DESCRIPTION:
Total RNA from the NAc and CPu were isolated from 12 adult male C57BL/6J mice (11 weeks old) within 1 h after the last session of oxycodone in a 14-day self-administration paradigm (4h/day, 0.25 mg/kg/infusion, FR1) or from yoked saline controls (6 oxycodone and 6 yoked saline controls). RNA-Seq libraries were prepared using Illumina's TruSeq® Stranded Total RNA LT kit. An Illumina HiSeq 2500 apparatus was used to obtain 100 bp single end reads for samples from the nucleus accumbens, whereas Illumina HiSeq 2000 was used to obtain 100 bp paired-end reads for samples from the CPu. The reads were aligned to the mouse reference genome (version mm10) using STAR. Aligned reads were then summarized through featureCounts with the gene model from Ensemble (Mus_musculus GRCm38.75.gtf) at gene level. Gene expressions were examined using using the miRNeasy Kit (Qiagen, Valencia, CA). Agilent 6000 RNA Nano Chips were used to examine the integrity of RNA in samples. DESeq2 was applied to the counts of protein coding genes to estimate the fold change between the treatment groups. False Discovery Rate (FDR) q < 0.1 were used to select genes that have a significant expression change. In the CPu, data from one saline control, and from one oxycodone-treated animals were excluded from downstream analysis. In the NAc, data from one oxycodone-treated animal was excluded from the downstream analysis. Statistical significance and fold change of oxycodone-induced alterations in expression of 32 axon guidance-related genes (integrins, semaphorins and ephrins, and their receptors) were extracted from the total list of differentially expressed genes in the RNA-seq data for the NAc and CPu in this study. To examine whether DE axon guidance genes may produce their effect in a cell type specific manner, we have studied potential enrichment in transcripts of the axon guidance genes in specific cell types such as astrocytes, neurons, microglial and endothelial cells. Publicly available RNA-Seq transcriptome data were downloaded from GEO (GSE52564). For each gene of integrin, semaphorin and ephrin gene families, that had a significant change (FDR < 0.1) in either NAc or CPu, expression fold change of each cell type was calculated as described recently (Table 2). For selection of a subset of genes related to axon guidance pathway, REACTOME was used. All genes from results are shown. From supplementary table 1s.
LABEL:
Axon guidance and integrin DEG mouse Nac 0.25mg/kg oxycodone vs control_qvalue
SCORE TYPE:
Q-Value
THRESHOLD:
<= 0.1
GENES IN THRESHOLD:
28
DATE ADDED:
DATE UPDATED:
SPECIES:
AUTHORS:
TITLE:
JOURNAL:
ABSTRACT:
Genes in threshold: 28
| Uploaded As | Gene Symbol | Homology | Score | Priority | LinkOuts | Emphasis |
|---|
GeneWeaver