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BMAP cDNA Resources

As part of BMAP gene discovery efforts, mouse brain cDNA libraries and Expressed Sequence Tags (ESTs) have been generated through NIMH/NINDS contract N01 MH80014 awarded to the University of Iowa (M.B. Soares, PI). Through this project a  BMAP mouse brain UniGene set consisting of over 24,000 non-redundant members of unique clusters has been developed from EST sequencing of more than 50,000 cDNA clones from 10 regions of adult mouse brain, spinal cord, and retina (  In 2001, NIMH along with NICHD, NIDDK, and NIDA, awarded a contract to the University of Iowa ( M.B. Soares, PI) to isolate full-length cDNA clones corresponding to genes expressed in the developing mouse nervous system and determine their full-coding sequences. The BMAP mouse brain EST sequences can be accessed at NCBI’s dbEST database (  Arrayed sets of BMAP mouse brain UniGenes and cDNA libraries, and individual BMAP cDNA clones can be purchased from Open Biosystems, Huntsville, AL  (


BMAP Funded Projects 

1. Gene Discovery in the Developing Nervous System (RFP NIMH-00-DB-006)

         Purpose: The main goals  of the propjects funded tunder this solicitation are: (1) to generate a comprehensive non-redundant collection of full-length cDNAs derived from mouse brain tissue at different stages of development, and (2) to determine the complete and accurate sequence of a significant number of these full-length cDNAs. Needless to say, the process of identification and sequencing of full-length cDNAs must be integrated with that of the NIH Mammalian Gene Collection (MGC) Program (

            Funded Projects:

  • The University of Iowa, M. Bento Soares, Principal Investigator and Thomas Casavant, Co-Principal Investigator
    Title: Gene Discovery in the Developing Nervous System (N01MH12006)

Full-length-enriched cDNA libraries from mouse brain tissue will be prepared at the following developmental stages: (a) 12.5, (b) E15.5, (c) E18.5, (d) pool of E13.5, E14.5, E16.5 and E17.5, (e) pool of P0, P5 and P15. In addition,  full-length-enriched libraries (i) from neural tissue at stage E9.5 dpc, when transcripts important for neural tube formation may be expressed, and (ii) from pools of eyes obtained at different developmental stages will be constructed. These cDNA libraries will be used to identify in the order of 9,000-10,000 candidate full-length cDNAs and to determine the complete and accurate sequence of approximately 1,000 of them. The remainder clones should be sequenced by the MGC consortia. 

2. Gene Expression Profiling in the Nervous System (MH-00-002)

      Purpose: This  Request for Applications (RFA) was to solicit feasibility studies for profiling gene    expression patterns in the mammalian nervous system.  Exploratory research projects supported under this RFA will utilize neural tissue-specific cDNA reagents and state-of-the-art microarray technologies, in order to quantify in a highly parallel way expression profiles of genes in mammalian neural tissue.  The creation of collaborative teams is encouraged, in which scientists with expertise in neuroscience research, genomics, and bioinformatics work to apply innovative approaches for analyzing microarray data.

    Such feasibility studies will permit functional analyses of mouse and human neural tissue that aim to understand genes influencing the nervous system in their full biological context.  The widespread availability of innovative methods for gene expression profiling will stimulate many avenues of research on nervous system functioning and complex behavioral disorders.

    Funded Projects:

  • Washington University, Dr. Joshua R. Sanes
    Title: Microarray Analysis of Single Retinal Ganglion Cells (R21NS41763)

  • University of Pennsylvania, Dr. James Eberwin
    Title: Robotized Expression Profiling of Mouse Amygdala

  • California Institute of Technology, Dr. David J. Anderson
    Title: Methods and Algorithms for RNA Profining in the Brain (R21MH62825)

  • University of Michigan at Ann Arbor, Dr. Sean J. Morrison
    Title: Gene Expression Profiling of Neural Crest Stem Cells (R21HD40760)

  • Dana- Farber Cancer Institute, Dr. David H. Rowitch
    Title: Functional Genomic Analysis of the Developing Cerebellum (R21NS41764)

