institut. Still expanding to include human brain atlas, developing brain, and mouse connectivity etc..
   ref)  Nature. (2007) 445:168-76.

  ISH database of embryo to early postnatal mouse
   ref)  J Physiol. (2006) 575:347-52.

  Zoomable high resolution image databases of brain sections from various model animals including those from primates.  There are several (although not many yet) good antibody-stained images.  Good links to various related sites.  
   ref)  Neuroimage. (2007) 35:9-15

Comparative Mammalian Brain Collections
  You can find photos of brains of various mammalian species, as well as stained sections of select animals.  Splendid place for educational purposes.  It's quite a fun just to browse.

Digital Brain Atlas of the Common Marmoset (Callithrix jacchus)
  Zoomable high resolution images of common marmoset brains. Includes immunostained images for a panel of antibodies useful for delineation of brain structures.

Brain Architecture Project
  Opened 2012 as the "hub" for brain architecture data, with mouse connection data as a core. By Cold Spring Harbor Laboratory.

Neuroscience information framework
  NIF is a dynamic portal providing access to neuroscience-relevant resources (data, tools, materials) from a single search interface. Supported by the NIH Blueprint consortium of neuroscience-related institutes.

<Gene databases>

Entrez Gene
  A section of NCBI(National Center for Biotechnology Information) homepage.  In this section, the sequence information is classified by genes.  There are usually several files for a particular gene submitted by different labs.  Quite often, each lab uses different names to designate the same gene.  There are also alternative transcripts and the same gene of different species.  In this database, these informations are neatly currated.  Linked to Pubmed (literature database), GENSAT (see above), BLAST (homology search).

NEDO database
HUGE database
Rouge database
  These are databases derived from the cDNA cloning projects performed by Kazusa DNA research institute and others.  You can obtain full-length cDNAs for long transcripts, which are difficult to clone by PCR.  There are also many useful information associated with each clone, including expression data.  


CoCoMac    Database for neural connectivity of macaque monkey brain.

Van Essen lab homepage
      You can obtain "Caret" and other softwares, used for surface-based analyses of cerebral cortex.  There are also surfaced-based atlases of human, macaque etc...

Translating Time
  A homepage for translating developmental time between different mammalian species.  

National Institute for Basic Biology

Yamamori Lab


> Contact

Send you questions and comments about this homepage to

Akiya Watakabe

brish @nibb.ac.jp (delete the space before @)

We welcome your feedback to make this website better and more useful.


> Copyright

Many of the photos presented in this website was used in our past publications.  The copyright of each photo belongs to the publisher of the journal cited.  We also borrowed some brain photos from Comparative mammalian brain collection (their copyright policy is presented in their top page). 

Other photos with no citations are unpublished data of Yamamori lab and we hold their copyright.  We (National Insitute for Basic Biology) also hold the copyright of other contents, including figures and explanations.  The basic design of this website was obtained from FreeCSSTemplates.org, which provides copyright-free materials.  

> Origins of the protocols etc

>> Origins of the protocols

* Floating ISH
We collaborated with Drs. FL and TH, who taught us their method (ref1).  Dr. ST was the first in our laboratory to use their technique for the analysis of area-specific genes.  With the effort of Dr. YK, we are now routinely using the technique for our study.   The protocol introduced in this homepage is based on the accumulation of experiences that our lab has gone through.

* Slideglass ISH
This method was first published by Dr. Schaeren-Wiemers et al (ref2), and was introduced into our laboratory by Dr. TK.

* Fluorescent double ISH
The signal amplification procedure for TSA kit was first optimized by AW.  Its application for double ISH was carried out by AW and YK.  There are several other groups that independently succeeded in the use of TSA kit for double ISH.  

* Protocol for homemade TSA-biotin
This protocol was obtained from Cepco lab homepage (here).  Other reference that we looked is this.  

>> Origins of the ISH probes.

The template plasmids for the ISH probes registered in the "Probe list" section was constructed by Yamamori lab.  The search engine in that section was programmed by Ms. HN in NIBB computer lab.