Cell Type Analysis

Attached below is a database (.xlsx) of genes that have been identified in previous scientific publications as having cell-type specific expression in neural tissue or cell culture, as discussed in the paper:

Inference of cell type content from human brain transcriptomic datasets illuminates the effects of age, manner of death, dissection, and psychiatric diagnosis

*Megan Hastings Hagenauer¹, Anton Schulmann², Jun Z. Li³, Marquis P. Vawter⁴, David M. Walsh⁴, Robert C. Thompson¹, Cortney A. Turner¹, William E. Bunney⁴, Richard M. Myers⁵, Jack D. Barchas⁶, Alan F. Schatzberg⁷, Stanley J. Watson¹, Huda Akil¹

https://doi.org/10.1371/journal.pone.0200003

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Supplementary Table 1. Master Database of Cortical Cell Type Specific Gene Expression. The attached Excel (.xlsx) file contains a single spreadsheet listing the genes defined as having cell type specific expression in our manuscript, including the species, age of the subjects, and brain region from which the cells were purified, the platform used to measure transcript, the statistical criteria and comparison cell types used to define “cell type specific expression”, the gene symbol or orthologous gene symbol in mouse/human (depending on the species used in the original experiment), and citation. If a gene was identified as having cell type specific expression in multiple experiments, there is an entry for each experiment – thus the full 3383 rows included in the spreadsheet do not represent 3383 individual cell type specific genes.

Supplementary Table 6. A .gmt file created using our database of cell type specific genes for use with Gene Set Enrichment Analysis (GSEA). This file should be in the correct format for usage with either GSEA (http://software.broadinstitute.org/gsea/index.jsp) or fGSEA.

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The full citations for the publications included in the database:

Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, Christopherson KS, et al. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci Off J Soc Neurosci. 2008 Jan 2;28(1):264–78.

Daneman R, Zhou L, Agalliu D, Cahoy JD, Kaushal A, Barres BA. The mouse blood-brain barrier transcriptome: a new resource for understanding the development and function of brain endothelial cells. PloS One. 2010;5(10):e13741.

Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, et al. A survey of human brain transcriptome diversity at the single cell level. Proc Natl Acad Sci U S A. 2015 Jun 9;112(23):7285–90.

Doyle JP, Dougherty JD, Heiman M, Schmidt EF, Stevens TR, Ma G, et al. Application of a translational profiling approach for the comparative analysis of CNS cell types. Cell. 2008 Nov 14;135(4):749–62.

GeneCards®: The Human Gene Database: http://www.genecards.org

Sugino K, Hempel CM, Miller MN, Hattox AM, Shapiro P, Wu C, et al. Molecular taxonomy of major neuronal classes in the adult mouse forebrain. Nat Neurosci. 2006 Jan;9(1):99–107.

Zeisel A, Muñoz-Manchado AB, Codeluppi S, Lönnerberg P, La Manno G, Juréus A, et al. Brain structure. Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq. Science. 2015 Mar 6;347(6226):1138–42.

Zhang Y, Chen K, Sloan SA, Bennett ML, Scholze AR, O’Keeffe S, et al. An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. J Neurosci Off J Soc Neurosci. 2014 Sep 3;34(36):11929–47.

{last updated 07-17-2018}