  • Univ of Texas MD Anderson Can Center, Dr. William H. Klein
    Title: Identification of Genes Regulating Retinal Ganglion Cell (R21EY13523)

  • Children's Research Institute, Dr. Eric P. Hoffman
    Title: Molecular Pathophysiology of Clinical variation in Spinal Cord Disease (R21NS41765)

  • Dartmouth College, Dr. Jay C. Dunlap
    Title: Gene Expression Profiling in the Mammalian Circadian System (R21MH62793)

  • University of Florida, Dr. William W. Hauswirth
    Title: Ribozyme-Mediated in vivo Photoreceptor expression Profiling (R21EY13522)

  • University of Pittsburgh, Dr. Karoly Mirnics
    Title: cDNA Microarray Analysis of Synaptic Transmission

  • Oregon Health Sciences University, Dr. Gary A. Banker
    Title: Gene Expression Profiling of Neural Cells in Culture

  • Mount Sinai School of Medicine of CUNY, Dr. Matthew L. Shapiro
    Title: Learning and Memory Dependent Gene Expression

  • Ernest Gallo Clinic and Research Center, Dr. Micheal F. Miles
    Title: Analyzing Gene Expression Profile Clusters by Comparison (R21DA14167)

  • University of Michigan at Ann Arbor, Dr. Margaret I.Lomax
    Title: Differential Gene Expression in Normal, Mutant and Aged (R21DC4920)

  • University of Cincinnati, Dr. Frank R. Sharp
    Title: Brain Genomic Response to Hypoxia (R21AG19561)

  • University of California, San Diego, Dr. Anthony J. Wynshaw-Boris
    Title: Defining the Neuronal Migration Regultory Network (R21MH62821)

  • University of California, Los Angeles, Dr. Harley I. Kornblum
    Title: Gene Expression in CNS Progenitors (R21MH62800)

  • McLean Hospital (Belmont, MA), Dr. Francine M. Benes
    Title: Hippocampal Gene Expression in Schizophrenia (R21MH62822)


3. Technologies For Gene Expression Analysis In The Nervous System (NS-99-003)

Purpose: This Request for Applications (RFA) solicited applications for research grants to develop new technologies or refine established technologies for gene discovery and gene expression analysis in the nervous system.  The nervous system poses unique challenges to gene expression analysis because of its extreme cellular heterogeneity and complex distributions of messenger RNAs within individual cells.  In addition, the nervous system is unusual in the degree to which it uses alternative splicing and RNA editing as mechanisms for regulating the spatial and temporal specificity of gene function.  The development of methods suited to the anatomical and molecular complexities of the nervous system is therefore critical for quantifying gene expression in this system, and for understanding how changes in gene expression may correlate with different developmental, pathological, or functional states.  Methods of interest would include, but are not limited to:  1) isolation of mRNA from single cells or small cell populations, 2) creation of high quality cDNA libraries from small amounts of tissue, 3) high throughput methods for quantifying the expression of large numbers of genes, 4) methods for quantifying multiple spliced or edited variants of a given transcript, 5) methods for comparing protein levels to corresponding mRNA levels for a given transcript within a cell or tissue sample, and 6) techniques for visualizing RNA distribution within cells and tissues.  The development of these methods is expected to improve our understanding of nervous system function in normal and disease conditions, and will aid in the diagnosis and treatment of neurological disorders.

    Funded Projects:

  • University of California, Berkely, Dr. John Ngai
    Title: Methods for Mapping Gene Expression in the CNS (MH61665)

  • University of Utah, Dr. Mahendra Rao 
    Title: Genes Involved In Long Term Neural Plasticity (R01DA13337)

  • University of California, Los Angeles, Dr. Kelsey Martin 
    Title: cDNA Libraries Prepared From Pure Neuronal Processes (R01 AA 12716)

  • University of Kentucky, Dr. Philip Landfield 
    Title: Novel Methods for Single Neuron Gene/Function Studies (R01 AG18228)

  • University of Kentucky, Dr. Timothy McClintock 
    Title: mRNA And Protein Dynamics In Identified Neurons (R01 AG18229)

