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gbb873-sup-0001-FigureS1.tiffTIFF image1603K Figure S1: Cocaine causes long-lasting locomotor sensitization. (a) Two sets of eight male mice were subjected to Saline or Cocaine injection as indicated, and locomotor activity for the subsequent 45 min was recorded. RNA from these individual mice was used for qPCR validation. (b) Two sets of eight male mice were subjected to Saline or 20 mg/kg Cocaine injection for 8 days followed by 30 min of locomotor monitoring. A third set of eight male mice received 20 mg/kg Cocaine for 8 days, was subjected to Withdrawal for 8 days, and then locomotion was monitored in three of the eight mice following a test injection of 20 mg/kg Cocaine. RNA from these mice was used for RNA-Seq. (c) An additional two sets of four male mice each were subjected to Saline or 20 mg/kg Cocaine injection daily for 7 days, followed by 15 min of locomotor monitoring; a third set of four mice received Cocaine for 7 days, was subjected to Withdrawal for 28 days, and then locomotion was monitored after a test injection of 20 mg/kg Cocaine. RNA from these individual mice was used for qPCR validation. Sal, Saline; Coc, Cocaine; W/D, Withdrawal. The number following the abbreviation indicated number of days in a given treatment paradigm.
gbb873-sup-0002-FigureS2.tiffTIFF image830K Figure S2: Contribution of reads mapping to mitochondrial chromosome. The proportion of mapped sequence reads from NAc lysate libraries aligning to the mitochondrial chromosome was determined. Sal, Saline; Coc, Cocaine; W/D, Withdrawal; chrM, mitochondrial chromosome.
gbb873-sup-0003-FigureS3.tiffTIFF image915K Figure S3: High-throughput sequence analysis of mitochondrial NAc mRNAs. Pairwise scatter plots of mRNA expression data for NAc lysate (a–c) libraries (Saline, Cocaine and Withdrawal) prepared from adult mouse; shown as log10(RPKM) per sample. Scatter plots include only mitochondrial genes (from GO:0005840). R2 values were calculated by least squares best fit. RPKM, reads per kilobase gene model per million mapped reads (Mortazavi et al. 2008).
gbb873-sup-0004-FigureS4.tiffTIFF image835K Figure S4: High-throughput sequence analysis of ribosomal NAc mRNAs. Pairwise scatter plots of mRNA expression data for NAc lysate (a–c) libraries (Saline, Cocaine and Withdrawal) prepared from adult mouse; shown as log10(RPKM) per sample. Scatter plots only include ribosomal genes (from GO:0005739). R2 values were calculated by least squares best fit. RPKM, reads per kilobase gene model per million mapped reads (Mortazavi et al. 2008).
gbb873-sup-0005-TableS1.pdfPDF document80K Table S1: Primers used for qPCR.
gbb873-sup-0006-TableS2.pdfPDF document1956K Table S2: Gene lists for Cocaine- and Withdrawal-regulated gene clusters expressed in NAc. Five worksheets provide complete gene lists for the five differentially regulated clusters (i–v) of genes identified through hierarchical gene expression clustering in Fig. 2a. + indicates functional group membership for selected genes. Coc, Cocaine; W/D, Withdrawal.
gbb873-sup-0007-TableS3.pdfPDF document444K Table S3: Complete Panther Pathway analysis of NAc Cocaine- and Withdrawal-regulated genes from clusters i, ii and v. Panther Pathway analysis for genes in clusters i, ii and v, identified through hierarchical gene expression clustering in Fig. 2a. Additional worksheets include gene lists for heterotrimeric G-protein signaling (Gαi and Gαs) from clusters i, ii and v. Coc, Cocaine; W/D, Withdrawal.
gbb873-sup-0008-TableS4.pdfPDF document402K Table S4: Full Panther Protein class gene lists for Cocaine-regulated genes at striatal PSDs. File includes the overall Panther Protein Class list for the Cocaine-regulated genes from striatal PSDs identified in Fig. 2.

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