Data from: Single-nucleus RNA-seq and ATAC-seq in outbred rats with divergent cocaine addiction behaviors reveal long-term changes in gene regulation and GABAergic inhibition in the amygdala

This dataset accompanies our publication titled: "Single-nucleus RNA-seq and ATAC-seq in outbred rats with divergent cocaine addiction behaviors reveal long-term changes in gene regulation and GABAergic inhibition in the amygdala." <strong>Files Included:</strong> <strong>1. geno.N26.vcf.gz</strong><br> - Description: Contains genotypes for 26 Heterogeneous Stock rats whose gene expression was predicted. <strong>2. pred_expr.Brain.N26.tsv</strong><br> - Description: This tab-delimited table contains predicted relative gene expression in the brain for 26 Heterogeneous Stock rats. <br> - Details: Predictions were made for 8,997 genes from linear models based on cis-eQTLs from whole brain hemisphere tissue downloaded from the RatGTEx Portal. A gene is included in the table if it had at least one significant cis-eQTL, and if its predicted expression in these 26 animals had nonzero variance. The values in the table give the predicted log2(relative expression), where log2(2) = 1 is the baseline expression from the two haplotypes of the gene if it had only reference alleles at all its regulatory loci.<br> - Additional Info: Predictions were generated using <strong>gene_expr_pred.py</strong> available at https://github.com/PejLab/gene_expr_pred<br> An explanation of the prediction model is given in https://doi.org/10.1101/2022.01.28.478116 <strong>3. Behavioral data.xlsx</strong><br> - Description: Contains behavioral data for the Heterogeneous Stock (HS) rats.<br> - Organization: Each sheet in the file corresponds to data for a specific figure. <strong>Additional Dataset Locations:</strong> The primary datasets generated during this study can be found on the Gene Expression Omnibus under accession number GSE212417 <strong>Publicly Available Datasets Utilized:</strong> - Rattus norvegicus Ensembl v98 reference genome and genome assembly: Rnor_6.0 <br> - JASPAR2022 transcription factor binding profiles for vertebrates: JASPAR<br> - ENCODE Honeybadger 2 ChIP-seq: Broad Institute<br> - Liu et al. 2019106 GWAS for tobacco and nicotine addiction summary statistics: PubMed<br> - RatGTEx Portal tissue-specific cis-eQTLs: RatGTEx Portal <br> - 1000 Genomes European reference panel: Alkes Group<br> - KEGG pathways: KEGG API