Literature DB >> 12763235

High-resolution voxelation mapping of human and rodent brain gene expression.

Ram P Singh1, Vanessa M Brown, Abhijit Chaudhari, Arshad H Khan, Alex Ossadtchi, Daniel M Sforza, A Ken Meadors, Simon R Cherry, Richard M Leahy, Desmond J Smith.   

Abstract

Voxelation allows high-throughput acquisition of multiple volumetric images of brain gene expression, similar to those obtained from biomedical imaging systems. To obtain these images, the method employs analysis of spatially registered voxels (cubes). For creation of high-resolution maps using voxelation, relatively small voxel sizes are necessary and instruments will be required for semiautomated harvesting of such voxels. Here, we describe two devices that allow spatially registered harvesting of voxels from the human and rodent brain, giving linear resolutions of 3.3 and 1 mm, respectively. Gene expression patterns obtained using these devices showed good agreement with known expression patterns. The voxelation instruments and their future iterations represent a valuable approach to the genome scale acquisition of gene expression patterns in the human and rodent brain.

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Year:  2003        PMID: 12763235     DOI: 10.1016/s0165-0270(03)00045-1

Source DB:  PubMed          Journal:  J Neurosci Methods        ISSN: 0165-0270            Impact factor:   2.390


  10 in total

1.  Investigation of different transcript quantitation tools for high-throughput mapping of brain gene expression using voxelation.

Authors:  Ram P Singh; Dahai Liu; Abhijit Chaudhari; Simon R Cherry; Richard M Leahy; Desmond J Smith
Journal:  J Mol Histol       Date:  2004-05       Impact factor: 2.611

2.  A genome-scale map of expression for a mouse brain section obtained using voxelation.

Authors:  Mark H Chin; Alex B Geng; Arshad H Khan; Wei-Jun Qian; Vladislav A Petyuk; Jyl Boline; Shawn Levy; Arthur W Toga; Richard D Smith; Richard M Leahy; Desmond J Smith
Journal:  Physiol Genomics       Date:  2007-05-15       Impact factor: 3.107

3.  Development and evaluation of a micro- and nanoscale proteomic sample preparation method.

Authors:  Haixing Wang; Wei-Jun Qian; Heather M Mottaz; Therese R W Clauss; David J Anderson; Ronald J Moore; David G Camp; Arshad H Khan; Daniel M Sforza; Maria Pallavicini; Desmond J Smith; Richard D Smith
Journal:  J Proteome Res       Date:  2005 Nov-Dec       Impact factor: 4.466

4.  Quantifying mRNA levels across tissue sections with 2D-RT-qPCR.

Authors:  Michael Armani; Michael A Tangrea; Benjamin Shapiro; Michael R Emmert-Buck; Elisabeth Smela
Journal:  Anal Bioanal Chem       Date:  2011-05-11       Impact factor: 4.142

5.  Anatomical methods for voxelation of the mammalian brain.

Authors:  Daniel M Sforza; Jacopo Annese; Dahai Liu; Shawn Levy; Arthur W Toga; Desmond J Smith
Journal:  Neurochem Res       Date:  2004-06       Impact factor: 3.996

6.  Transcriptome tomography for brain analysis in the web-accessible anatomical space.

Authors:  Yuko Okamura-Oho; Kazuro Shimokawa; Satoko Takemoto; Asami Hirakiyama; Sakiko Nakamura; Yuki Tsujimura; Masaomi Nishimura; Takeya Kasukawa; Koh-hei Masumoto; Itoshi Nikaido; Yasufumi Shigeyoshi; Hiroki R Ueda; Gang Song; James Gee; Ryutaro Himeno; Hideo Yokota
Journal:  PLoS One       Date:  2012-09-19       Impact factor: 3.240

7.  Learning pair-wise gene functional similarity by multiplex gene expression maps.

Authors:  Li An; Haibin Ling; Zoran Obradovic; Desmond J Smith; Vasileios Megalooikonomou
Journal:  BMC Bioinformatics       Date:  2012-03-21       Impact factor: 3.169

8.  Analysis of multiplex gene expression maps obtained by voxelation.

Authors:  Li An; Hongbo Xie; Mark H Chin; Zoran Obradovic; Desmond J Smith; Vasileios Megalooikonomou
Journal:  BMC Bioinformatics       Date:  2009-04-29       Impact factor: 3.169

9.  NeuroTerrain--a client-server system for browsing 3D biomedical image data sets.

Authors:  Carl Gustafson; William J Bug; Jonathan Nissanov
Journal:  BMC Bioinformatics       Date:  2007-02-05       Impact factor: 3.169

10.  Quantitative methods for genome-scale analysis of in situ hybridization and correlation with microarray data.

Authors:  Chang-Kyu Lee; Susan M Sunkin; Chihchau Kuan; Carol L Thompson; Sayan Pathak; Lydia Ng; Chris Lau; Shanna Fischer; Marty Mortrud; Cliff Slaughterbeck; Allan Jones; Ed Lein; Michael Hawrylycz
Journal:  Genome Biol       Date:  2008-01-30       Impact factor: 13.583

  10 in total

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