  • University of Rochester, Dr. Howard Federoff 
    Title: Methods For Analysis Of Gene Function In Neural Networks (R01 AG 18231)

  • Public Health Research Institute, Dr. Sanjay Tyagi 
    Title: Detecting mRNAs in Living Cells With Molecular Beacons (R01 ES 10536)

  • Harvard University (Medical School), Dr. Constance Cepko 
    Title: Gene Expression In Single Identified CNS Cells (R01 EY 13092)

  • Medical College of Georgia, Dr. Shuo Lin 
    Title: Embryonic Neuronal Cdna Libraries: Transgenic Zebrafish (R01 HD 39121)

  • University of Wisconsin Madison, Dr. James Malter 
    Title: Cloning Of Early Response Genes From The Nervous System (R01 MH 61666)

  • Battelle Pacific Northwest Lab., Dr. Richard Smith
    Title: Technology for Nervous System Proteome Analysis (R01 NS 39617)

  • University of Calgary, Dr. Derrick Rancourt 
    Title: Neural Gene Discovery And Expression Analysis (R01 NS 39621).

  • Rockefeller University, Dr. Nathaniel Heintz 
    Title: Use Of Bacs For Analysis Of Cns Specific Genes (R01 NS 39636)

  • Rockefeller University, Dr. Jeffrey Friedman 
    Title: Expression Microarrays For Scoring Of Neurophenotypes (NS 39662)

  • University of Iowa, Dr. Jack Lilien
    Title: Efficient Screen For Interacting Neuronal Gene Products (R21 AA 12717) 

4. Mouse Brain Atlas For Functional Genomics (PAS-99-060)

    Purpose: This Program Announcement (PA) solicited grant applications to research and develop a digital multidimensional atlas that ultimately will serve as a platform to organize and integrate genomic data obtained from the mouse nervous system. Early efforts are likely to primarily focus on atlases of the brain, due to the technologies available and its relative geometric simplicity, but it is envisioned that atlases and related tools would ultimately accommodate data from the entire central nervous system, the peripheral nervous system and special sense organs (herein, collectively referred to as the "nervous system"). 

   This atlas will likely comprise an array of interoperating informatics tools and approaches for handling gene expression data obtained from the mouse nervous system.  It is not expected that any one research group would develop all of the tools needed or atlases of all parts of the nervous system. The algorithms and their implementations resulting from grants funded under this PA must be extensible and scalable, and, ideally, should be modifiable to accommodate genomic data obtained from the human nervous system. It is thus important that informatics tools and approaches supported by this initiative are designed to allow for articulation with other such tools and approaches. 

   The research and development supported under this PA will be iterative, with early versions providing basic functions that would be elaborated upon in subsequent versions.  The intention is to introduce early versions of these tools to the research community generating gene expression data and to develop an atlas of the nervous system of the C57BL6/J strain of mouse. Ultimately, it is expected that uses of the tools and approaches developed under this PA will extend beyond functional genomics. Atlases, informatics tools, and other materials and information generated in projects funded under this PA will be made widely available to the scientific community.

    Funded Projects:

  • University of Califiornia, Los Angeles, Dr. Arthur Toga
    Title: A Multimodal Multidimensional Map Of The Mouse Brain (R01 MH61223)

5. BMAP Gene Discovery RFP (N01 MH80014)

    Purpose: This Request for Proposal (RFP) invited proposals for the production of high-quality, representative cDNA libraries from specific anatomical regions of the adult mouse brain, and for assessment of the utility of the cDNA libraries for novel gene discovery. It is expected that one contract shall be awarded for the requirements specified in this RFP. The primary goal of this contract is the discovery of novel genes expressed in the adult mouse brain. Given this goal, it is not essential to utilize tissue from finely localized brain regions. The identification of genes from more coarsely localized regions at this point will facilitate the development of resources for future studiesof gene expression patterns in which neuroanatomical regions are finely mapped. The cDNA libraries and resulting sequence data are available for wide distribution to the scientific community.

Funded Projects:

  • University of Iowa, Dr. M. Bento Soares 
    Title: Brain Molecular Anatomy Project: Gene Discovery (N01 MH80014)