Entire transcriptome

Neuroglia, edited by Helmut Kettenmann and Bruce R. Ransom, Third Edition, Oxford University Press 2012

Chapter 28

Ditte Lovatt and Maiken Nedergaard
nedergaard@urmc.rochester.edu   Lovatt@upenn.edu
Center for Translational Neuromedicine
University of Rochester
601 Elmwood Ave, Box 645
Rochester NY 14642

Table 28.S2: The astrocyte transcriptome (download)

Analysis from Lovatt et al. (2007) was produced by comparing adult cortical GFAP-GFP+/GLT1+ astrocytes to GFAP-GFP–/GLT1– cells (n=3). Analysis from Cahoy et al. (2008) was produced by comparing postnatal (P)16-17 fluorescence activated cell sorting- (FACS) and panning-isolated astrocytes (n=5) to P16-17 panning-isolated neurons (n=3). Analysis from Doyle et al. (2008) was produced by comparing TRAP affinity-purified mRNA from BAC-transgenic Aldh1l1 mice. From Doyle et al. (2008), each sample (n=4) derived from several 8-10 week old mice, and was compared to unbound affinity-purified samples (n=2). Each of the three datasets was normalized individually using the RMA algorithm in R/Bioconductor. The same software was used to calculate statistical values using the limma package. Fold changes are log base 2. P-values are FDR-corrected. A representative probe was chosen for cases where a gene has more than one probeset for the platform. This was done by choosing the probeset with the lowest p-value for that gene. When there was a p-value tie, the probeset with the higher value fold change was chosen.

Lovatt D, Sonnewald U, Waagepetersen HS, Schousboe A, He W, Lin JH, et al. 2007. The transcriptome and metabolic gene signature of protoplasmic astrocytes in the adult murine cortex. J Neurosci 27(45):12255–12266.
Cahoy JD, Emery B, Kaushal A, Foo LC, Zamanian JL, Christopherson KS, et al. 2008. A transcriptome database for astrocytes, neurons, and oligodendrocytes: a new resource for understanding brain development and function. J Neurosci 28(1):264–278.
Doyle JP, Dougherty JD, Heiman M, Schmidt EF, Stevens TR, Ma G, et al. 2008. Application of a translational profi ling approach for the comparative analysis of CNS cell types. Cell 135(4):749–762.

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