Molecular diversity of astrocytes with implications for neurological disorders

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Fig. 5. Replicates within a given experimental modality or tissue type demonstrated a high degree of reproducibility and, when analyzed as groups, highlighted the distinctiveness of the astrocyte profile from the profiles of neurons, NSCs, and embryonic cortex.

Fig. 6. Experimental strategy to identify the astrocyte transcriptome. Embryonic NSCs were differentiated into astrocytes by exposure to either to serum (from 24 h to 5 days), or CNTF, BMP2, or PACAP for 5 days. Primary cortical astrocyte cultures were isolated from P1--P2 mice. Pure neuronal cultures were derived from E13.5 hippocampus. In addition, the GM, CC, and GL were microdissected from coronal sections of the telencephalon of P0, P2, P5, P10, and adult mice. RNA was isolated from all of the above samples was hybridized to the Affimetrix U74 oligonucleotide microarrays. The arrays were analyzed by using D-CHIP software (the Wong Laboratory). Differentially expressed genes were analyzed by (i) UHC, (ii) R-SVM, and (iii) threshold criteria. Genes differentially expressed by neurons (more than three LBFCs) were subtracted from the data. Candidate astrocyte genes were validated by RNA ISH combined with immunohistochemistry. Finally, we use a clustering algorithm (see Methods in the main text for details) to identify additional astrocyte specific genes that tightly cluster with the validated astrocyte genes

Table 1. Validation of astrocyte candidate genes by combination of ISH and immunohistochemistry.

Table 2. A total of 394/458 genes/probe sets coclustered with GFAP by UHC.

Table 3. A total of 153 astrocyte candidate genes identified by R-SVM, common in vitro, and common in vivo

Table 4. A total of 33/41 genes/probe sets that were up-regulated in CC and at least one culture system.

Table 5. A total of 29/37 genes/probe sets that were up-regulated in GM and at least one culture system.

Table 6. A total of 23/30 genes/probe sets that were up-regulated in GL and at least one culture system.

Table 7. Twenty-six validated astrocyte genes and corresponding 42 probe sets.

Table 8. Significant Gene Ontology (GO) functional categories.

Supporting CEL Files. All data used in the paper in Affymetrix CEL file format (sample labels).

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